@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}
@article {pmid41522492,
year = {2026},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2610588},
pmid = {41522492},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.<br><br>OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.<br><br>DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.<br><br>RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. &#x3b2;-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.<br><br>CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.},
}
@article {pmid41521629,
year = {2026},
author = {Shelton, BR and Larrere, J and Yusta Belsham, D and Omacini, M and Argüelles-Moyao, A and Buscardo, E and Alves da Silva, DK and Zhao, X and Nakamura, N and Ángeles-Argáiz, R and Paz, C and Matías-Ferrer, N and Hart, MM},
title = {Fungal ecology in the age of 'omics.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70900},
pmid = {41521629},
issn = {1469-8137},
abstract = {The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with the macroscopic world, than ever before. However, fungal studies that use meta'omic technologies have been sparse compared with bacterial and plant-focused studies. In this review, we highlight the ways that meta'omics can help to address pressing questions in belowground plant-fungal ecology, show consistencies that are emerging - and discrepancies that still exist - among analysis pipelines, and advocate for reporting standards that will allow meta'omic research to more fully benefit fungal ecology.},
}
@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}
@article {pmid41521100,
year = {2026},
author = {Zhu, NQ and Zhang, QB and Wang, ZX and Li, RD},
title = {Bacteroides in Bile Detected by Metagenomic Next-Generation Sequencing: Potential Novel Indicator for Early Allograft Dysfunction After Liver Transplantation.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2025.11.001},
pmid = {41521100},
issn = {1873-2623},
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) is an effective method for the detection of microorganisms. Early allograft dysfunction (EAD) is a common complication after liver transplantation. The association between early postoperative microorganisms in bile and EAD is unclear, so we evaluated the association of microorganisms and other potential risk factors with EAD.<br><br>METHODS: A total of 100 patients who underwent orthotopic liver transplantation with biliary T tube placement in Huashan Hospital Fudan University from March 2021 to July 2022 were studied. Clinical data, the occurrence of EAD, and bile microorganisms' information detected by mNGS were collected.<br><br>RESULTS: EAD occurred in 22 recipients (22%). Patients with EAD had a longer length of postoperative hospital stay. Bacteroides spp. detected by mNGS in bile was identified as an independent risk factor for EAD. Also, operation time, the MELD score of the recipient, and donor AST level were also independent risk factors for EAD.<br><br>CONCLUSION: Bacteroides spp. detected by mNGS in bile after liver transplantation was identified as an independent risk factor for EAD, which may reflect the translocation of intestinal flora into the biliary tract and may serve as a potential early warning indicator of poor quality of the donor liver. Recipients with EAD had longer LOS, which may indicate a poor short-term prognosis.},
}
@article {pmid41519985,
year = {2026},
author = {Bodhe, I and Gokuladoss, V},
title = {Sustainable CO2 valorization for PHB production towards circular economy: metagenomic insights on enriched indigenous microbial cultures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26791-7},
pmid = {41519985},
issn = {2045-2322},
}
@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41519950},
issn = {1530-0447},
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.<br><br>METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.<br><br>RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.<br><br>CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.<br><br>IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut&#x2012;brain axis.},
}
@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {},
number = {},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by circadian rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Circadian rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.<br><br>RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.<br><br>DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the circadian rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.<br><br>CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for circadian rhythm-targeted interventions in metabolic diseases.},
}
@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}
@article {pmid41518832,
year = {2025},
author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R},
title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.},
journal = {Water research},
volume = {292},
number = {},
pages = {125272},
doi = {10.1016/j.watres.2025.125272},
pmid = {41518832},
issn = {1879-2448},
abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.},
}
@article {pmid41518812,
year = {2026},
author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Yu, Z and Liu, J},
title = {Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes and metal(loid) interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141092},
doi = {10.1016/j.jhazmat.2026.141092},
pmid = {41518812},
issn = {1873-3336},
abstract = {Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10[4] copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.},
}
@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}
@article {pmid41518728,
year = {2026},
author = {Sun, J and Lyons, R and Weigh, KV and Lieske, S and Newsham, KK and Hopkins, DW and Dennis, PG},
title = {Putative drivers of maritime Antarctic soil resistomes in the early 21st century: A baseline for monitoring environmental change and human influence.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181361},
doi = {10.1016/j.scitotenv.2026.181361},
pmid = {41518728},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) are present in all ecosystems and encode the defences that microorganisms have naturally evolved to defend themselves against antimicrobial agents. The use and synthesis of antibiotics by humans, however, has led to a proliferation of ARGs, resulting in their consideration as emerging environmental pollutants, even in some of the most pristine terrestrial ecosystems on Earth. Here we used shotgun metagenomics to characterise the abundance and diversity of ARGs in 29 maritime Antarctic soils collected in the 2007-2008 austral summer that varied in edaphic conditions and levels of human visitation. In total, 1831 ARGs were identified, spanning 29 naturally occurring ARGs that confer resistance to either single or multiple drug classes, such as glycopeptide, fluoroquinolone and tetracycline. The ARG profiles were not significantly associated with predicted levels of human visitation and harboured novel and potentially ancient ARGs, suggesting that these soils were relatively pristine. Furthermore, we observed that the abundance and diversity of ARGs was strongly associated with soil pH and mean annual surface air temperature (MASAT), as well as moisture content, C:N ratio, DOC and Mg concentration, albeit to a lesser extent. Our study provides a useful baseline for future studies, greatly expands the geographical coverage of Antarctic soil resistomes, and highlights putative environmental drivers of ARGs for the early 21st century including pH and MASAT, the latter of which is predicted to rise towards the end of this century.},
}
@article {pmid41518205,
year = {2026},
author = {Ren, H and Jiao, X and Wang, R and Liu, J and Wu, D and Liu, J and Wang, M and Shangguan, W and Cao, S and Chen, P},
title = {DSN-based Host DNA Depletion for Simultaneous Detection of DNA and RNA Pathogens in next-generation sequencing.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf145},
pmid = {41518205},
issn = {1472-765X},
abstract = {In recent years, nucleic acid sequencing has been increasingly used in clinical pathogen detection. Typically, 20-100 million metagenomic reads are generated per sample, but 90-99% originate from host nucleic acids, leaving only 1-2 million for microbial identification-potentially compromising detection sensitivity. Here, we present a novel duplex-specific nuclease (DSN)-based method to reduce host nucleic acid content in next-generation sequencing. Validated using mock communities and clinical samples, it yielded a 2- to 3-fold increase in pathogen RPM (reads per million) in metagenomic NGS (mNGS) and a more pronounced 3- to 10-fold improvement in probe-based targeted NGS (tNGS). Optimal performance was achieved with: 65°C annealing temperature; 2 μg Cot-1 DNA and 50 μmol rProbe as driver DNA; and 150 mmol·L-1 tetramethylammonium chloride (TMAC)-using 25 ng input nucleic acid for library preparation. The DSN workflow adds less than 30 minutes to library preparation and enables rapid, low-loss microbial enrichment, enhancing pathogen detection in clinical NGS. While effective, its host depletion efficiency could be further improved by expanding driver DNA coverage to additional abundant human genomic regions, such as LINE and LTR repeats.},
}
@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R&#x2009;+&#x2009;D&#x2009;+&#x2009;I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}
@article {pmid41517763,
year = {2026},
author = {Zhu, Q and Liu, Q},
title = {Early diagnosis of Lemierre syndrome using targeted next-generation sequencing combined with metagenomics capture: A case report and literature review.},
journal = {Medicine},
volume = {105},
number = {2},
pages = {e46988},
doi = {10.1097/MD.0000000000046988},
pmid = {41517763},
issn = {1536-5964},
support = {2022KC22269//Project of Xuzhou Key Research and Development Program/ ; },
mesh = {Humans ; Female ; *Lemierre Syndrome/diagnosis/microbiology/therapy ; Adolescent ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Fusobacterium necrophorum/isolation &amp; purification/genetics ; Early Diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {RATIONALE: Lemierre syndrome (LS) is a rare but life-threatening complication of acute oropharyngeal infections. It is characterized by septic thrombophlebitis of the internal jugular vein and subsequent metastatic abscess formation. The most common causative pathogen of LS is Fusobacterium necrophorum (FN). This paper presents the case of a 17-year-old female patient with LS, in whom FN was rapidly detected and LS was diagnosed using targeted next-generation sequencing (tNGS) combined with metagenomics capture (MetaCAP). This approach enabled timely detection of FN and guided appropriate treatment.<br><br>PATIENT CONCERNS: The patient, a female 17-year-old student, experienced a fever after catching a cold, with a peak temperature of 39.8 &#xb0;C on May 22, 2024, accompanied by chills and shivering, sore throat, right chest pain, back pain, cough, and hemoptysis.<br><br>DIAGNOSES: The patient was initially diagnosed with non-severe community-acquired pneumonia at admission on May 26, 2024. She was finally diagnosed with LS after FN was detected using bronchoalveolar lavage fluid tNGS combined with serum MetaCAP.<br><br>INTERVENTIONS: The patient received targeted antimicrobial therapy and thorough thoracic drainage in the shortest time after being definitely diagnosed with LS using tNGS and MetaCAP technologies.<br><br>OUTCOMES: The clinical symptoms of the patient were significantly improved. A chest computed tomography scan on July 15, 2024 indicated complete resolution of exudates and solid lesions in both lungs.<br><br>LESSONS: This case underscores the significant role of tNGS combined with MetaCAP in the early detection of FN and timely diagnosis of LS, systematically explores the epidemiology, clinical features, diagnosis and treatment of LS, thus providing a reference for clinicians to rapidly diagnose and treat LS.},
}
@article {pmid41517713,
year = {2026},
author = {Sun, Z and Xu, K and Huo, L and Zhang, X and Chen, B},
title = {Family psittacosis cluster diagnosed by metagenomic next-generation sequencing in Hangzhou City, Eastern China: A case series.},
journal = {Medicine},
volume = {105},
number = {2},
pages = {e47139},
doi = {10.1097/MD.0000000000047139},
pmid = {41517713},
issn = {1536-5964},
mesh = {Humans ; *Psittacosis/diagnosis/drug therapy/microbiology ; *Chlamydophila psittaci/genetics/isolation &amp; purification ; China ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Metagenomics/methods ; Adult ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Animals ; Moxifloxacin/therapeutic use ; },
abstract = {RATIONALE: Psittacosis, a human infection caused by Chlamydia psittaci (C psittaci), is often underdiagnosed due to its nonspecific presentation and the limitations of conventional diagnostic methods. This diagnostic challenge can lead to missed outbreaks and delays in appropriate treatment. This report aims to highlight the critical role of metagenomic next-generation sequencing (mNGS) in rapidly identifying C psittaci and facilitating the investigation of a family cluster, thereby providing a clearer rationale for its application in similar scenarios.<br><br>PATIENT CONCERNS: In this study, we report a family cluster of psittacosis cases. All affected individuals had a history of direct or indirect contact with backyard poultry during a visit to a rural village before symptom onset. The index case (Case 1) presented with fever and chills and was subsequently hospitalized. The 2 secondary cases (Cases 2 and 3) exhibited similar clinical manifestations and were treated at the same hospital, where doctors promptly collected specimens for testing based on their shared medical history.<br><br>DIAGNOSES: The diagnosis of C psittaci pneumonia was confirmed by mNGS analysis of bronchoalveolar lavage fluid obtained from 3 patients through bronchoscopy.<br><br>INTERVENTIONS: Combination therapy involving intravenous moxifloxacin and doxycycline was administered for the treatment of infectious pneumonia.<br><br>OUTCOMES: Following timely diagnosis and targeted antimicrobial therapy, all 3 patients attained full clinical recovery.<br><br>LESSONS: C psittaci pneumonia presents with nonspecific clinical and radiographic features that are indistinguishable from other causes of community-acquired pneumonia. mNGS markedly enhances diagnostic accuracy and shortens the time to diagnosis, proving to be an invaluable tool for early identification and management of outbreaks, particularly in patients with avian or poultry exposure.},
}
@article {pmid41517247,
year = {2026},
author = {Shah, SMH and Volpe, S and Colonna, F and Valentino, V and De Filippis, F and Torrieri, E and Cavella, S},
title = {Combined Effect of Plasma-Activated Water, Edible Coating, and Active Packaging on Cherry Tomato Shelf-Life: Kinetics and Microbiome Approach.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517247},
issn = {2304-8158},
support = {817936//European Commission/ ; },
abstract = {Cherry tomatoes are highly appreciated for their nutritional value but remain highly perishable due to rapid respiration and senescence. This study evaluated a multi-hurdle strategy combining plasma-activated water (PAW), sodium caseinate-based edible coating, and antioxidant active packaging to preserve minimally processed (MP) cherry tomatoes stored at 1 °C, 4 °C, and 8 °C for 15 days. Quality evolution was monitored through physical, chemical, nutritional, and microbiological parameters and described using pseudo-zero- and first-order kinetic models, with temperature dependence expressed by the Arrhenius equation. The combined treatment (prototype) slowed the degradation rates of pH, titratable acidity, total polyphenols, and antioxidant capacity, as reflected by consistently lower kinetic rate constants across all temperatures. Prototype samples showed better retention of polyphenols and antioxidant capacity, particularly at 1 °C and 4 °C, without detrimental effects on visual appearance. Metagenomic analysis revealed that the multi-hurdle treatment reshaped the microbial community, reducing the relative abundance of potentially problematic taxa such as Acinetobacter johnsonii and limiting the occurrence of antimicrobial resistance (AMR) genes at the end of storage. This study provides the first integrated assessment of PAW, edible coating, and antioxidant active packaging as a synergistic multi-hurdle strategy, demonstrating their combined ability to extend shelf life while modulating the microbiome and resistome of minimally processed cherry tomatoes.},
}
@article {pmid41516169,
year = {2025},
author = {Uvarova, YE and Khlebodarova, TM and Vasilieva, AR and Shipova, AA and Babenko, VN and Zadorozhny, AV and Slynko, NM and Bogacheva, NV and Bukatich, EY and Shlyakhtun, VN and Korzhuk, AV and Pavlova, EY and Chesnokov, DO and Peltek, SE},
title = {Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516169},
issn = {1422-0067},
support = {075-15-2025-516//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical program for genetic technologies development for 2019-2030)/ ; FWNR- 2022-0022//Ministry of Science and Higher Education project "Study of metabolic control networks in living systems under environmental interaction, including in genetically modified organisms."/ ; },
mesh = {*Lactococcus lactis/genetics/classification/isolation &amp; purification/metabolism ; *Cheese/microbiology ; Food Microbiology ; Phylogeny ; Genome, Bacterial ; Fermentation ; Microbiota/genetics ; },
abstract = {The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of Lactococcus lactis. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the rpoB gene grouped the isolates into three clusters, each corresponding to a distinct strain of Lactococcus lactis subsp. diacetilactis. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of L. l. subsp. diacetilactis, namely, diacetyl and CO2. The functional properties and metabolic characteristics of this starter consortium are discussed.},
}
@article {pmid41516078,
year = {2025},
author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD},
title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516078},
issn = {1422-0067},
support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/therapy ; Middle Aged ; Biomarkers/blood ; *Artificial Intelligence ; Feces/microbiology ; Inflammation/microbiology ; Metagenomics/methods ; Treatment Outcome ; Young Adult ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.},
}
@article {pmid41515236,
year = {2025},
author = {Zhang, Z and Wang, S and Sun, G and Pan, D},
title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515236},
issn = {2072-6643},
support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; },
mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Humans ; *Gastrointestinal Microbiome/physiology ; *Fasting ; Blood Glucose/metabolism ; Animals ; Dysbiosis ; Intermittent Fasting ; },
abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.},
}
@article {pmid41515159,
year = {2025},
author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR},
title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515159},
issn = {2072-6643},
support = {na/MRA/Melanoma Research Alliance/United States ; na//Andrew Sabin Family Fellowship/ ; na//MD Anderson Melanoma Moon Shot/ ; 1P30CA016672/NH/NIH HHS/United States ; 1R01CA291965/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; },
mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Patient Reported Outcome Measures ; *Cancer Survivors/psychology ; *Diet ; Aged ; Adult ; *Immunotherapy/adverse effects ; Quality of Life ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Depression ; Anxiety ; Prospective Studies ; Exercise ; },
abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.},
}
@article {pmid41514837,
year = {2026},
author = {Li, L and Zhang, H and Zhan, L and Guan, W and Hu, J and Wei, Z and Wu, W and Wu, Y and Xing, Q and Wu, J and Li, Z and Liu, Q and Chen, J and Yuan, A and Guo, D and Ouyang, K and Yang, J and Hu, W and Zhao, X},
title = {Synergistic Regulation of Bile Acid-Driven Nitrogen Metabolism by Swollenin in Ruminants: A Microbiota-Targeted Strategy to Improve Nitrogen Use Efficiency.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
pmid = {41514837},
issn = {2076-2615},
support = {32160804//National Natural Science Foundation of China/ ; 32202762//National Natural Science Foundation of China/ ; 32360855//National Natural Science Foundation of China/ ; 32460886//National Natural Science Foundation of China/ ; 20224BAB215037//Jiangxi Provincial Natural Science Foundation/ ; 20252BAC240611//Jiangxi Provincial Natural Science Foundation/ ; 20224ACB205007//Jiangxi Provincial Natural Science Foundation/ ; 20232BBF60009//Key Project Under the Key R&amp;D Program of Jiangxi Provincial Department of Science and Technology/ ; },
abstract = {The annual nitrogen loss from the livestock production sector poses a significant threat to the global natural environment. Therefore, it is urgent to focus on improving the nutrient utilization efficiency of ruminants and promoting the sustainable development of livestock production. Twelve 60-day-old Ganxi goats with similar body weights were selected and randomly assigned to two dietary treatment groups. The control group was fed only a basal diet, while the treatment group was supplemented with 32 mg/d of Swollenin. The experiment lasted for 30 days. At the end of the experimental period, the goats were euthanized, and their intestinal contents were collected, rapidly frozen, and stored at -80 °C for subsequent metagenomic and metabolomic analyses. In the Swollenin group, we observed changes in gut microbiota structure and significantly enhanced feed conversion efficiency compared to the control group. Notably, genera such as Bacteroides, Ruminococcus, and Bifidobacterium exhibited significantly higher abundance. Following Swollenin supplementation, the gene abundance associated with the secondary bile acid biosynthesis pathway in the intestinal tract of young goats was significantly higher. The levels of primary bile acids (BAs), including taurocholic acid, glycocholic acid, taurochenodeoxycholic acid, and glycochenodeoxycholic acid, were significantly lower, while the concentrations of secondary BAs such as ursodeoxycholic acid and deoxycholic acid were significantly higher. The abundance of nitrogen-fixing and nitrogen-assimilating genes in the gut of young goats in the Swollenin group was significantly higher. Furthermore, co-occurrence network analysis revealed a strong correlation between bile acid metabolism and nitrogen metabolism pathways. These results suggest that nutritional regulation may serve as a preventive strategy to optimize the symbiotic development of animals and their gut microbiota, ultimately improving nitrogen utilization.},
}
@article {pmid41514742,
year = {2025},
author = {Song, Y and Hu, Z and Yang, X and An, Y and Lu, Y},
title = {Duckweed as a Sustainable Aquafeed: Effects on Growth, Muscle Composition, Antioxidant and Immune Markers in Grass Carp.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
pmid = {41514742},
issn = {2076-2615},
support = {2020B1111530002//Guangdong Foundation for Program of Science and Technology Research/ ; },
abstract = {Duckweed (Spirodela polyrhiza), a fast-growing aquatic plant rich in protein and bioactive compounds, offers a sustainable alternative to conventional aquafeed protein sources. This study evaluated the effects of incorporating 25-75% duckweed meal into a commercial feed on grass carp (Ctenopharyngodon idella) over a 6-week trial. Fish meal, wheat starch, and vegetable oil was added in amounts to obtain isonitrogenous and isoenergetic diets. Additionally, another grass carps were used for extended feeding until they reached approximately 1000 g, using the feed with the optimal duckweed inclusion rate (25%). Fish fed a diet consisting of 75% commercial feed and 25% duckweed meal (F75D25) exhibited significantly higher weight gain. Muscle analysis revealed increased protein content (up 15%, p < 0.05) and improved amino acid and fatty acid profiles. Liver, muscle, and blood assays showed elevated antioxidant enzyme activities (SOD up 20%, LYS up 18%; p < 0.05) and immune markers (CRP, GOT; p < 0.05), indicating enhanced health status. Transcriptomic and metagenomic analyses confirmed the upregulation of immune-related genes (e.g., SOD1, IL-6; fold change > 2, p < 0.01) and beneficial shifts in gut microbiota (e.g., increased Firmicutes). These findings highlight duckweed's potential as a nutrient-rich, health-promoting ingredient for sustainable aquaculture diets.},
}
@article {pmid41514654,
year = {2025},
author = {Liu, KYP and Huang, A and Pepin, C and Shen, Y and Tsang, P and Poh, CF},
title = {Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
pmid = {41514654},
issn = {2072-6694},
abstract = {The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages-from collection to analysis-is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers.},
}
@article {pmid41514452,
year = {2026},
author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K},
title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02307-3},
pmid = {41514452},
issn = {2049-2618},
support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium f&#xfc;r Forschung, Technologie &amp; Raumfahrt/ ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.<br><br>RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.<br><br>CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.},
}
@article {pmid41381025,
year = {2026},
author = {Zabaleta, WDB and Gomez, JDR and Santofimio Villa, LF and Angarita, NB and Alzate, JF and Garzón, YEG and Cantillo-Barraza, O and Triana-Chavez, O and Vargas, PAO and Urrea, DA},
title = {Metatranscriptomic insights into feeding preferences, bacterial diversity, and insect-specific viruses genomics in Aedes aegypti populations from Ibagué, Colombia.},
journal = {Acta tropica},
volume = {273},
number = {},
pages = {107941},
doi = {10.1016/j.actatropica.2025.107941},
pmid = {41381025},
issn = {1873-6254},
mesh = {Animals ; *Aedes/virology/microbiology/physiology ; Colombia ; Female ; *Mosquito Vectors/virology/microbiology ; *Feeding Behavior ; *Bacteria/classification/genetics/isolation &amp; purification ; *Insect Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; Genome, Viral ; },
abstract = {Aedes aegypti is not only the primary vector of medically important arboviruses worldwide, but also a host of a wide range of arthropod-specific viruses (ISVs), whose genomic and biological diversity remains largely unknown across most regions of Colombia. Investigating its associated microbiota including viruses and bacteria is essential, as these interactions can influence vector competence. Metatranscriptomic analysis of this vector provides quantitative insights into the presence of such microorganisms and their potential links to blood meal sources. In this study, we analyzed 320 blood-fed female A. aegypti mosquitoes collected from urban areas of Ibagué, Colombia, using RNA-Seq to identify eukaryotic, prokaryotic, and viral sequences, with particular emphasis on insect-specific viruses (ISVs). This approach allowed us to assess the diversity and relative abundance of microorganisms across four mosquito populations, infer potential feeding sources, identify and recover complete viral genomes, and detect parasite families. Despite inherent limitations related to taxonomic classification based on databases, our findings contribute to a better understanding of the ecological and epidemiological characteristics of A. aegypti populations circulating in Ibagué, Colombia, and their vector-pathogen-host interactions.},
}
@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02318-0},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.<br><br>RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.<br><br>CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}
@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02309-1},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&amp;D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.<br><br>RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen &#x3b1;-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.<br><br>CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through &#x3b1;-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}
@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04678-x},
pmid = {41514203},
issn = {1471-2180},
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}
@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02679-x},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andaluc&#xed;a/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}
@article {pmid41513932,
year = {2026},
author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A},
title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35033-3},
pmid = {41513932},
issn = {2045-2322},
support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d&#xb4;Educaci&#xf3;, Cultura, Universitats i Ocupaci&#xf3;, cofinan&#xe7;at per la Uni&#xf3; Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d&#xb4;Educaci&#xf3;, Cultura, Universitats i Ocupaci&#xf3;/ ; },
}
@article {pmid41513032,
year = {2026},
author = {Liu, S and Liu, Z and Xia, X},
title = {Primary cutaneous blastomycosis in a Chinese-Canadian girl following an insect bite.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108374},
doi = {10.1016/j.ijid.2026.108374},
pmid = {41513032},
issn = {1878-3511},
abstract = {BACKGROUND: Blastomycosis is a disease caused by the dimorphic fungus Blastomyces species. This infection occurs most frequently among individuals residing in the midwestern, southeastern, and south-central United States, as well as in Canadian provinces bordering the Great Lakes and the St. Lawrence Seaway. Sporadic cases have been reported in China, the diagnosis of imported cases remains a significant challenge.<br><br>CASE PRESENTATION: We report a diagnostically challenging case of primary cutaneous blastomycosis in a Chinese-Canadian girl, presenting as two nodules of different sizes on her left lower leg and left arm. The patient was initially diagnosed with insect bite dermatitis in Canada, which showed poor response to treatment. Direct microscopic examination revealed large spherical yeast cells, some with broad-based budding, initially interpreted as protothecosis or coccidioidomycosis. However, metagenomic next-generation sequencing (mNGS) indicated B. dermatitidis, which was subsequently confirmed by fungal culture and ITS sequencing. The patient was prescribed oral itraconazole at 50 mg/day and has since returned to Canada to continue treatment.<br><br>CONCLUSIONS: For diagnosing infections caused by highly pathogenic pathogens such as imported blastomycosis, the combination of mNGS and direct microscopic examination represents a valuable diagnostic approach.},
}
@article {pmid41512899,
year = {2026},
author = {Chu, VT and Spottiswoode, N and Ward, R and Yokoe, DS and Ramirez-Avila, L and Phelps, MS and Glascock, A and Crawford, ED and Kamm, J and Hao, S and Li, L and Dynerman, D and Waltari, E and Nafees, S and Kalantar, KL and Caldera, S and Madera, S and Guerrero, ES and Ivashin, D and Serpa, PH and Love, C and Mwakibete, LL and Doernberg, SB and Kistler, A and Alvino, R and Engel, J and Chiu, CY and Pak, C and Cunningham, G and Reyes, H and Buie, B and Messacar, K and Leroue, M and Prince, BC and Detweiler, AM and Stanley, K and Caughell, C and McNeil, N and Neff, N and Nichols, A and Miller, S and DeRisi, JL and Tato, CM and Langelier, CR},
title = {Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101277},
doi = {10.1016/j.lanmic.2025.101277},
pmid = {41512899},
issn = {2666-5247},
abstract = {Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical centre. In collaboration with the hospital infection-prevention team, the RR programme uses whole-genome sequencing and metagenomic next-generation sequencing for outbreak investigations, special interest analyses of emerging pathogens, and surveillance of high-priority microbes. Over 7 years (2017-24), the RR programme conducted a diversity of outbreak investigations and other analyses; most investigations ruled out transmission, and the rapid turnaround of genomic results averted further resource-intensive work. Longitudinal surveillance enabled early detection of changing incidence trends and guided timely infection-prevention responses. Our experiences with the RR programme build upon growing evidence that genomic epidemiology programmes enhance hospital infection prevention and control, augment priority pathogen surveillance, and improve patient safety.},
}
@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}
@article {pmid41512751,
year = {2025},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}
@article {pmid41512717,
year = {2026},
author = {Li, L and Shang, G and Guo, Y and Zhang, J and Qi, Y and Wang, H and Flores, M and Belloch, C and Liu, Y and Jing, W and Li, X and Woldemariam, KY},
title = {Unlocking the genomic landscape of Staphylococcus equorum and understanding the functional role and technological application in dry-cured fermented meat products: A review.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111618},
doi = {10.1016/j.ijfoodmicro.2025.111618},
pmid = {41512717},
issn = {1879-3460},
abstract = {In Dry-cured fermented meat products, the role of Staphylococcus equorum has been given less attention. S. equorum enhances the flavour, colour, texture, and nutritional quality, and produces antimicrobial compounds that inhibit pathogens in dry-cured fermented meat products. This review aims to provide a comprehensive evaluation of S. equorum as a potential starter culture in dry-cured fermented meat products, examines the main genomic and metabolic characteristics, and highlights the regulatory mechanisms. S. equorum is a gram-positive, catalase-positive coccus with high salt tolerance and optimal growth at 4-10 °C and pH 5-5.6. Modern PCR-based sequencing and metagenomics allow accurate identification of S. equorum using the major genes, including superoxide dismutase (sodA) and recombinase A (recA). Identification of this species has been made from different dry-cured fermented meat products, including Spanish dry-cured ham and "Chorizo" sausages from Spain, artisanal "Soppressata" fermented sausage from Italy. The functional role of S. equorum in protein and lipid hydrolysis contributes to key flavour and aroma compounds. Moreover, it has potential in the prevention of secondary lipid oxidation (superoxide dismutase (SOD)), contributes to nitrate reductase activity (NOS pathway), and biosynthesis of antibacterial peptide (micrococcin P1), which improves the quality and safety of dry-cured fermented meat products. Keeping this into account, the studies conducted on the S. equorum application as a starter culture in dry-cured fermented meat products are in their early stages and require further investigation and analysis.},
}
@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
doi = {10.1016/j.psj.2026.106384},
pmid = {41512665},
issn = {1525-3171},
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}
@article {pmid41511111,
year = {2026},
author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M},
title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/msystems.01405-25},
pmid = {41511111},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.<br><br>IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.},
}
@article {pmid41511092,
year = {2026},
author = {Jabir, T and Venkatachalam, S and Surya Prakash, L},
title = {Metagenome-assembled genomes of bacterial communities in the eastern Southwest Indian Ridge, Indian Ocean.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0087025},
doi = {10.1128/mra.00870-25},
pmid = {41511092},
issn = {2576-098X},
abstract = {This paper presents high-quality metagenome-assembled genomes (MAGs) recovered from hydrothermal plume at the 67.67°E vent field along the eastern Southwest Indian Ridge. A total of 24 high-quality MAGs were obtained having 21 different genera. These MAGs, associated with chemosynthetic pathways including methane, metal, and sulfur metabolism, offer crucial insights into microbial transformation in deep-sea hydrothermal vents.},
}
@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}
@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}
@article {pmid41510448,
year = {2025},
author = {Tohya, M and Murase, K and Minagawa, M and Saiura, A and Nakagawa, I and Kirikae, T and Watanabe, S},
title = {Single-Cell Sequencing of a Bile Sample From an Acute Cholecystitis Patient.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98748},
pmid = {41510448},
issn = {2168-8184},
abstract = {Single-cell sequencing is a novel approach to genome sequencing of clinical samples. However, there are only few studies using single-cell sequencing of genomes for bacterial infections. A 71-year-old woman presented to the emergency department with epigastric pain, 38.5°C fever, and a history of hypertension and hyperuricemia. From blood test results, acute cholecystitis was suspected. The surgery went well and bilirubin calcium stones were found in the gallbladder. Single-cell sequencing was used to investigate a bile sample from a patient with acute cholecystitis. The sample, cultured on a MacConkey agar plate, produced four colonies, all identified as Escherichia coli by bacteriological and biochemical properties. Whole genome sequences of the four strains were determined using the single-cell amplified genome (SAG) sequencing technique. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all four were 99.98-100% and 100%, respectively, indicating that they were the same bacterial species. Compared with type strains, these four strains were closest to Shigella sonnei (ANI 98.65-98.66%; dDDH 88.5%) than E. coli (ANI 96.79-96.80%; dDDH 74.2%), despite lacking stx1, stx2 and ipaH, which Shigella species harbor. 16S metagenome analysis identified E. coli as the predominant bacterial genome in the sample, comprising 93.15%. SAG raw data had a relatively high level of quality, with 98.4-98.7% of the read numbers used after quality trimming. However, the genome sequencing coverage was only 9.45-42.88% when compared to a complete genome of an isolate with a mapping quality set above 99%, resulting in gaps compared to conventional whole genome sequence data of these isolates. The procedures of the SAG sequencing technique should be revised to improve the sequencing coverage and reduce gaps in the sequence data. Nonetheless, single-cell genome sequencing can provide novel information for bacterial infections.},
}
@article {pmid41510411,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, H and Feng, J},
title = {A Case of Severe Fever With Thrombocytopenia Syndrome Co-infected With Pseudomonas aeruginosa and Aspergillus fumigatus.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98752},
pmid = {41510411},
issn = {2168-8184},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne infectious disease with a high mortality rate. Co-infections with SFTS virus (SFTSV) and other pathogens can exacerbate the condition, leading to rapidly progressive multiple organ failure. We reported a case of SFTS complicated by Pseudomonas aeruginosa and Aspergillus fumigatus. Despite active symptomatic supportive treatment (including anti-virus, anti-infection, anti-antifungal treatment, liver protection, and other advanced life supports), the patient's condition deteriorated rapidly, leading to multiple organ failure. The patient was discharged home and died on the same day. The next day, her blood test results reported that SFTSV, Pseudomonas aeruginosa and Aspergillus fumigatus were detected through metagenomic next-generation sequencing (mNGS). It suggests that early pathogen screening and targeted anti-infective treatment are crucial for improving the prognosis.},
}
@article {pmid41510275,
year = {2025},
author = {De Vlaminck, I and Mzava, O and Djomnang, LA and Cheng, A and Gomez-Escobar, L and Lenz, J and Belcher, E and Schenck, E},
title = {Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8148988/v1},
pmid = {41510275},
issn = {2693-5015},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated response to infection. Early identification of pathogens and accurate assessment of organ injury are critical for improving outcomes, but current methods are often inadequate, especially after initiation of antibiotic treatment. Metagenomic sequencing of cell-free DNA (cfDNA) offers a promising alternative, enabling simultaneous pathogen detection and tissue-of-origin profiling. Contamination, however, can limit its accuracy in low-biomass samples. Here, we apply the Sample-Intrinsic Microbial DNA Found by Tagging and Sequencing (SIFT-seq) assay, which reduces contamination and allows detection of pathogens and organ injury simultaneously. We analyzed 142 plasma specimens: 105 from sepsis patients, 103 collected after initiation of antibiotic treatment, 24 from non-sepsis ICU controls, and 13 from healthy controls. SIFT-seq identified sepsis-causing pathogens in good agreement with pre-antibiotic blood cultures, revealed elevated immune activity and organ injury in sepsis patients, and, when combined with the SOFA score in a multivariate model, improved diagnostic performance (AUC = 0.874). These findings highlight the potential of integrated cfDNA profiling to enhance sepsis diagnosis.},
}
@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {},
number = {},
pages = {15357597251412104},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.<br><br>METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.<br><br>RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.<br><br>SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}
@article {pmid41509497,
year = {2025},
author = {Shen, Z and Eckert, J and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA},
title = {Skin microbiome composition and function in the development of atopic diseases during infancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.22.696050},
pmid = {41509497},
issn = {2692-8205},
abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.<br><br>OBJECTIVE: To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.<br><br>METHODS: We analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status.<br><br>RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae . At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae . Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.<br><br>CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.},
}
@article {pmid41509203,
year = {2025},
author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G},
title = {Quantum implementation of multi-pattern string matching for k-mer detection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.21.695808},
pmid = {41509203},
issn = {2692-8205},
abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.<br><br>METHOD: We implement two quantum algorithms for DNA multi pattern string matching for k-mer detection based on Grover's amplitude amplification with quantum random access memory (QRAM). The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O(&#x221a;S) query complexity for S text positions but requiring O(m&#xb7;L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O(&#x221a;S &#xb7; &#x221a;m) in total.<br><br>RESULTS: We present two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.<br><br>CONCLUSIONS: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.<br><br>To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.},
}
@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Geologic Sediments/virology ; Tibet ; Metagenomics ; Phylogeny ; *Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}
@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.<br><br>SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}
@article {pmid41421789,
year = {2025},
author = {Wang, X and Wu, J and Huang, J and Zeng, Y and Xu, Z and Li, C},
title = {Ectopic paragonimiasis presenting as massive pericardial effusion in a child: A rare diagnostic challenge.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {164},
number = {},
pages = {108326},
doi = {10.1016/j.ijid.2025.108326},
pmid = {41421789},
issn = {1878-3511},
abstract = {OBJECTIVES: To report a rare pediatric case of ectopic paragonimiasis presenting as isolated massive pericardial effusion and to emphasize key diagnostic clues for early recognition in endemic regions.<br><br>DESIGN OR METHODS: We describe a 10-year-old boy from an endemic area in China who presented with acute gastrointestinal symptoms and recurrent massive pericardial effusion without respiratory manifestations. Diagnostic evaluation included pericardial fluid analysis, microbiological testing, echocardiography, cardiac magnetic resonance imaging(MRI), serological testing for Paragonimus IgG, therapeutic response assessment, and histopathological examination following surgery.<br><br>RESULTS: Despite repeated pericardiocenteses and empirical anti-infective therapy, the effusion persisted. Laboratory testing revealed exudative pericardial fluid with negative cytology, acid-fast staining, and metagenomic next-generation sequencing(mNGS), while peripheral eosinophilia and stool ova were absent. Echocardiography showed a characteristic "cocoon-like" pericardial pattern, and serology was positive for Paragonimus IgG.The patient improved after praziquantel and corticosteroids, but progressive pericardial thickening required pericardiectomy, which confirmed necrotizing granulomatous inflammation. The patient recovered with no recurrence during follow-up.<br><br>CONCLUSION: Paragonimiasis should be considered in children from endemic areas with unexplained or recurrent pericardial effusion, even in the absence of pulmonary involvement or eosinophilia. Epidemiological exposure, characteristic echocardiographic findings, and serology are critical for diagnosis, and timely anti-parasitic therapy with surgical intervention when necessary may prevent constrictive pericarditis.},
}
@article {pmid41388147,
year = {2026},
author = {Osipova, E and Balakrishnan, CN and Spottiswoode, CN and Lund, J and DaCosta, JM and Hauber, ME and Warren, WC and Sorenson, MD and Sackton, TB},
title = {Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism.},
journal = {Nature ecology &amp; evolution},
volume = {10},
number = {1},
pages = {128-139},
pmid = {41388147},
issn = {2397-334X},
support = {DEB-1754397//National Science Foundation (NSF)/ ; IOS-1456524//National Science Foundation (NSF)/ ; DEB-1754406//National Science Foundation (NSF)/ ; DEB-1754311//National Science Foundation (NSF)/ ; DEB-1754643//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Nesting Behavior ; Male ; *Adaptation, Physiological/genetics ; *Biological Evolution ; *Finches/genetics/physiology ; Female ; *Adaptation, Biological ; Metagenomics ; },
abstract = {Parental care evolved as a strategy to enhance offspring survival at the cost of reduced adult survival and fecundity. While 99% of bird species provide parental care, obligate brood parasites circumvent this trade-off by exploiting the parental behaviours of other species. This radical life-history shift occurred independently seven times in birds, offering an outstanding opportunity to test for convergent adaptation. To investigate genomic adaptations underlying this transition, we analyse population resequencing data from five brood-parasitic species across three independent origins of brood parasitism-three parasitic finches, a honeyguide and a cowbird-alongside related non-parasitic outgroups. Using the McDonald-Kreitman framework, we find evidence for adaptation in genes involved in sperm function in multiple parasitic clades, but not in the matched, non-parasitic outgroups, consistent with evidence for increased male-male competition in parasitic lineages following the loss of parental care. We also detect selective sweeps near genes associated with nervous system development in parasitic lineages, perhaps associated with improved spatial cognition that aids brood parasites in locating and monitoring host nests. Finally, we detect more selective sweeps in the genomes of host specialist brood parasites as compared to non-parasitic outgroups, perhaps reflecting ongoing host-parasite coevolutionary arms races.},
}
@article {pmid41508467,
year = {2026},
author = {Chang, H and Zhang, Q and Soro, PL and Zhang, W and Ma, L and Feng, Z and Gu, C},
title = {Integrative metagenomic, metabolomic, and transcriptomic analyses unravel flavor development driven by a defined starter cocktail in cocoa fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118042},
doi = {10.1016/j.foodres.2025.118042},
pmid = {41508467},
issn = {1873-7145},
mesh = {*Fermentation ; *Cacao/microbiology/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Saccharomyces cerevisiae/metabolism/genetics ; Gene Expression Profiling ; Odorants/analysis ; Transcriptome ; Food Microbiology ; Hanseniaspora/metabolism ; Gas Chromatography-Mass Spectrometry ; },
abstract = {This study investigated the impact of a defined starter cocktail (Hanseniaspora uvarum XY23.1, Saccharomyces cerevisiae XY23.2, Lactiplantibacillus plantarum XY23.1, and Gluconobacter oxydans XY23.2) on Trinitario cocoa fermentation in Hainan, China. A multi-omic approach integrating shotgun metagenomics, metabolomics (LC-MS and GC-MS), and transcriptomics was employed to comprehensively assess microbial succession, metabolite dynamics, and functional gene expression. Starter inoculation accelerated cocoa fermentation and stabilized microbial succession, and the four introduced strains remained dominance during the process. Metabolomic analysis revealed that the inoculated group had a remarkable increase in the content of the aromatic volatiles phenylethyl alcohol, 3-methylbutyl acetate, and delta-decalactone, which contributes to fruity and floral aroma characteristics. Shotgun metagenomics revealed enrichment of genes involved in carbohydrate utilization, amino acid catabolism, and acetate ester biosynthesis. Transcriptomics also indicated that S. cerevisiae upregulated Ehrlich pathway and glyoxylate cycle under co-culture conditions, demonstrating its central role in aroma formation and redox balance, while H. uvarum upregulated sugar transporters and stress-response genes, demonstrating a putative regulatory role in nutrient competition and interspecies interaction. Overall, our findings elucidate that defined starter cultures can shape cocoa fermentation toward improved consistency and aroma outcomes, providing a foundation for designing function-driven microbial consortia for controlled fermentation applications.},
}
@article {pmid41508436,
year = {2026},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Corrigendum to "Aldehyde metabolism in Maotai-flavor baijiu: insights from integrated metagenomic and metaproteomic analyses" [Food Res. Int. 221(Part 3) (2025) 117518].},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {117954},
doi = {10.1016/j.foodres.2025.117954},
pmid = {41508436},
issn = {1873-7145},
}
@article {pmid41508161,
year = {2026},
author = {Villafuerte, AB and Comeau, AM and Soria, R and Ortega, R and Wright, RJ and Miralles, I},
title = {Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00845-9},
pmid = {41508161},
issn = {2524-6372},
support = {FIRESOIL CNS2023-14150//Ministerio de Ciencia e Innovaci&#xf3;n (Spain), Agencia Estatal de Investigaci&#xf3;n (Spain) and European Union/ ; BIOQUALIRES-PID2021-1275910B-100//Ministerio de Ciencia e Innovaci&#xf3;n (Spain), Agencia Estatal de Investigaci&#xf3;n (Spain) and European Union/ ; P_FORT_GRUPOS_2023/69//Research Plan of the University of Almeria/ ; TECHBIOSOL-PID2024-156189OB- I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {BACKGROUND: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.<br><br>RESULTS: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.<br><br>CONCLUSIONS: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.},
}
@article {pmid41508143,
year = {2026},
author = {Gong, Y and Shen, S and Cao, Z and Zou, X and Zhou, S and Jiang, R and Kang, X and Liu, S and Tian, Y},
title = {Prophylactic impact of cecal fermentation broth against gut microbiota dysbiosis of broiler chickens challenged with Escherichia coli.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00514-9},
pmid = {41508143},
issn = {2524-4671},
support = {2024CXZX009//The Science and Technology Innovation Fund of Henan Agricultural University/ ; 30601985//The Scientific Studio of Zhongyuan Scholars/ ; },
}
@article {pmid41508107,
year = {2026},
author = {Bay, P and Cappy, P and Rodriguez, C and Mongardon, N and Petit, M and Voiriot, G and Sonneville, R and Pineton de Chambrun, M and Urbina, T and Pham, T and Decavèle, M and Benghanem, S and Contou, D and Lepeule, R and Melica, G and de Prost, N and Angebault, C and Mekontso Dessap, A and Woerther, PL and Razazi, K},
title = {Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.},
journal = {Critical care (London, England)},
volume = {30},
number = {1},
pages = {18},
pmid = {41508107},
issn = {1466-609X},
}
@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04707-9},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.<br><br>OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.<br><br>METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.<br><br>RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.<br><br>CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}
@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.<br><br>STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.<br><br>RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.<br><br>CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}
@article {pmid41507619,
year = {2026},
author = {Mohamad, M and Sergaki, C and Patel, VC},
title = {Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {3},
pmid = {41507619},
issn = {2731-8745},
abstract = {Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.},
}
@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}
@article {pmid41507173,
year = {2026},
author = {Han, Y and Liao, J and Li, C and Xing, F and Peng, J and Liu, X and Xie, W and Wu, F and Jian, H and Cheng, R and Dong, X},
title = {Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68174-6},
pmid = {41507173},
issn = {2041-1723},
abstract = {Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.},
}
@article {pmid41506580,
year = {2026},
author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM},
title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104768},
doi = {10.1016/j.ijpara.2025.104768},
pmid = {41506580},
issn = {1879-0135},
abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.},
}
@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}
@article {pmid41506454,
year = {2026},
author = {Shi, T and Xu, S and Lin, Y and Zheng, X and Ruan, H and Shi, W and Zhang, R and Chen, H and Chen, T and Chen, H and Wang, H},
title = {The Clinical Application of Metagenomic Next-Generation Sequencing in Pathogen Identification of Postoperative Spinal Implant Infection.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.01.004},
pmid = {41506454},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Postoperative spinal implant infection (PSII) poses significant diagnostic challenges and can lead to serious clinical outcomes. Traditional microbial culture methods are limited by prolonged turnaround times and low sensitivity, which have long hindered a comprehensive understanding of the pathogen spectrum in PSII. Metagenomic next-generation sequencing (mNGS) offers rapid, broad-spectrum, and highly sensitive pathogen detection, providing a promising solution to the diagnostic difficulties associated with PSII.<br><br>PURPOSE: This study aimed to evaluate the clinical utility of mNGS for the pathogenic diagnosis of PSII.<br><br>STUDY DESIGN/SETTING: Retrospective cohort study.<br><br>PATIENT SAMPLE: A retrospective analysis was conducted on clinical data from 122 patients with suspected surgical site infection following spinal implant-related surgery between January 2020 and July 2025.<br><br>OUTCOME MEASURES: Identification of pathogenic bacteria in patients.<br><br>METHODS: According to the National Healthcare Safety Network (NHSN) criteria, patients were classified into the PSII group (n&#x202f;=&#x202f;89) and the non-PSII group (n&#x202f;=&#x202f;33). Pathogen spectrum characteristics of PSII detected by mNGS were analyzed, and the diagnostic performance of mNGS was compared with that of traditional microbial culture, laboratory tests, and imaging studies.<br><br>RESULTS: The pathogen detection rate of mNGS was significantly higher than that of traditional culture (79.78% vs. 38.20%, P < 0.001). mNGS successfully detected pathogens in 42.70% (38/89) of culture-negative PSII cases. The main pathogens identified by mNGS included Staphylococcus aureus and coagulase-negative staphylococci (20.00% each, 15/75), Mycobacterium tuberculosis (18.67%, 14/75), and anaerobic bacteria (14.67%, 11/75). Among the 33 patients positive by both mNGS and culture, species-level concordance was 69.70%. No significant difference in the distribution of major pathogens was observed between early-onset (&#x2264;3 months) and late-onset (>3 months) infection groups. Antibiotic appropriateness evaluation revealed that only 32.58% (29/89) of patients had initial antibiotic regimens that provided complete coverage against the detected pathogens. The overall diagnostic performance of mNGS for PSII was superior to that of culture, with significantly higher sensitivity (79.78% vs. 38.20%), specificity (100.00% vs. 93.94%), positive predictive value (100.00% vs. 94.44%), negative predictive value (64.71% vs. 36.05%), accuracy (85.25% vs. 53.28%), and AUC (0.8989 vs. 0.6607).<br><br>CONCLUSION: mNGS significantly improves the detection of difficult-to-culture pathogens such as M. tuberculosis and anaerobic bacteria in PSII. It is recommended to combine mNGS with conventional methods, thereby improving diagnostic accuracy, guiding rational antibiotic use, and enhancing treatment outcomes.},
}
@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.<br><br>OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.<br><br>METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).<br><br>RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2]&#x202f;=&#x202f;0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.<br><br>CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}
@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of Sediment Microbial Community Composition and Function to Mangrove Restoration from an Aquaculture Pond in Southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}
@article {pmid41505815,
year = {2026},
author = {Liu, F and Sun, S and Zhang, Y and Wang, F and Yang, X and Zhang, B and Fan, S and Jia, H},
title = {Possible tuberculous meningitis presenting with predominant voiding dysfunction in an elderly patient: A case report.},
journal = {Journal of infection and public health},
volume = {19},
number = {3},
pages = {103128},
doi = {10.1016/j.jiph.2025.103128},
pmid = {41505815},
issn = {1876-035X},
abstract = {Tuberculous meningitis (TBM) typically presents with neurological symptoms. Voiding dysfunction in TBM is usually attributed to spinal cord involvement. We report a rare case of possible TBM co-existing with possible prostatic tuberculosis, presenting primarily with urinary symptoms in the absence of spinal pathology. A 69-year-old male presented with a two-year history of progressive urinary retention, urgency, and frequency. Initial management for benign prostatic hyperplasia was ineffective. He subsequently developed fever, headache, and dizziness. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis and elevated protein. Despite extensive testing, including CSF culture, Xpert MTB/RIF, and metagenomic next-generation sequencing (mNGS), no pathogen was identified. However, a history of untreated testicular tuberculosis, pulmonary nodules on CT, and a prostatic nodule on MRI raised suspicion of disseminated tuberculosis. A clinical diagnosis of possible TBM was made based on a Marais score of 11. An intensive anti-tuberculosis regimen including moxifloxacin and linezolid led to complete resolution of neurological and urinary symptoms. This case suggests that voiding dysfunction in TBM patients may stem from concurrent genitourinary tuberculosis rather than spinal cord involvement. It highlights the importance of considering hematogenous dissemination from latent genitourinary foci in elderly patients and the utility of the Marais criteria for the diagnosis of TBM when microbiological evidence is elusive.},
}
@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}
@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}
@article {pmid41504847,
year = {2026},
author = {Wang, W and Li, Y and Sun, J and Jiang, C and Hao, J},
title = {Semi-Rational Design of a Deep-Sea Metagenomic Sucrose Phosphorylase for Enhanced α-Arbutin Biosynthesis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41504847},
issn = {1559-0291},
support = {2022YFC2805101//National Key Research and Development Program of China/ ; 2022QNLM030003-2//Qingdao Marine Science and Technology Center/ ; 2023TD71//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
}
@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}
@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).<br><br>METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.<br><br>RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced &#x3b1;-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.<br><br>CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}
@article {pmid41503923,
year = {2026},
author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H},
title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70231},
pmid = {41503923},
issn = {1744-7917},
support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.},
}
@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
doi = {10.1080/19490976.2025.2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.<br><br>RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.<br><br>CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}
@article {pmid41503787,
year = {2026},
author = {Wang, Y and Yu, Y and Xu, N and Zhang, Z and Chen, B and Song, M and Zhang, Q and Wang, T and Ma, Y and Lu, T and Sun, L and Qian, H},
title = {Genes for Vitamin B Synthesis and Their Distribution in Microbial Producers.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11883},
pmid = {41503787},
issn = {1520-5118},
abstract = {B vitamins (VBs) are essential micronutrients, yet their microbial production across natural habitats remains poorly understood. We analyzed 126,931 metagenome-assembled genomes to map the distribution of VB producers and constructed a database of 87 VB synthesis genes, identifying VB-independent producers and their environmental drivers. Soil and freshwater habitats harbored the greatest diversity of VB1, VB2, VB7, VB9, and VB12 producers, whereas marine systems contained fewer. Biosynthetic capacity was rare for VB5 and was limited for VB3 and VB6. Gammaproteobacteria are prolific producers, synthesizing up to eight VB types. Soil sulfur content and conductivity significantly enhanced VB production potential, linking beneficial microbes to improved soil health. We further validated VB3 and VB7 synthesis in Acinetobacter kookii, supporting our predictive framework. Because the identified producers include both beneficial and pathogenic taxa, careful evaluation is required. This work provides a robust gene database and a foundation for optimizing microbial VB production in agriculture and biotechnology.},
}
@article {pmid41503705,
year = {2026},
author = {Liu, W and Du, Y and Ning, J and Zheng, S and Qiu, W and Wang, Y},
title = {Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11156},
pmid = {41503705},
issn = {1520-5851},
abstract = {Elevated geogenic ammonium (NH4[+]) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH4[+] accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH4[+] enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH4[+] sources, whereas nitrification served as the primary sink by oxidizing NH4[+] to nitrate. At low NH4[+] levels, NH4[+] was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH4[+] levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH4[+]-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH4[+] production. These findings could advance our understanding of microbially mediated NH4[+] enrichment mechanisms and offer implications for the management of NH4[+] and other geogenic contaminants in organic-rich aquifers.},
}
@article {pmid41503571,
year = {2026},
author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM},
title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101634},
pmid = {41503571},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.<br><br>METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.<br><br>RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.<br><br>CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.<br><br>IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.<br><br>TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.},
}
@article {pmid41503531,
year = {2026},
author = {Burd, EM},
title = {Metagenomic next-generation sequencing reveals cross-reactivity of lateral flow cryptococcal antigen assay with Trichosporon inkin.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503531},
issn = {2996-2684},
abstract = {Metagenomic next-generation sequencing (mNGS) in plasma, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid is a relatively new technology that offers a means to potentially provide a diagnosis in cases where infection is suspected, but conventional diagnostic testing has not revealed a pathogen. There have been many publications of individual cases and overall appraisals of its utility in detecting bacteria, fungi, and DNA viruses associated with otherwise undiagnosed systemic infections. A recent article by Phillips et al. published in ASM Case Reports (2:e00053-25, 2025, https://doi.org/10.1128/asmcr.00053-25) presents a case of meningitis in an immunosuppressed child that was ultimately determined to be caused by Trichosporon inkin using mNGS. Elevated ß-1,3-D-glucan (BDG) levels in CSF and serum projected a diagnosis of fungal meningitis. Bacterial, fungal, and mycobacterial cultures were negative. Positive lateral flow cryptococcal antigen titers in serum and CSF complicated the anticipated diagnosis since Cryptococcus spp. are thought to not have sufficient cell wall BDG to produce positive test results. Given the ultimate diagnosis of T. inkin meningitis and the known cross-reactivity with Trichosporon asahii per package insert, the unexpected cryptococcal antigen results raised the possibility of additional cross-reactivity. The authors uncovered this possibility by testing three known clinical isolates of T. inkin which generated positive results. This case adds to the growing literature that highlights the utility of mNGS in providing a diagnosis in otherwise unresolved cases and shows that mNGS can be further instructive in elucidating limitations in commonly used diagnostic tests.},
}
@article {pmid41503526,
year = {2026},
author = {Phillips, K and Acker, KP and Han, JY and Salvatore, CM and Permar, SR and Rolón, RM and Marino, J and Dysart, C and Berman, DM and Chiu, CY and Kidd, SE and Westblade, LF and Dubois, MM},
title = {Trichosporon inkin meningitis in a pediatric patient diagnosed via metagenomic sequencing.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503526},
issn = {2996-2684},
abstract = {BACKGROUND: Trichosporon has emerged as an important cause of invasive fungal infections in immunocompromised patients. There are limited data on invasive Trichosporon infections in children.<br><br>CASE SUMMARY: We report a case of culture-negative Trichosporon inkin meningitis diagnosed via metagenomic next-generation sequencing of plasma and cerebrospinal fluid in an infant with retinoblastoma. In addition, we highlight the role of &#x3b2;-1,3-D-glucan in the diagnosis and therapeutic monitoring of trichosporonosis, and cross-reactivity of the cryptococcal antigen lateral flow assay with T. inkin.<br><br>CONCLUSION: This diagnosis, which was challenging to make in the absence of a positive culture, highlights the utility of metagenomic sequencing methods and fungal biomarkers in identifying infectious agents and ensuring timely diagnosis and management of patients with rare fungal infections of the central nervous system.},
}
@article {pmid41503489,
year = {2026},
author = {Goddard, TR and Carlson-Jones, JA and Morton, J and Ooi, CY and Tai, A and Warner, MS and Wong, J and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA},
title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.28.25342520},
pmid = {41503489},
abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.},
}
@article {pmid41503361,
year = {2025},
author = {Uddin, MN and Hartog, C and Murray, E and Loveless, JB and Roberson, L and Aslan, A and Cubas, F and Rowles, LS},
title = {Advancing Circular Bioeconomy through a Systems-Level Assessment of Food Waste and Industrial Sludge Codigestion.},
journal = {ACS environmental Au},
volume = {5},
number = {5},
pages = {479-489},
pmid = {41503361},
issn = {2694-2518},
abstract = {Disposal of food waste (FW) in landfills remains an unsustainable practice for organic waste management. Simultaneously, pulp and paper mills produce significant amounts of recalcitrant organic waste that is difficult to decompose due to its high lignocellulosic content. In this study, we developed an innovative approach to improve the digestion of pulp and paper mill sludge (PPMS) by amending FW to produce a low chemical oxygen demand (COD) sludge while recovering methane in the process. This codigestion process was evaluated through lab-scale biogas production experiments coupled with a comprehensive economic and environmental sustainability assessment. Biomethane production results revealed that the FW-PPMS codigestion methane yield was 36% higher on average than the PPMS monodigestion. Additionally, metagenomic analysis revealed that microbial communities for both systems transitioned from highly heterogeneous to more adapted uniform communities after digestion. Improved microbial communities contributed to higher COD removal (92%) in the FW-PPMS system compared to monodigestion (80% removal). The sustainability analysis revealed that the codigestion of FW-PPMS had median costs of 236.64 USD·tonne[-1]·day[-1] and emissions of 228.30 kg CO2 eq·tonne[-1]·day[-1], a significant reduction compared to directly disposing the FW in landfills (median costs of 405.13 USD·tonne[-1]·day[-1] and emissions of 556.27 kg CO2 eq·tonne[-1]·day[-1]). A nationwide contextual analysis revealed that out of six regions, the US Northeast had the lowest median costs and emissions, while the Mountain Plains region had the highest, highlighting the importance of geographical and infrastructural factors in implementation. Overall, codigesting FW with PPMS is revealed to be a sustainable waste management option to decrease landfill disposal of valuable organic waste.},
}
@article {pmid41502951,
year = {2025},
author = {Oliveira, RA and McSpadden, E and Pandey, B and Lee, K and Yousef, M and Chen, RY and Triebold, C and Haro, F and Aksianiuk, V and Patel, R and Shriram, K and Ramanujam, R and Kuehn, S and Raman, AS},
title = {Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.28.582635},
pmid = {41502951},
issn = {2692-8205},
abstract = {Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments [1-6] . Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp -MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp -MH258 across in vitro , ex vivo , and in vivo environments, matching the efficacy of a fecal microbiome transplant in a clinically relevant murine model of infection. The mechanism of suppression by SynCom15 was related to fatty acid production coupled with environmental acidification. SynCom15 also suppressed other pathogens- Clostridioides difficile , Escherichia coli , and other K. pneumoniae strains-but through different mechanisms. Sensitivity analysis revealed models trained on strain presence/absence captured the statistical structure of pathogen suppression, illustrating that community representation was key to our approach succeeding. Our framework, 'Constraint Distillation', could be a general and efficient strategy for building emergent complex systems, offering a path towards synthetic ecology more broadly.},
}
@article {pmid41502900,
year = {2025},
author = {Hou, Y and Xie, W and Duan, J and Li, X and Wu, Z},
title = {Challenge of Cupriavidus gilardii infection in an immunocompromised child: a case report.},
journal = {Translational pediatrics},
volume = {14},
number = {12},
pages = {3498-3503},
pmid = {41502900},
issn = {2224-4344},
abstract = {BACKGROUND: Cupriavidus gilardii is a multidrug-resistant (MDR) pathogen found in soil and water. Human infection is extremely rare, with only two pediatric cases reported to date, and its clinical features and the antimicrobial strategies remain unclear. The pathogen's MDR nature often poses a therapeutic challenge. This case provides valuable clinical evidence regarding the management of C. gilardii infection in immunocompromised pediatric patients.<br><br>CASE DESCRIPTION: A 4-year-old boy with acute lymphoblastic leukemia developed severe immunosuppression after reinduction cyclophosphamide, cytarabine (Ara-C), mercaptopurine (CAM) chemotherapy according to the SCCCG-ALL-2023 protocol. The patient initially presented with recurrent fever, septic shock, and progressive respiratory distress. Despite an aggressive empirical antibiotic regimen including meropenem, imipenem, piperacillin-tazobactam, linezolid, and levofloxacin, his condition continued to worsen. Blood cultures and metagenomic next-generation sequencing (mNGS) subsequently confirmed C. gilardii infection. Based on susceptibility testing, therapy was adjusted to a combination of ceftazidime-avibactam (CAZ-AVI) and tigecycline. After this adjustment, the patient showed marked clinical improvement, with decreased inflammatory indicators and nearly completed clearance of the pathogen. Unfortunately, on hospital day 26, he developed sudden massive hemoptysis due to Aspergillus pulmonary artery invasion and died despite emergency treatment.<br><br>CONCLUSIONS: This case demonstrates that CAZ-AVI may offer effective antimicrobial control for C. gilardii infection in immunocompromised pediatric patients. Although the patient succumbed to secondary fungal complications, successful microbiological control demonstrates that CAZ-AVI may serve as a potential salvage therapy for rare MDR Gram-negative bacteria and provides clinical insight into the management of uncommon pediatric infections.},
}
@article {pmid41502854,
year = {2025},
author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX},
title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1744013},
pmid = {41502854},
issn = {2297-1769},
abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.<br><br>METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.<br><br>RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.<br><br>CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.},
}
@article {pmid41502470,
year = {2026},
author = {Shukla, A and Yadav, M and Malik, MZ and Aditya, AK and Kumar, A and Tandon, R and Shalimar, and Ray, AK},
title = {Soil influences on rural versus urban human gut microbiota and implications on cardio-metabolic health: a comparative pilot study.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {62},
pmid = {41502470},
issn = {2190-572X},
abstract = {UNLABELLED: Humans are exposed to surrounding soil environment and this exposure has reduced with growing urbanisation. Limited evidence exists on how rural and urban soils shape human gut microbiome and related functions. Here, we performed metagenomic analysis, functional prediction, gene ontology using QIIME2, PICRUSt, and DAVID by taking human stool and soil samples (n = 20) from rural and urban settings to characterise gut microbiota and their resemblance to their respective soil microbiota and its functional implications. Our findings demonstrated that soil environment affects gut microbial diversity and abundance of its immediate human inhabitants in both groups and observed shared microbial and functional properties in rural- and urban-guts characteristic of their respective soil microbiota. In rural-group, phylum Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, class Actinobacteria were major overlapping features, while in the urban-counterpart phylum Proteobacteria, Firmicutes, class Gammaproteobacteria were observed. We also demonstrated implication of this differential composition on human health in both settings, and observed enrichment of cytokines like IL-12, IFN-ϒ, and oxidative phosphorylation pathway in rural group vital to metabolic homeostasis. While enrichment of response to toxic substances, methane metabolism, and potentially low levels of alanine in the urban counterpart, linked to impaired immune response and metabolism, suggests urban group may be prone to the cardio-metabolic disease risk. These observations were consistent with other findings emphasising rural groups have healthy sets of microbiome compared to their urban counterpart. In conclusion, our findings unveil the significance of soil microbiota in evolution and shaping of human gut microbiota, thereby potentially beneficial to human health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04675-x.},
}
@article {pmid41502282,
year = {2025},
author = {Sheng, YP and Kong, LJ and Chu, PP and Xia, YL and Shen, CT and Sun, JF},
title = {[Clinical Analysis of Torque Teno Virus Infection after Hematopoietic Stem Cell Transplantation in Children].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {6},
pages = {1784-1789},
doi = {10.19746/j.cnki.issn.1009-2137.2025.06.036},
pmid = {41502282},
issn = {1009-2137},
mesh = {Humans ; *Torque teno virus ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *DNA Virus Infections ; Child ; Male ; Female ; Incidence ; Child, Preschool ; Adolescent ; },
abstract = {OBJECTIVE: To investigate the incidence, clinical characteristics, and complications of Torque teno virus (TTV) in children after hematopoietic stem cell transplantation (HSCT).<br><br>METHODS: A total of 40 children with hematological diseases who underwent HSCT were selected, and metagenomic next-generation sequencing (mNGS) technology was used to detect the gene sequences of pathogenic microorganisms in the blood. Combined with clinical data, the characteristics of TTV infection were analyzed.<br><br>RESULTS: Among the 40 pediatric patients post-HSCT, the TTV positive rate was 42.5% (17/40). There were no statistically significant differences between the TTV-positive group and the TTV-negative group in sex, age, white blood cell count(WBC), red blood cell count(RBC), hemoglobin, platelet count, neutrophil count, lymphocyte count, and high-sensitivity C-reactive protein (all P >0.05). The incidence of TTV infection was significantly higher in children who underwent haploidentical HSCT and in those with bone marrow stem cells (BMSC) as the transplant source (P <0.05). However, there were no significant differences in the TTV infection rate among patients with different disease types, different HLA matching statuses, or different engraftment times of neutrophils and platelets (all P >0.05). Among 17 children infected with TTV, 13(76.5%) had co-infections with other viruses, mainly including cytomegalovirus (58.8%, 10/17), human polyomavirus (41.2%, 7/17), and Epstein-Barr virus (17.6%, 3/17). In children with TTV infection, the most common complications were sepsis (82.4%), graft-versus-host disease (GVHD) (70.6%), pulmonary infection (41.2%), and hemorrhagic cystitis (17.6%). The incidence of GVHD in the TTV-positive group was significantly higher than that in the TTV-negative group (P <0.05).<br><br>CONCLUSION: TTV infection is common in children undergoing HSCT, and it is prone to be complicated with cytomegalovirus infection and GVHD, which has an important influence on the clinical outcomes.},
}
@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}
@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
doi = {10.1111/1462-2920.70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Thermus/metabolism/growth &amp; development/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; Iceland ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; Metagenomics ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}
@article {pmid41502155,
year = {2026},
author = {Kim, SS and D'Agostino, E and Needham, DM},
title = {Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70215},
doi = {10.1111/1462-2920.70215},
pmid = {41502155},
issn = {1462-2920},
support = {//Helmholtz Association/ ; NE 2754/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Nitrification ; *Archaea/genetics/metabolism/classification/isolation &amp; purification ; Seasons ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Phylogeny ; Ammonia/metabolism ; Genomics ; Nitrogen/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Nitrates/metabolism ; },
abstract = {Nitrification is widespread across marine systems, yet the ecological and evolutionary drivers shaping nitrifier populations remain largely unknown. The Baltic Sea, a brackish basin with pronounced gradients in salinity, oxygen, nutrients and strong seasonality, is a valuable model environment to investigate these questions. Here, we combined metagenomics and rRNA gene sequencing to characterise the spatiotemporal dynamics and genomic diversity of nitrifiers, alongside physicochemical measurements. Nitrifiers were persistently abundant throughout aphotic waters, with vertical niche partitioning and seasonal peaks in surface waters from late fall to early spring. The seasonal peaks were positively correlated with nitrite, nitrate and diverse other prokaryotes, and negatively correlated with solar radiation and chlorophyll. To probe the genomic basis of these ecological patterns of the numerically dominant nitrifier, we recovered five novel genomes of ammonia-oxidising archaea through metagenomics of bulk samples and selective enrichments, including the dominant taxon from aphotic depths. Comparative genomics showed high gene conservation, with variation largely in genes linked to interactions with the external environment and nitrogen and phosphorus metabolism between central surface and deep types. Together, our study provides insights into niches of Baltic Sea nitrifiers and begins the process of understanding the mechanisms and functional implications of these patterns.},
}
@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Metagenomics ; Pacific Ocean ; *Microbiota/genetics ; *Metagenome ; Photosynthesis/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Chlorophyll/metabolism ; Nitrites/metabolism ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}
@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02300-w},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.<br><br>RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial&#xa0;symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.<br><br>CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}
@article {pmid41501755,
year = {2026},
author = {Li, JL and Hu, W and Pu, LH and Sun, J and Ortúzar, M and Lv, ZH and Yang, ZF and Zhu, D and Xie, KQ and Yang, LQ and Yin, YR},
title = {Molecular cloning and characterization of a GH10 thermophilic xylanase from hot spring and its potential application in promoting probiotic growth.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01096-9},
pmid = {41501755},
issn = {1472-6750},
support = {202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; },
}
@article {pmid41501434,
year = {2026},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {46},
pmid = {41501434},
issn = {1432-8798},
mesh = {*Rivers/virology ; Phylogeny ; Genome, Viral ; *Metagenomics ; *Fungal Viruses/genetics/classification/isolation &amp; purification ; Germany ; Open Reading Frames ; },
abstract = {Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae - three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used.},
}
@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33939-y},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}
@article {pmid41501123,
year = {2026},
author = {Alexandrino, DAM and Semedo, M and Cao, W and Azevedo, J and Magalhães, C and Osório, H and Jia, Z and Campos, A and Mucha, AP and Almeida, CMR and Carvalho, MF},
title = {Insights into the biodegradation of two persistent fluorinated fungicides by coupling metabolic modelling with metaproteogenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31941-y},
pmid = {41501123},
issn = {2045-2322},
abstract = {Epoxiconazole (EPO) and fludioxonil (FLU) are fluorinated fungicides known for their extremely high environmental persistence and significant ecotoxicological impact. Given their decades-old use in the agrochemical sector, EPO and FLU became frequent pollutants of terrestrial and aquatic ecosystems. And yet, not much is known regarding how these pesticides biodegrade in the natural environment or how to develop suitable bioremediation approaches capable of tackling their inherent recalcitrance. As such, this work focused on providing new insights into the bacterial degradation of EPO and FLU, by surveying the catabolic activity of a previously obtained EPO-enriched bacterial consortium through chemical and metaproteogenomic analyses guided by different metabolic modelling tools. The bacterial consortium was capable of extensively degrading EPO and FLU in 21 days, with fungicide removals of over 90% and defluorination efficiencies of up to 80%, but none of the subproducts predicted in silico were identified for either pesticide. Despite this, the combination of metabolic modelling tools and metaproteogenomic surveys suggested that EPO and FLU were first attacked in their N-heterocyclic moieties and that the targets of defluorination were the resulting aromatic fluorinated intermediates. This catabolic cascade is consistent with the experimental data gathered in this study and with the existing literature on this topic. Also, the degrading consortium remained stable at the taxonomical and functional levels, highlighting its catabolic plasticity in biodegrading and defluorinating two chemically distinct fluorinated compounds. This work offers a conceptual framework with novel observations that can guide future efforts to further elucidate the pathways of microbial transformation of these pesticides, ultimately contributing to better environmental risk management practices for these pollutants.},
}
@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}
@article {pmid41500138,
year = {2026},
author = {Bellekom, B and Troman, C and Fitz, S and Akello, JO and Grassly, NC and Shaw, AG},
title = {Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181333},
doi = {10.1016/j.scitotenv.2025.181333},
pmid = {41500138},
issn = {1879-1026},
abstract = {Timely and accurate pathogen detection is critical for the successful implementation of wastewater surveillance and has broad implications for public health. A wide range of surveillance tools are currently available, offering both quantitative and qualitative insights into the wastewater virome. Careful consideration of molecular methodology is required to successfully implement an effective wastewater surveillance scheme. Using SARS-CoV-2 as a model organism, we compared detection success across multiple approaches, including targeted (RT-PCR, qPCR, random priming RT-PCR) and target-agnostic (Rapid SMART-9N metagenomics) methods. We also estimated the copy number required for reliable detection, examined how the ratio of target to off-target genomes in wastewater affects detection and genome coverage using metagenomics, and assessed the efficacy of hybrid capture enrichment of target genomes in improving metagenomic detection. Our results show significant differences between methods, targeted RT-PCR and qPCR were more likely (68 % and 65 % respectively) to detect SARS-CoV-2 than target agnostic approaches. The inclusion of carrier RNA during extraction significantly increased the likelihood of target detection. Our target-agnostic metagenomic approach was consistently unable to detect our target, and, even in the presence of high concentrations that are atypical for wastewater, detection was limited. Target enrichment increased SARS-CoV-2 detection and maximum coverage by metagenomics (SMART-9N), though was outperformed by targeted amplicon sequencing. Overall, our findings support the use of targeted approaches for the routine surveillance of viral pathogens in wastewater. Whilst metagenomics provides broad insights into the virome, enrichment strategies are essential when using it to detect specific viruses, particularly in complex wastewater matrices.},
}
@article {pmid41500047,
year = {2025},
author = {Gutfreund, MC and Callado, GY and Pardo, I and Hsieh, MK and Celeghini, PD and Lopes, GOV and Marra, PS and Cheng, YR and Kobayashi, T and Pinho, JRR and Generoso, JR and Bulgarelli, L and Mendonça, EA and Deliberato, RO and Amgarten, DE and Malta, FM and Edmond, MB and Marra, AR},
title = {Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {4},
pages = {117248},
doi = {10.1016/j.diagmicrobio.2025.117248},
pmid = {41500047},
issn = {1879-0070},
abstract = {BACKGROUND: Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.<br><br>METHODS: This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (&#x2264;21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.<br><br>RESULTS: Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82-0.86) and 0.71 (95% CI: 0.66-0.75), respectively, compared with 0.40 (95% CI: 0.37-0.43) and 0.82 (95% CI: 0.78-0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.<br><br>CONCLUSIONS: mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.},
}
@article {pmid41499937,
year = {2025},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.<br><br>PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.<br><br>METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPK&#x3b1; signaling pathways.<br><br>RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPK&#x3b1; signaling.<br><br>CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPK&#x3b1; signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}
@article {pmid41499920,
year = {2025},
author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S},
title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106558},
doi = {10.1016/j.clnu.2025.106558},
pmid = {41499920},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.<br><br>METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.<br><br>RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.<br><br>CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.<br><br>CLINICALTRIALS: gov ID NCT06317883.},
}
@article {pmid41499832,
year = {2026},
author = {Wang, Y and Yao, C and Zhou, J and Liu, B and Qi, L and Wang, B and Ma, C and Hou, L and Liu, M and Zheng, Y},
title = {Co-occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems.},
journal = {Water research},
volume = {292},
number = {},
pages = {125307},
doi = {10.1016/j.watres.2025.125307},
pmid = {41499832},
issn = {1879-2448},
abstract = {Estuaries worldwide are experiencing intensifying acidification and hypoxia, driven synergistically by anthropogenic activities and global climate change. Nevertheless, their combined impact on the emissions of the potent greenhouse gas methane (CH4) and its underlying regulatory mechanisms remains poorly understood, undermining our ability to project climate feedbacks. Here, we integrated [13]C stable isotope tracing, DNA/mRNA-based qPCR, and amplicon/metagenomic sequencing to unravel how acidification-hypoxia interactions regulate the complex balance between CH4 production and consumption in estuarine sediments. Results showed that aquatic acidification and hypoxia combined to significantly increase CH4 emissions from estuarine sediments (P < 0.05), in a non-additive (antagonistic) manner where oxygen availability was the dominant factor governing this response. Notably, acidification increased CH4 emissions by suppressing methanotrophy more strongly than methanogenesis, whereas hypoxia preferentially stimulated methanogenic activity over CH4 oxidation. These response patterns were further demonstrated by metagenomic sequencing and mRNA-based quantitative PCR analyses, which revealed coordinated shifts in both the relative abundance and transcriptional activity of key functional genes. These findings uncover a previously overlooked mechanism whereby the worldwide co-occurrence of acidification and hypoxia in estuarine ecosystems jointly promote CH4 emissions, providing a scientific basis for improving predictive models of the global CH4 cycle and its climate feedbacks under combined anthropogenic and climatic stressors.},
}
@article {pmid41499829,
year = {2026},
author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125312},
doi = {10.1016/j.watres.2025.125312},
pmid = {41499829},
issn = {1879-2448},
abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.},
}
@article {pmid41499817,
year = {2026},
author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z},
title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119669},
doi = {10.1016/j.ecoenv.2025.119669},
pmid = {41499817},
issn = {1090-2414},
abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.<br><br>METHODS: C57BL/6 mice (n&#x202f;=&#x202f;10 per group) were orally gavaged with DnPP (1-100&#x202f;mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).<br><br>RESULTS: DnPP exposure induced dose-dependent villus degeneration (100&#x202f;mg/kg/d, P&#x202f;<&#x202f;0.05) and colon shortening (P&#x202f;<&#x202f;0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-&#x3b1;) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P&#x202f;<&#x202f;0.001) and elevated antibiotic resistance genes (CARD, P&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.},
}
@article {pmid41499533,
year = {2026},
author = {Liu, T and Song, Z and Zhang, L and Liu, F and Sun, L},
title = {Clinicopathological Features of Orf Virus Infection in the Human: A Rare Case Report of Extensive Skin Infections and Meta-Analysis.},
journal = {Journal of medical virology},
volume = {98},
number = {1},
pages = {e70794},
doi = {10.1002/jmv.70794},
pmid = {41499533},
issn = {1096-9071},
support = {//Beijing Ditan Hospital, Xuzhou Hospital, Capital Medical University, Special Program for Clinical Research and Scientific Innovation Transformation (KCZL202510)./ ; //Training Program for High-level Public Health Technical Talents Construction Project (academic backbone-03-21)/ ; },
mesh = {Humans ; *Orf virus/isolation &amp; purification/genetics ; *Ecthyma, Contagious/pathology/virology/diagnosis ; Male ; Adult ; Animals ; Female ; Sheep ; Middle Aged ; Skin/pathology/virology ; Young Adult ; },
abstract = {The Orf virus is responsible for causing contagious ecthyma in sheep and goats. Humans are primarily infected with Orf virus result in zoonotic skin diseases. We reported a rare case of orf virus infection affecting the face and thoracodorsal regions and performed pathological examination and metagenomic pathogen detection technology(MethPath[TM]) test on the patient. A meta-analysis of the reported cases was also presented. All cases of human infection with orf virus were searched in PubMed and web of science databases. The pathology revealed eosinophilic inclusion bodies visible in the epidermal cells, and the demonstrated orf virus infection by MetaPath™. We identified 99 articles reporting 159 cases of human orf virus infection. The average (±SD) age of all patients was 34.96 ± 16.82 years. Male gender was predominant; hand infections were the most frequent. 81.3% of the patients were infected by contact with sheep. The observed recovery time averaged 42.7 days, with a median of 40 days. The most typical histopathological finding is characterized by the presence of eosinophilic inclusions within vacuolated epidermal cells. When facial nodular lesions are present, obtaining a detailed medical history is essential to aid in considering orf virus infection in the differential diagnosis.},
}
@article {pmid41499519,
year = {2026},
author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E},
title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0323038},
doi = {10.1371/journal.pone.0323038},
pmid = {41499519},
issn = {1932-6203},
mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Food Microbiology ; },
abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.},
}
@article {pmid41499369,
year = {2026},
author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J},
title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70092},
pmid = {41499369},
issn = {1755-0998},
support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; },
abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.},
}
@article {pmid41499358,
year = {2026},
author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H},
title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {16},
number = {1},
pages = {e70579},
pmid = {41499358},
issn = {2001-1326},
support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science &amp; Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.<br><br>METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.<br><br>RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs&#xa0;>&#xa0;.85.<br><br>CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.<br><br>TRIAL REGISTRATION: NCT05244837.<br><br>KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.},
}
@article {pmid41498995,
year = {2026},
author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A},
title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {32},
pmid = {41498995},
issn = {1573-0972},
support = {42430404//National Natural Science Foundation of China/ ; },
}
@article {pmid41498484,
year = {2026},
author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J},
title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70155},
pmid = {41498484},
issn = {1097-0290},
support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; },
abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.},
}
@article {pmid41497396,
year = {2025},
author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T},
title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114029},
pmid = {41497396},
issn = {2589-0042},
abstract = {Metagenomic read classification is a fundamental task in computational biology but remains challenging due to the scale and diversity of sequencing data. We present a run-length compressed BWT-based index using the move structure for efficient multi-class classification. Our method finds all super-maximal exact matches (SMEMs) of length ≥ L between a read and a reference and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs and their class identifiers into a single classification. We are the first to perform run-length compressed read classification using full rather than semi-SMEMs. We evaluated on long and short reads across two datasets: a large bacterial pan-genome with few classes and a smaller 16S rRNA gene database spanning thousands of genera. Our method outperforms SPUMONI 2 in accuracy and runtime while maintaining run-length compressed memory complexity and surpasses Cliffy in memory efficiency with comparable accuracy.},
}
@article {pmid41497123,
year = {2026},
author = {Mehmood, MS and Hajj, F},
title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {997-998},
pmid = {41497123},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.},
}
@article {pmid41496931,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {955-956},
pmid = {41496931},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.},
}
@article {pmid41350554,
year = {2025},
author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M},
title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {560},
pmid = {41350554},
issn = {2045-2322},
abstract = {UNLABELLED: The gut microbiome (GM) is increasingly recognized as a key modulator of neurodevelopment via the microbiome-gut-brain axis. Fragile X syndrome (FXS), the most common inherited monogenic cause of intellectual disability, shares behavioural and molecular features with other neurodevelopmental disorders (NDDs), yet the role of the GM in FXS remains largely unexplored. In this open-label, single-arm trial, 15 children with genetically confirmed FXS received a daily probiotic formulation containing Lactobacillus casei, Lactobacillus salivarius, and Bifidobacterium breve for 12 weeks. Behavioural analysis and metagenomic sequencing with network and pathway analyses were performed before and after probiotic supplementation. Significant improvements were observed in irritability (-3.9, SD: ± 5.2; p = 0.027), communication (+ 1.7, SD: ± 2.5; p = 0.022), socialization (+ 1.4, SD: ± 2.1; p = 0.033), and adaptive behaviour (+ 1.3, SD: ± 1.4; p = 0.004). While overall microbial diversity remained stable, SparCC network analysis revealed increases in connectivity measures such as edge count and clustering coefficient, indicating denser microbial interactions and greater community coordination after probiotic supplementation. Functional profiling showed trends toward increased microbial activity in fatty acid biosynthesis, NAD salvage, and starch degradation pathways. This pilot study provides initial evidence that probiotics may modulate structural and functional properties of the GM, with potential links to improved behavioural outcomes in children with FXS. Larger, controlled trials are needed to validate the therapeutic potential of GM-targeted interventions in FXS and related NDDs.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29896-1.},
}
@article {pmid41496864,
year = {2025},
author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y},
title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf242},
pmid = {41496864},
issn = {2730-6151},
abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.},
}
@article {pmid41496862,
year = {2025},
author = {Rojas-Vargas, J and Samperio-Ramos, G and Camacho-Ibar, VF and Pajares, S},
title = {Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf241},
pmid = {41496862},
issn = {2730-6151},
abstract = {Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.},
}
@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}
@article {pmid41496335,
year = {2026},
author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K},
title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {194},
number = {},
pages = {118923},
doi = {10.1016/j.biopha.2025.118923},
pmid = {41496335},
issn = {1950-6007},
abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.<br><br>OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.<br><br>METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).<br><br>RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.<br><br>CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.},
}
@article {pmid41496236,
year = {2025},
author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y},
title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.},
journal = {Environment international},
volume = {207},
number = {},
pages = {110030},
doi = {10.1016/j.envint.2025.110030},
pmid = {41496236},
issn = {1873-6750},
abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.},
}
@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
doi = {10.1097/MD.0000000000046594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTD&#xe3;&#x20ac;"2025&#xe3;&#x20ac;&#x2022;046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.<br><br>METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.<br><br>RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.<br><br>CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}
@article {pmid41495893,
year = {2026},
author = {Bouras, G and Grigson, SR and Mirdita, M and Heinzinger, M and Papudeshi, B and Mallawaarachchi, V and Green, R and Kim, RS and Mihalia, V and Psaltis, AJ and Wormald, PJ and Vreugde, S and Steinegger, M and Edwards, RA},
title = {Protein structure-informed bacteriophage genome annotation with Phold.},
journal = {Nucleic acids research},
volume = {54},
number = {1},
pages = {},
doi = {10.1093/nar/gkaf1448},
pmid = {41495893},
issn = {1362-4962},
mesh = {*Genome, Viral ; *Molecular Sequence Annotation/methods ; *Bacteriophages/genetics ; *Viral Proteins/chemistry/genetics ; *Software ; Protein Conformation ; },
abstract = {Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here, we introduce Phold, an annotation framework utilizing protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high-quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency, and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveal that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.},
}
@article {pmid41495863,
year = {2026},
author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z},
title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00842-y},
pmid = {41495863},
issn = {2524-6372},
support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; },
abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.<br><br>RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p&#x2009;<&#x2009;0.001) in summer than in winter while the community maturity index was higher (p&#x2009;<&#x2009;0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p&#x2009;<&#x2009;0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p&#x2009;<&#x2009;0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p&#x2009;<&#x2009;0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R&#x2009;=&#x2009;0.222, p&#x2009;=&#x2009;0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).<br><br>CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.},
}
@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34186-x},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}
@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02654-6},
pmid = {41495312},
issn = {1432-184X},
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}
@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.<br><br>OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.<br><br>DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, &#xcd;ndice de Alimentaci&#xf3;n Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6&#x2009;months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.<br><br>RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.<br><br>CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}
@article {pmid41494342,
year = {2026},
author = {Hu, P and Chen, S and Qian, Y and Hong, Y and Lin, JG and He, B and Gu, JD},
title = {Efficient nitrogen removal by coupling with methane metabolism in three landfill leachate wastewater treatment systems.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141035},
doi = {10.1016/j.jhazmat.2026.141035},
pmid = {41494342},
issn = {1873-3336},
abstract = {High concentration of ammonium-nitrogen (NH4[+]-N) is a widley known characteristic of landfill leachate, and therefore, a thorough understanding of the active nitrogen-related microorganisms is essential for designing an efficient landfill leachate treatment system. Here, we analyze the microbial nitrogen cycling and metabolic interactions at three full-scale landfill leachate treatment plants. Specifically, using metagenomics and metatranscriptomics techniques, we elucidate the mechanisms underlying high NH4[+]-N removal rates achieved through distinct N removal strategies (nitrification-denitrification system at Jilong (JL), denitrification-ammonia oxidation-partial nitrification system at Xinfeng (XF), and simultaneous nitrification-denitrification-ammonia oxidation system at Wenshan (WS)), all three plants achieved efficient NH4[+]-N removal of 96 %, 97.96 % and 97.33 % for JL, XF, and WS, respectively. Highly active methane (CH4)-associated microorganisms, particularly CH4-catabolizing bacteria, exhibited strong interactions with denitrifying bacteria in all three treatment plants, promoting effective nitrogen removal in the landfill treatment systems. In addition, enhanced anammox activity in WS treatment plant in 2023 and 2015 was compared using nitrogen-15 isotope labeling and in situ transcriptome analysis. By comparing microbial metabolic activity, strong interactions were observed between anammox bacteria and other nitrogen-transforming microbes. Meanwhile, detailed physicochemical parameter analysis revealed that optimal Fe[3] [+] concentrations significantly promote the enrichment and enhanced activity of anammox bacteria. Collectively, this study highlights strategies for microbial-mediated high-efficiency ammonia nitrogen removal in full-scale landfill leachate and explains the underlying mechanisms that may lead to increased abundance and activity of anammox bacteria.},
}
@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
doi = {10.1016/j.redox.2026.104005},
pmid = {41494287},
issn = {2213-2317},
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}
@article {pmid41494246,
year = {2026},
author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F},
title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.},
journal = {Waste management (New York, N.Y.)},
volume = {212},
number = {},
pages = {115332},
doi = {10.1016/j.wasman.2026.115332},
pmid = {41494246},
issn = {1879-2456},
abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.},
}
@article {pmid41493405,
year = {2025},
author = {Seidel, F and Nygren, TM and Opgen-Rhein, B and Hecht, T and Boehne, M and Weickmann, J and Anderheiden, F and Reineker, K and Böcker, D and Rentzsch, A and Wiegand, G and Fischer, M and Kiski, D and Frede, W and Ruf, B and Tarusinov, G and Papakostas, K and Logeswaran, T and Schiebel, A and Voges, I and Kaestner, M and Kramp, J and Kerst, G and Khedim, M and Gatzweiler, E and Wannenmacher, B and Knirsch, W and Meyer-Dobkowitz, L and Donner, B and Klingner, J and Rau, C and Haller, S and Brinkmann, A and Nitsche, A and Noldt, M and Schmoock, G and Herzmann, C and Degenhardt, U and Bühler, S and Enders, M and Hermes, J and Rolfs, N and Manuylova, T and Schwarzkopf, E and Beudt, J and Siffczyk, C and Schubert, S and Sandfort, M and Klingel, K},
title = {Severe Myocarditis Increase in Children Associated With Parvovirus B19 Infection: MYKKE Registry and German Surveillance Data.},
journal = {JACC. Heart failure},
volume = {},
number = {},
pages = {102854},
doi = {10.1016/j.jchf.2025.102854},
pmid = {41493405},
issn = {2213-1787},
abstract = {BACKGROUND: Following a surge in myocarditis in Germany since August 2023, many with parvovirus B19 (B19V) detection, concerns arose about causes and countermeasures.<br><br>OBJECTIVES: The authors aimed to verify the association among B19V, myocarditis increase, and severity.<br><br>METHODS: Data from the pediatric multicenter registry (MYKKE) from 27 centers were analyzed. B19V myocarditis cases were defined by polymerase chain reaction (PCR) positivity in blood or myocardium with clinical or histopathologic myocarditis evidence. Comprehensive clinical, histopathologic, and epidemiologic analyses were conducted. Past patients were hospitalized from 2013 to July 2023, current from August 2023 to November 2024. Registry data were compared with surveillance and consultant laboratory data. Specimens of current cases underwent metagenomic analysis and B19V sequencing.<br><br>RESULTS: Since 2013, 922 myocarditis patients including 126 (13.6%) with B19V myocarditis were enrolled. With 57 of 126 (45.2%) current cases, B19V myocarditis increased, compared with other myocarditis causes. Most current cases were patients who were <2 years of age (64.9%), 56.1% were female. The ratio of B19V myocarditis to incidence did not increase compared with the earlier period. Current cases presented with more reduced ejection fraction (29.0% vs 34.5%; P = 0.007), linked to severe cardiac T-cell infiltration and high numbers of B19V copies. Increased severity was associated with younger age. Phylogenetic analysis identified B19V genotype 1A, without sequence variants indicating increased virulence.<br><br>CONCLUSIONS: The increase in pediatric myocarditis since August 2023 was associated with B19V, more likely explained by disproportionately young current cases and young children's vulnerability than a virulent strain. Raising clinicians' awareness and proactive, interdisciplinary approaches are essential for improving prevention of B19V infection, management of myocarditis, and treatment strategies in this vulnerable cohort. (Myocarditis Registry for Children and Adolescents [MYKKE]; NCT02590341).},
}
@article {pmid41493389,
year = {2026},
author = {Buchheister, S and Bolsega, S and Rösel-Birk, S and Smoczek, A and Scheele, T and Bleich, A and Basic, M},
title = {Unraveling potential bacterial contamination in germ-free husbandry using bacterial viability staining.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag001},
pmid = {41493389},
issn = {1365-2672},
abstract = {AIMS: Hygienic monitoring (HM) of germ-free (GF) mouse colonies is exceptionally challenging. The test accuracy of the applied diagnostic methodology has to be outstanding to provide proof of absence of all living microorganisms confirming the GF status. In this context, microscopy of native intestinal content serves as a highly sensitive diagnostic tool for the detection of bacterial contaminants. However, with this method residual microorganisms may be detected. To overcome this risk of false-positive results, we complemented our analyses with a bacterial viability staining of the intestinal content of GF mice.<br><br>METHODS AND RESULTS: Intestinal contents of GF mice (n=13) from five isolators were analyzed by bacterial culture and phase-contrast microscopy. Additionally, 16S rRNA gene PCR analysis and metagenomic sequencing were performed. To distinguish between live and dead bacteria, intestinal content was stained by a Bacterial Viability Kit and analyzed by fluorescence microscopy.While culture medium proved sterility of a sample material, increased amounts of scattered bacterial structures were detected during microscopic analysis, indicating potential contamination. Molecular techniques pointed to a presence of environmental bacteria. However, viability staining revealed the presence of only dead (double-stained) bacteria in all samples. Likewise, non-viable bacteria have been identified in samples obtained from irradiated feed, probably being the source of bacterial structures found in GF mice.<br><br>CONCLUSIONS: Altogether, detected bacterial structures were proven to be non-viable and therefore should not be interpreted as isolator contaminants. Thus, in our hands, with the herein described report of suspected contamination we prove, that bacterial viability staining served as a highly valuable screening tool, enhancing diagnostic quality of the HM of GF colonies.},
}
@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}
@article {pmid41493376,
year = {2026},
author = {Shklyar, AA and Mesentsev, YS and Smirnov, AV and Nassonova, ES},
title = {Nucleophaga amutiana, sp. nov.-a novel intranuclear parasite of amoebae from the Far East of Russia expands the diversity and biogeography of microsporidia-like organisms.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/00275514.2025.2586430},
pmid = {41493376},
issn = {1557-2536},
abstract = {The genus Nucleophaga comprises poorly studied intranuclear parasites that infect amoebae. Currently classified within the phylum Rozellomycota, this genus belongs among numerous lineages with unresolved taxonomic positions, primarily identified through metagenomic studies. Three species of Nucleophaga were described at the morphological and molecular levels-N. amoebae, N. terricolae, and N. striatae, all isolated in Europe. Here, we report the discovery of a fourth species of the genus, isolated from the Far East of Russia, infecting nuclei of Thecamoeba sp. A detailed light microscopic study revealed several remarkable morphological features of this organism. For the first time, the division of Nucleophaga plasmodium was illustrated. Experimental infections demonstrated that Thecamoeba quadrilineata and T. foliovenanda can support the development of the parasite, whereas Nucleophaga showed abnormal development in T. onigiri and was unable to survive in T. vumurta. Phylogenetic analysis, based on the nuc 18S rRNA gene sequences, placed the new isolate as a distinct lineage within the genus Nucleophaga. Based on its molecular characteristics, the studied isolate was described as a new species, Nucleophaga amutiana.},
}
@article {pmid41493186,
year = {2026},
author = {Queiroz, VF and Jivaji, AM and Aylward, FO},
title = {Tiny giants in a big ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0299225},
doi = {10.1128/spectrum.02992-25},
pmid = {41493186},
issn = {2165-0497},
abstract = {Prasinoviruses infect some of the most abundant photosynthetic eukaryotes in the ocean, shaping microbial dynamics and playing a major role in nutrient cycling. Despite their ecological significance, they have only been explored in a few marine systems. In a recent study, A. B. de Silva, S. W. Polson, C. R. Schvarcz, G. F. Steward, and K. F. Edwards (Microbiol Spectr 13:e02583-24, 2025, https://doi.org/10.1128/spectrum.02583-24) describe four new prasinoviruses isolated from the tropical North Pacific. The comparative analyses highlighted the placement of these viruses within known prasinovirus lineages while also revealing novel genetic features. To assess their ecological reach, the authors mapped metagenomic reads from global data sets, demonstrating that these viruses are not confined to the Pacific but are globally distributed. These findings expand our understanding of prasinovirus diversity and evolution and highlight their widespread occurrence across oceanic regions.},
}
@article {pmid41492995,
year = {2026},
author = {Sathaye, SB and Sharma, N and Bhaumik, J and Sahoo, D and Rai, AK and Singh, SP},
title = {Novel Glutamate Decarboxylase from Ethnic Food Metagenome: A Potential Biocatalyst to Produce a Nonproteinaceous Amino Acid, γ-Aminobutyric Acid.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11421},
pmid = {41492995},
issn = {1520-5118},
abstract = {This study reports the biochemical characterization of a novel variant of glutamate decarboxylase (mtGAD), identified from an ethnic food, Kinema. The mtgad gene was cloned from the Kinema metagenome and expressed in a heterologous host, Escherichia coli. The enzyme mtGAD was extracted and purified for biochemical characterization. The enzyme showed optimal activity for γ-aminobutyric acid (GABA) synthesis at 50 °C and pH 4.5. The kinetic parameters of mtGAD were computed to be 29.2 mM Km, 561.8 s[-1] kcat, and 23.2 mM[-1] s[-1] kcat/Km. The in silico protein structure analysis, followed by molecular docking and molecular dynamics simulation, revealed that the binding with pyridoxal-5'-phosphate (PLP; a cofactor for mtGAD) reduces the fluctuations in the structure at high temperatures, contributing to the thermal stability of mtGAD. Furthermore, the conversion of about 60% monosodium glutamate (MSG) into GABA was achieved in approximately 3 h of catalytic reaction with 200 mM MSG, treated with 6.67 U mtGAD. A high turnover number with moderate thermal and pH stability makes mtGAD a potential biocatalyst for GABA production.},
}
@article {pmid41492410,
year = {2025},
author = {Wallau, GDL and Barbier, E and Machado, LC and da Silva, AF and Dias, YJM and Dezordi, FZ and Tomazatos, A and Horváth, B and Lins, RD and Bernard, E and Cadar, D},
title = {Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf094},
pmid = {41492410},
issn = {2057-1577},
abstract = {Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.},
}
@article {pmid41492364,
year = {2025},
author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M},
title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.},
journal = {Plant and soil},
volume = {516},
number = {1},
pages = {705-723},
pmid = {41492364},
issn = {0032-079X},
abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.<br><br>METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.<br><br>RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.<br><br>CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.},
}
@article {pmid41492358,
year = {2026},
author = {Pan, D and Jiang, M and Wang, Y and He, J and Tang, J and Liu, S and Li, M and Jiang, X and Xu, Q},
title = {Multi-omics reveals associations between the microbiota-gut-brain axis and antidepressant effects of vagus nerve stimulation.},
journal = {Neurobiology of stress},
volume = {40},
number = {},
pages = {100777},
pmid = {41492358},
issn = {2352-2895},
abstract = {BACKGROUND: Major depressive disorder is a severe mental health condition characterized by persistent depressed mood and loss of interest. Current first-line pharmacotherapies often exhibit limited therapeutic performance and adverse side effects. Transcutaneous auricular vagus nerve stimulation (taVNS) is a promising, safe, and noninvasive alternative intervention with demonstrated neuromodulatory efficacy. Nevertheless, its mechanisms remain unclear. This study investigated whether the antidepressant properties of taVNS are associated with the microbiota-gut-brain axis, focusing on the potential crosstalk between differentially expressed hippocampal proteins and the gut microbiota.<br><br>METHODS: A chronic unpredictable mild stress (CUMS) rat model of depression was established, and taVNS was administered for 14 days. Hippocampal proteomic profiling was performed using data-independent acquisition. Fecal metagenomic sequencing was conducted to characterize alterations in gut microbial communities. Key signaling pathways were validated using Western blot, qRT-PCR, HE staining, and transmission electron microscopy, all of which were employed to systematically assess behavioral, proteomic, microbial, and molecular changes.<br><br>RESULTS: Proteomics and molecular analyses revealed that taVNS upregulated hippocampal expression of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 1 (GluN1) and brain-derived neurotrophic factor (BDNF), while simultaneously restoring mitogen-activated protein kinase (MAPK) signaling activity. Metagenomic profiling demonstrated that taVNS increased the abundance of Akkermansia muciniphila and reduced Ligilactobacillus reuteri. Ligilactobacillus levels were positively correlated with synaptogyrin-1 (Syngr1), indicating their potential association in enhancing the antidepressant effects mediated by the GluN1/MAPK/BDNF signaling cascade.<br><br>CONCLUSION: TaVNS significantly alleviated depression-like behaviors in CUMS-exposed rats. The underlying mechanism may involve the restoration of synaptic function of glutamatergic neurons by regulating the GluN1/MAPK/BDNF signaling pathway. In addition, taVNS reshaped the gut microbiota, markedly increasing the abundance of Akkermansia muciniphila and Ligilactobacillus murinus while reducing Limosilactobacillus reuteri and Lactobacillus johnsonii. The positive correlation between Syngr1 protein level and Ligilactobacillus abundance in the hippocampus suggests that the microbiota-gut-brain axis may play a key role in the antidepressant effects of taVNS.},
}
@article {pmid41492297,
year = {2025},
author = {Cordeiro, NF and Coppola, N and Ferreira, F and Vignoli, R and Bado, I},
title = {What are we eating?. Detection of antibiotic resistance mechanisms in frozen chicken nuggets imported from Brazil.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101171},
pmid = {41492297},
issn = {2352-7714},
abstract = {The rise of antibiotic resistance is a growing challenge, affecting humans, the environment, and animals. Under the One Health framework, this study investigated resistance mechanisms to critically important antibiotics in frozen chicken nuggets imported from Brazil. Eighty nugget samples were cultured on selective media containing ceftriaxone, ciprofloxacin, or colistin. Isolates were identified using MALDI-TOF, and antibiotic susceptibility was assessed by disk diffusion. Eight samples were also analyzed using shotgun metagenomic sequencing processed through the SqueezeMeta pipeline. Nineteen Enterobacterales resistant mainly to β-lactams and to a lesser extent, to quinolones and aminoglycosides, were identified. Eight Pseudomonas spp. were recovered, including one P. fulva resistant to colistin. Metagenomics revealed predominant Firmicutes, (Bacillaceae, Lactobacillaceae, and Paenibacillaceae) with low γ-Proteobacteria levels. Additionally, we detected resistance genes against several antibiotics. This study highlights the role of imported food in spreading AMR and the value of combining metagenomics with conventional microbiology to strengthen One Health surveillance.},
}
@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.<br><br>RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20&#xa0;&#xb0;C, and -80&#xa0;&#xb0;C), revealed no significant impact on microbial composition. Additionally, the NEBNext&#xae; Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.<br><br>CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04523-1.},
}
@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03905-y},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.<br><br>RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.<br><br>CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}
@article {pmid41491676,
year = {2026},
author = {Long, Y and Guo, J and Dai, L and Jiang, J},
title = {Interactions between phytoplankton and bacterioplankton communities in Caohai plateau lake, revealed by environmental DNA metagenomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {4},
pmid = {41491676},
issn = {1471-2180},
support = {QKHJC-ZK[2023]YB233//Guizhou Provincial Science and Technology Projects, China/ ; 32360036//National Natural science Foundation of china/ ; QSS2024001//Talent Team Proiect of Guizhou lnstitute of Biology,china/ ; QKHPT[2025]015//Guizhou Provincial science and Technology Projects, China/ ; },
mesh = {*Phytoplankton/genetics/classification/physiology ; *Lakes/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; China ; *DNA, Environmental/genetics ; *Plankton/genetics/classification ; Ecosystem ; *Microbial Interactions ; },
abstract = {Phytoplankton-bacterioplankton interactions critically influence aquatic ecosystem stability, yet their dynamics remain poorly understood in eutrophic plateau lakes. This study employed environmental DNA (eDNA) metagenomics to investigate these cross-kingdom relationships in Caohai Plateau Lake, a vulnerable wetland undergoing macrophyte-to-algae regime shifts, integrating correlation analysis, niche overlap, redundancy analysis (RDA), co-occurrence networks, and neutral community model (NCM). A total of 331 phytoplankton species across 10 phyla were characterized in the phytoplankton community, dominated by Cyanophyta with Microcystis as the representative genus, while bacterioplankton communities were primarily structured by Proteobacteria and Sphingomonas. The assembly of phytoplankton community was primarily driven by stochastic processes (R[2]>0.90). Co-occurrence network analysis showed phytoplankton interactions were dominated by positive effects (84.25%), whereas bacterioplankton networks exhibited balanced positive and negative effects. Metabolic specialization emerged through LEfSe analysis: phytoplankton specialized in photosynthesis and carbon storage, while bacterioplankton dominated anaerobic respiration (propanoate metabolism). The positive interactions were more prevalent than negative ones; combined with the metabolic complementarity of phytoplankton and bacterioplankton, this suggests that mutualism is more dominant than competition in cross-kingdom interactions. High niche overlap under sufficient nutrients (TP) facilitated species coexistence of phytoplankton and bacterioplankton by minimizing resource competition, thereby promoting stochastic community assembly, while keystone taxa (Cyanothece, Sphingobium) mediated ecosystem stability. This work demonstrates that nutrient enrichment promote stochastic assembly in eutrophic plateau lakes.},
}
@article {pmid41491168,
year = {2026},
author = {Zhao, Y and Dai, L and Wang, L and Wang, L},
title = {Case report: a case of neonatal Candida osteomyelitis with septic arthritis and literature review.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {9},
pmid = {41491168},
issn = {1471-2431},
abstract = {A preterm infant who previously experienced Candida septicemia at 18 days of life and was treated with standard antifungal therapy presented one month later with signs of multifocal osteomyelitis and arthritis. Causative Candida albicans was detected by metagenomic next-generation sequencing (mNGS). Since the symptoms of neonatal candidal osteomyelitis are typically insidious, early diagnosis and appropriate treatment are crucial. Moreover, incision and drainage of the affected joint are essential for a favorable prognosis.},
}
@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02283-8},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.<br><br>RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n&#x2009;=&#x2009;24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.<br><br>CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}
@article {pmid41491235,
year = {2026},
author = {Huang, J and Feng, Z and Fu, J and Zou, J and Xiang, Q and Liu, X and Li, L and Yu, R},
title = {Amelioration of acute lung injury by Salvia miltiorrhiza-derived extracellular vesicles: through repair of the vascular barrier and modulation of lung microbiota.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {6},
pmid = {41491235},
issn = {1749-8546},
support = {2025JJ80078//Natural Science Foundation of Hunan Province/ ; 23B0379//Education Department of Hunan Province/ ; A2024010//Health Commission of Hunan Province/ ; kq2402183//Science and Technology Bureau, Changsha/ ; 22JBZ002//Hunan University of Chinese Medicine/ ; 24YS003//Hunan University of Chinese Medicine/ ; },
abstract = {BACKGROUND: Acute lung injury (ALI) is a severe respiratory disease characterized by diffuse lung injury, vascular barrier dysfunction, and inflammatory responses. Its current treatments such as corticosteroids often involve adverse effects, highlighting the need for alternative therapies. Salvia miltiorrhiza-derived extracellular vesicles (SMEVs) have shown a potential therapeutic value for ALI due to their anti-inflammatory and barrier-protective properties, but the specific mechanisms remain unclear.<br><br>METHODS: SMEVs were extracted and purified through differential centrifugation coupled with sucrose density gradient centrifugation, and were analyzed by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Biosafety assessment was then conducted in zebrafish embryos, mouse organs, and human umbilical vein endothelial cells (HUVEC). Subsequently, the treatment efficacy of SMEV on LPS-induced HUVEC inflammation was evaluated in vitro. LPS-induced ALI mice were then treated with SMEVs to further evaluate the posttreatment lung histopathology, vascular barrier markers, and microbial composition using metagenomics in vivo.<br><br>RESULTS: SMEVs exhibited a typical bilayer structure (average size: 177.7&#xa0;nm) and excellent biosafety properties. In vitro, SMEVs effectively reduced LPS-induced inflammation (IL-1&#x3b2;, IL-6, TNF-&#x3b1;) and promoted wound healing in HUVEC, while in vivo, SMEVs ameliorated pulmonary edema and inflammation, and restored the VE-cadherin expression. Metagenomic analysis revealed that SMEVs were capable of regulating lung microbiota and reducing the pathogenic bacterial (e.g., g-Listeria, g-Streptococcus) and microbial diversity and richness after LPS stimulation.<br><br>CONCLUSION: SMEVs can ameliorate ALI by repairing the vascular barrier and modulating lung microbiota, offering a novel therapeutic strategy for this disease. Future research may focus on the SMEV-microbiota-immune interaction targeting ALI treatment.},
}
@article {pmid41491053,
year = {2026},
author = {Manirakiza, B and Zhang, S and Addo, FG and Ifon, BE and James, N and Kiribou, R and Nadine, NIA and Nyandwi, V and Sebaziga, JN and Mukasekuru, R and de Dieu Uwizelimana, J},
title = {Untapped Microbial Diversity, Assemblages, and Interactions in Rwandan Geothermal Spring Mats, Africa.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {123},
pmid = {41491053},
issn = {1432-0991},
support = {E51879084//National Natural Science Foundation of China/ ; E51579075//National Natural Science Foundation of China/ ; },
mesh = {*Hot Springs/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Rwanda ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; *Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {Research on prokaryotes living in geothermal ecosystems have broadened our understanding of their compositions and response to extreme environmental stresses, especially for plankton bacterial communities in hot spring water. However, the comprehensive exploration of microbial diversity, assemblages, and interactions in geothermal spring mats in Africa, particularly in Rwanda, remain underexplored. This study explored the bacterial and eukaryotic communities' biodiversity, assemblages, and interactions within microbial mats from the Bugarama hot pool (BHP; 40-47 °C) and Gisenyi hot springs (GHS; 58-71.4 °C) in Rwanda, using high-throughput sequencing of the 16S rRNA gene and 18S rRNA gene, complemented by null and neutral community models and physicochemical analytical methods. Interestingly, the bacterial Shannon, Evenness, and Simpson indices were significantly different (P < 0.05) among geothermal spring mats. In BHP and GHS, the abundances of Chloroflexota, Proteobacteria, Firmicutes, and Acidobacteriota were significantly higher in BHP (P < 0.05) than in GHS, whereas Cyanobacteria, Bacteroidota, Planctomycetota, Verrucomicrobiota, and Spirochaetota were significantly more abundant in GHS (P < 0.01). Conversely, Chloroplastida, Mucoromycota, Arthropoda, and Cryptomycota were significantly more prevalent in BHP (P < 0.05), while the SAR supergroup, Ascomycota, Nematoda, and Amoebozoa dominated in GHS (P < 0.05). Through null and neutral modeling, stochastic processes exerted greater influence on bacterial and eukaryotic community assembly in fine-scale variations within geothermal spring mats. Despite this stochastic predominance, abiotic environmental factors (deterministic processes) such as temperature, pH, salinity (EC and TDS), and nitrate cannot be entirely ruled out. Moreover, Co-occurrence network analysis (|r|> 0.7, P < 0.05) revealed more complex and stable microbial interactions at higher temperatures (GHS). These findings highlight the rich underexplored microbial diversity and interactions in Rwandan geothermal spring mats through metagenomic analysis, shedding light on ecological processes and dynamics in extreme environments. Despite being ignored in metagenomic studies, eukaryotic communities highlight novel temperature-tolerant taxa: Echinamoeba and Tubulinea in phylum Amoebozoa, Monhysterida in phylum Nematoda, and Novel_Clade_Gran-5 in phylum Cercozoa, which are both pathogens and fierce predators thriving in geothermal habitats.},
}
@article {pmid41490675,
year = {2026},
author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C},
title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133923},
doi = {10.1016/j.biortech.2026.133923},
pmid = {41490675},
issn = {1873-2976},
abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.},
}
@article {pmid41490674,
year = {2026},
author = {Hao, X and Zeng, W and Gong, Q and Zhan, M and Miao, H and Yuan, C and Peng, Y},
title = {Biochar derived from waste iron-rich biosludge promotes iron-nitrogen coupled nitrogen removal in wastewater treatment.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133935},
doi = {10.1016/j.biortech.2026.133935},
pmid = {41490674},
issn = {1873-2976},
abstract = {Traditional biological nitrogen removal faces sustainability challenges due to high energy consumption and chemical demands. This study developed a novel autotrophic process leveraging the Fe-N cycle, enhanced by biochar derived from waste iron-rich biosludge (BC-Fe). During 150-day operation, adding 1 g/L BC-Fe (450 °C) achieved a total nitrogen removal efficiency of 94 ± 1 %, reducing aeration energy by 68 % and eliminating the need for external carbon sources compared to conventional nitrification-denitrification. BC-Fe served as a substrate and electron shuttle, facilitating Fe(III) reduction coupled with anaerobic ammonium oxidation (Feammox), nitrate-dependent Fe(II) oxidation, and denitrification, thereby supplying nitrite for Anammox. It enhanced iron bioavailability and established integrated carbon, nitrogen, and iron cycles, promoting microbial metabolism and system resilience. Metagenomics revealed Candidatus Brocadia fulgida performing Feammox via hao, compensating for hzs/hdh deficiency, while Saprospiraceae utilized biochar-derived organics for denitrification. This work provides a scalable solution to promote circular economy principles in wastewater treatment.},
}
@article {pmid41490614,
year = {2026},
author = {Campos-Silva, R and Rahimi, F and Joshi, J and Voiniciuc, C and Zhou, J and Hanson, AD},
title = {Mining bacterial (meta)genomes for enzymes active in aerobic, mesophilic conditions.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116045},
doi = {10.1016/j.ab.2026.116045},
pmid = {41490614},
issn = {1096-0309},
abstract = {Enzyme biochemistry can now draw on hundreds of thousands of prokaryotic genomes and metagenomes to identify orthologous genes for research, biocatalysis, and metabolic engineering. In many applications, adaptation to O2 and mild temperatures are essential. But as organism lifestyle information can be poor or absent (especially for metagenomes), it is challenging to avoid orthologous genes from anaerobes and extremophiles. Taking bacterial sulfide-dependent THI4 thiazole synthases as test-cases, we built computational pipelines that use only DNA sequence inputs to explore (i) the average oxidation state of carbon (ZC) in orthologous enzymes and (ii) the presence of O2-metabolism genes in the corresponding (meta)genomes. ZC has been proposed to be highest (least negative) in proteins of organisms from O2-rich, mesophilic environments. We found that ZC values of 2,300 THI4s ranged from -0.107 (relatively oxidized) to -0.302 (strongly reduced). As predicted, genes specifying cytochrome c or o oxidases (supporting respiration at relatively high O2 levels) and, to a lesser extent, cytochrome bd oxidases (which can function to scavenge O2) were more frequent in genomes encoding THI4s with high ZC values. Eight THI4s with ZC values in the top 5% and from (meta)genomes having cytochrome oxidases were tested for ability to complement a THI4Δ yeast strain in aerobic conditions. Three THI4 genes from a metagenome with cytochrome c/o oxidase (but without cytochrome bd) were active. These results support the feasibility of combining ZC and cytochrome oxidase profiles to identify bacterial orthologous enzymes that work in aerobic, mild temperature conditions.},
}
@article {pmid41490375,
year = {2025},
author = {Hou, S and Xie, E and Si, B and Xiao, Y and Ding, J and Yan, Z and Zhou, H and Cheng, H and Shen, Y and Li, Y},
title = {Nanobubble aeration accelerates manure wastewater sanitisation and enhances nitrogen retention while reduces greenhouse gas emissions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125267},
doi = {10.1016/j.watres.2025.125267},
pmid = {41490375},
issn = {1879-2448},
abstract = {Manure wastewater is an organic effluent rich in nitrogen and is often regarded as a valuable recycled nutrient source for crop production; however, it also contains high concentrations of organic pollutants and pathogenic microorganisms, and inadequate treatment can lead to serious environmental and public health risks. Nanobubbles (NBs) aeration is an emerging high-efficiency gas-liquid mass-transfer technology, but its role in nitrogen conservation and hygienic stabilisation of nutrient-rich manure wastewater remains unclear. Here, a 180-day experiment with piggery wastewater compared four NBs and conventional aeration regimes against natural storage. We quantified sanitisation performance, nitrogen transformation, greenhouse-gas emissions, microbial communities and virulence factors, and determined oxygen transfer rate (OTR), oxygen transfer efficiency (OTE) and volumetric mass-transfer coefficient (kLa) under identical airflow. NBs aeration markedly increased dissolved oxygen and ·OH generation, thereby enhancing COD, BOD5 and Escherichia coliremoval and shortening the time to reach hygienic standards by 60 and 150 days compared with conventional aeration and natural storage, respectively.Although TN decreased in all treatments, the shorter sanitisation period under NBs aeration led to higher residual TN at compliance. The TN loss rate was 13.96% and 15.39% lower than under CA and CK, and cumulative N2O emissions were 30.21% lower than under conventional aeration. Network and metagenomic analyses showed that NBs aeration reshaped bacterial, fungal and archaeal communities, weakened virulence-factor connectivity, and strengthened the coupling between nitrogen-cycling microbes and gaseous nitrogen pathways. Quantification of OTR, OTE and kLa demonstrated that these benefits arise from the intrinsic mass-transfer properties of nanobubbles rather than an increased oxygen supply rate. Overall, this work provides new mechanistic insight and engineering evidence that NBs aeration can simultaneously accelerate manure wastewater sanitisation and improve nitrogen management for subsequent fertiliser reuse.},
}
@article {pmid41489359,
year = {2026},
author = {Yancey, CE and Hart, LN and Dick, GJ},
title = {Secondary metabolism of Microcystis: current understanding and recent advances in unlocking genomic and chemical diversity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0163425},
doi = {10.1128/aem.01634-25},
pmid = {41489359},
issn = {1098-5336},
abstract = {The cyanobacterial genus Microcystis is globally distributed and known for its ability to produce microcystins, a structurally diverse group of cyanotoxins. However, the biosynthetic capacity of Microcystis is vast; its diverse genomes contain a variety of biosynthetic gene clusters (BGCs) encoding the synthesis of metabolites that may be toxic, have important ecological function, or have applications for biotechnology or drug discovery. Recent studies illustrate that these BGCs vary significantly across Microcystis strains, can be highly expressed in environmental conditions, and may play key roles in cellular physiology, grazer deterrence, and microbial interactions. However, many of these BGCs and metabolites remain poorly characterized or completely uncharacterized, having been identified only through genome sequencing or mass spectrometry, respectively, leaving no knowledge of their structure, bioactivity, or physiological or ecological functions. Here, we synthesize the current body of knowledge regarding the secondary metabolism of Microcystis in terms of genetic and chemical diversity, potential drivers of synthesis, and physiological and ecological functions. This review highlights the need for further research to characterize the largely unexplored genetic and chemical diversity of Microcystis in communities in the environment and discusses the challenges and opportunities of integrating high-throughput multiomic approaches to link uncharacterized gene clusters with their corresponding metabolites. Microcystis will continue to be a rich source for secondary metabolite research as its genetic and chemical potential likely plays a critical role in the persistence and observed dynamics of harmful algal blooms and may harbor uncharacterized toxins and metabolites.},
}
@article {pmid41489358,
year = {2026},
author = {Surgenor, K and McCormick, C},
title = {Diving into the hidden viral world of marine protists.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0126225},
doi = {10.1128/jvi.01262-25},
pmid = {41489358},
issn = {1098-5514},
abstract = {As the most abundant biological entities in the ocean, viruses of microbes play important roles in regulating host population dynamics and influencing biogeochemical cycles. Metagenomic surveys have revealed an astounding reservoir of viral genetic diversity in single-celled marine eukaryotes known as protists, but the vast majority of these viruses have not been directly observed, and information about their protist hosts remains fragmentary. The 2023 discovery of mirusviruses provides a striking example, whereby metagenomic surveys of samples collected by the Tara Oceans expedition led to the discovery of a new phylum of viruses, the Mirusviricota, with remarkable chimeric genomes encoding structural proteins from herpesviruses and enzymes from giant eukaryotic viruses. However, because mirusviruses were detected indirectly by metagenomics, their host range remained unclear, and their biological properties unexplored. Here, we provide new insights into research approaches to identify bona fide protist hosts for marine viruses and characterize virus-host interactions. A greater understanding of these viruses and their natural hosts will unlock opportunities to understand the roles that they play in regulating biogeochemical processes in marine habitats.},
}
@article {pmid41489025,
year = {2026},
author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M},
title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70719},
pmid = {41489025},
issn = {1399-3054},
mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; },
abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.},
}
@article {pmid41488896,
year = {2025},
author = {Liu, J and Huang, L},
title = {Case Report: Simultaneous Paragonimus skrjabini infection in twin girls with spontaneous emergence of a juvenile worm from the eyelid of the elder sister.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1708963},
pmid = {41488896},
issn = {2296-2360},
abstract = {We reported a rare case of paragonimiasis occurring in twin sisters who had eaten raw crabs 7 months ago. The elder sister complained of eyelid swelling and migratory lumps, while the younger sister was asymptomatic. Laboratory tests showed eosinophilia and elevated levels of inflammatory indicators in the two sisters. The brain MRI of the elder twin showed hyperintensity in the frontal lobe, suggesting cerebral hemorrhage. The chest CT image of the twins showed pulmonary involvement. Enzyme-linked immunosorbent assay (ELISA) for serum antibody test and metagenomic next-generation sequencing (mNGS) of subcutaneous tissue from the eyelid-obtained via sterile puncture aspiration under local anesthesia-confirmed Paragonimus skrjabini infection. After praziquantel treatment, both of the sisters recovered. This study aims to enhance clinical awareness and highlight the application of advanced molecular diagnostic technologies for identifying rare parasitic infections.},
}
@article {pmid41488894,
year = {2025},
author = {Lin, B and Zhu, Z and Yang, X and Li, Z and Zhou, H and Luo, M and Guan, J and Zou, Y and Chen, H and Zhuang, Z and Meng, S and Li, W and Yang, Q and Dai, D},
title = {Protocol for the efficacy and safety of fecal microbiota transplantation in children with autism spectrum disorder: a prospective single-center, single-arm interventional study.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1660773},
pmid = {41488894},
issn = {2296-2360},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental condition affecting 0.7% of children globally, with 90% experiencing comorbid gastrointestinal (GI) symptoms. Fecal microbiota transplantation (FMT) may modulate ASD symptoms via the microbiota-gut-brain axis (MGBA).<br><br>METHODS: This open-label single-arm trial enrolls 30 children (2-12 years) with moderate-to-severe ASD, defined as a Childhood Autism Rating Scale (CARS) score of &#x2265;36. Participants receive 3 nasojejunal FMTs (5&#x2005;mL/kg) over 5 days. The primary outcomes are GI symptom improvement, assessed using the Gastrointestinal Symptom Rating Scale (GSRS), and ASD severity, assessed using the CARS. Secondary outcomes include social responsiveness (Social Responsiveness Scale, SRS), aberrant behaviors (Aberrant Behavior Checklist, ABC), and gut microbiota changes assessed by metagenomic next-generation sequencing (mNGS).<br><br>ETHICS AND DISSEMINATION: Ethical approval obtained from Shenzhen Children's Hospital Ethics Committee. Results will be disseminated via peer-reviewed publications and conference presentations.Clinical Trial Registration: https://www.chictr.org.cn/showproj.html?proj=229136, identifier ChiCTR2400083998. Registered on 2024-05-08. Registered title: "Efficacy and safety of fecal microbiota transplantation in treatment of autism spectrum disorder: a prospective single-center intervention study".},
}
@article {pmid41488762,
year = {2025},
author = {Zhao, Y and Hu, X and Li, C and Huang, J and Guo, K and Pan, Q and Yu, Z},
title = {Comprehensive Analysis of Vaginal and Gut Microbiome Alterations in Endometriosis Patients.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {5775-5786},
pmid = {41488762},
issn = {1179-1411},
abstract = {PURPOSE: Endometriosis (EMS) is a chronic gynecological disorder with unclear pathogenesis. While the vaginal and gut microbiomes are known to influence EMS, few studies have analyzed both microbiomes integrally. This study aims to characterize the vaginal and gut microbiome profiles in EMS patients and evaluate their diagnostic potential.<br><br>PATIENTS AND METHODS: We conducted metagenomic sequencing on 22 paired vaginal and fecal samples from EMS patients and controls. Microbial composition, diversity, and metabolic pathways were analyzed. Machine learning models were employed to assess the predictive performance of microbiome features in EMS diagnosis.<br><br>RESULTS: EMS patients exhibited pronounced shifts in the vaginal microbiome, characterized by reduced Lactobacillus and increased Bifidobacterium and Gardnerella, which correlated with elevated luteinizing hormone (LH) and follicle-stimulating hormone (FSH) levels. The gut microbiome displayed decreased diversity, with a depletion of beneficial taxa such as Ruminococcus and Prevotella, alongside an enrichment of Dialister. Metabolic pathways in both microbial communities were significantly altered. Machine learning analyses demonstrated that gut microbiome features outperformed both vaginal microbiome and hormonal indices in predicting EMS, highlighting their strong diagnostic potential.<br><br>CONCLUSION: This study underscores the pivotal role of the gut microbiota in EMS and elucidates the complex interplay between microbial dysbiosis and disease pathogenesis. Our findings indicate that gut microbiome signatures may serve as superior diagnostic biomarkers for EMS, thereby paving the way for microbiome-based diagnostic and therapeutic strategies.},
}
@article {pmid41488684,
year = {2026},
author = {Zeng, A and Yang, M and Yang, T and Yang, W and Zhang, J},
title = {Effects of hot water treatment, silver hydroxide ion solution and carboxymethyl chitosan on Lanxangia tsao-ko quality.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100326},
pmid = {41488684},
issn = {2666-5662},
abstract = {The fruit of Lanxangia tsao - ko (LT), a widely used spice, is highly perishable during storage and transportation making it essential to develop effective preservation methods. This study employed multi-omics techniques to evaluate the effects of three different treatments on the quality of LT during short-term storage. Results demonstrated that, compared to the tap water control group (TW), the hot water treatment group (HW), carboxymethyl chitosan treatment group (CMC), and hydrogen peroxide‑silver ion solution treatment group (SP) significantly suppressed the increase in color change intensity (ΔE), browning index (BI), weight loss rate (W%), and rot rate (R%) of LT. Furthermore, these treatments promoted the accumulation of beneficial flavor substances, while reducing the level of unfavorable ones. Both CMC and SP were effective in inhibiting the increase of LT's respiration intensity and the relative abundance of pathogenic microorganisms like Rhizopus microsporus and Rhizopus arrhizus. However, HW led to an abnormal decrease in respiration intensity and increases the relative abundance of certain pathogenic microorganisms. In summary, although the temperature setting in the hot water treatment group was not ideal, hot water treatment still significantly inhibited the spoilage and discoloration phenomenon. Both CMC and SP can effectively extend the storage and transportation period of LT in all aspects. This study provides a new idea for the preservation of LT.},
}
@article {pmid41488305,
year = {2025},
author = {Liu, Y and Wang, J and Wei, W and Xia, M and Ji, D and Wang, F and Zhang, X and Wang, W},
title = {Depth differentiation of microbial communities and nutrient cycling functional genes in semi-arid riparian soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717707},
pmid = {41488305},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial communities and their associated carbon, nitrogen, and phosphorus metabolic processes play a role in maintaining ecological functions and nutrient cycling in riparian zones. However, systematic research on the coupling mechanisms of carbon, nitrogen, and phosphorus biogeochemical processes in soil profiles of semi-arid riparian soil is still limited.<br><br>METHODS: This study focused on the riparian zone of the Tuwei River, a typical semi-arid river. Metagenomic sequencing was used to analyze the composition of microbial communities and their carbon, nitrogen, and phosphorus metabolic functions across different soil depths along the river.<br><br>RESULTS: The dominant taxa across all depths and river sections were Proteobacteria (average relative abundance 49.85%) and Serratia (11.23%). Results from ANOVA and Tukey-Kramer post-hoc multiple comparison tests showed that microbial diversity significantly decreased with increasing soil depth (p <&#x202f;0.05). Gene families associated with carbon fixation (accC, pccB), denitrification (nosZ, nirK), and phosphorus metabolism (purC, guaB, pyrG) were significantly enriched in surface soils and showed clear depth-dependent declines (p <&#x202f;0.05). Partial Mantel tests revealed that microbial metabolic functions were significantly correlated with porosity (p <&#x202f;0.05), soil organic carbon, total nitrogen, and total phosphorus, confirming that nutrient availability and soil structure are key regulators of microbial biogeochemical functions.<br><br>CONCLUSION: Our findings reveal that nutrient availability and soil structure jointly regulate the vertical distribution of microbial metabolic functions. These insights provide a scientific basis for ecological restoration and soil management in semi-arid riparian zones, where optimizing surface structure and nutrient inputs can stimulate microbial-driven biogeochemical cycling. Key functional taxa and genes may also serve as sensitive indicators for evaluating restoration effectiveness under climate-induced stress.},
}
@article {pmid41488304,
year = {2025},
author = {Duan, Y and Li, X and Chai, Y and Chen, H and Hou, H},
title = {Adlercreutzia-modulated polyunsaturated fatty acid metabolism underlies nicotine's anti-obesity effects.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682370},
pmid = {41488304},
issn = {1664-302X},
abstract = {BACKGROUND: The regulatory effects of nicotine on energy balance through central and peripheral mechanisms have been reported. However, its impact on obesity and gut microbiota at safe doses remains unclear.<br><br>RESULTS: In this study, it was found that chronic oral nicotine administration daily at relative low dose (0.5 mg/kg) significantly alleviated high-fat diet (HFD)-induced obesity phenotypes in mice, including body weight gain, fat deposits, hepatic steatosis, inflammation and metabolic dysfunction. Gut microbiota depletion and fecal microbiota transplantation (FMT) confirmed that these beneficial effects were microbiota-dependent. Metagenomic sequencing confirmed that nicotine administration reshaped gut microbiota composition, and specifically enriched the commensal genus Adlercreutzia, whose increased abundance correlated with improved biochemical indicators related to obesity. Furthermore, transplantation of Adlercreutzia reproduced anti-obesogenic effects, suggesting it was a key factor for nicotine reducing HFD-induced obesity. Untargeted metabolomics analysis combined association analysis further demonstrated that nicotine modulated host metabolic profiles via gut microbiota-metabolite axis, particularly enhancing Adlercreutzia-linked lipid metabolites involved in polyunsaturated fatty acid (PUFA) metabolism.<br><br>CONCLUSION: Collectively, our study elucidates the critical involvement of gut microbiota in nicotine-induced obesity amelioration, uncovers a novel Adlercreutzia-PUFA metabolic axis mediating nicotine's anti-obesity effects, and highlight Adlercreutzia potentiation as a promising microbiota-directed invention strategy for obesity and metabolic syndrome.},
}
@article {pmid41488077,
year = {2025},
author = {Sun, X and Jiao, Q and Fu, X and Xie, T and Xie, W and Cheng, H and Chen, S},
title = {Case Report: Severe psittacosis in an elderly patient without avian exposure: diagnosis via metagenomic next-generation sequencing and rapid response to doxycycline.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1689333},
pmid = {41488077},
issn = {2296-858X},
abstract = {Chlamydia psittaci causes psittacosis in both birds and humans, typically following avian exposure. We present a case of severe psittacosis in a 73-year-old woman with no documented bird contact. The diagnosis was ultimately achieved through metagenomic next-generation sequencing (mNGS) after initial conventional serologic tests failed to identify a pathogen. The patient presented with fever and pneumonia that were unresponsive to broad-spectrum antibiotics. mNGS performed on a whole-blood sample collected on hospital day 5 detected C. psittaci, albeit with a low number of specific sequence reads (only 14 reads mapping to the C. psittaci genome). Oral doxycycline (100 mg q12h) was initiated promptly, resulting in defervescence within 24 h and resolution of inflammatory markers. Although community pet parrots were identified as a potential source, the patient denied any direct contact. This case highlights the risk of environmental aerosol transmission in the absence of direct avian exposure, demonstrates the critical role of mNGS in diagnosing culture-negative pneumonia, and underscores the efficacy of early doxycycline therapy. Strengthened public health surveillance of avian reservoirs is imperative to mitigate unrecognized transmission.},
}
@article {pmid41487523,
year = {2025},
author = {Gómez-Cebrián, N and Trull, MC and Gras-Colomer, E and Edo Solsona, MD and Poveda Andrés, JL and Puchades-Carrasco, L},
title = {Systemic metabolic reprogramming and microbial dysbiosis in Fabry disease: Multi-omics mechanisms and implications for drug development.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1702682},
pmid = {41487523},
issn = {1663-9812},
abstract = {Current treatments, including enzyme replacement and pharmacological chaperones, have improved disease outcomes but often fail to fully prevent progression or alleviate persistent symptoms, underscoring the need for novel therapeutic strategies. Recent systems biology and multi-omics approaches have revealed consistent and previously underappreciated alterations in systemic metabolism and the gut microbiota in FD. Here, we synthesize evidence from metabolomic, lipidomic, transcriptomic, and metagenomic studies in patients and experimental models, highlighting disturbances in redox balance, mitochondrial function, energy metabolism, and microbiota-derived metabolites such as short-chain fatty acids and tryptophan catabolites. These findings point to new mechanisms underlying gastrointestinal, inflammatory, and metabolic complications in FD, with direct implications for biomarker discovery and drug development. We further discuss the challenges of integrating multi-omics data into clinical research, the value of mechanistic studies in disease models, and the potential for translating omics-derived insights into precision diagnostics and targeted therapies. By framing FD as a systemic disorder of metabolic and microbial dysregulation, this review outlines a roadmap for mechanism-based interventions that extend beyond canonical glycosphingolipid targets.},
}
@article {pmid41487461,
year = {2026},
author = {Huang, MY and Li, Z and Zhang, W and Chen, HY and Liu, J and Li, CX},
title = {EBV+ and Kaposi's Sarcoma Herpesvirus-Associated Multicentric Castleman Disease in a Patient With HIV Infection: A Case Report.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {5567369},
pmid = {41487461},
issn = {2090-6625},
abstract = {Multicentric Castleman disease is a rare proliferative disease of lymphoid tissue. It has rarely been reported in Asian countries, particularly in HIV-positive patients. Here, we report a case of Kaposi's sarcoma herpesvirus-associated Multicentric Castleman disease (KSHV-MCD). A 44-year-old male HIV patient with a good response to antiretroviral therapy presented with recurrent fever and bilateral axillary masses. He was hospitalized for recurrent exacerbations, and it took 7 years from onset to definitive diagnosis. Lymph node biopsy suggested Castleman disease. Metagenomic next-generation sequencing (mNGS) of the blood showed that the patient was infected with KSHV (8327 sequence reads) and EBV (283 sequence reads). The patient was administered rituximab, thalidomide, sodium phosphonates, and ganciclovir. The patient's symptoms were completely relieved, and all indicators returned to normal, with no recurrence during follow-up. This case underlines that it is necessary to perform multiple lymph node biopsies or repeat the biopsies multiple times for the diagnosis of KSHV-MCD.},
}
@article {pmid41487438,
year = {2025},
author = {Chen, W and Liu, R and Qi, Q and Xu, L and Sun, G},
title = {Comparative Evaluation of mNGS and Traditional Culture Methods in Pathogen Detection for Pulmonary Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6991-6998},
pmid = {41487438},
issn = {1178-6973},
abstract = {PURPOSE: This study aimed to evaluate the diagnostic accuracy and clinical applicability of metagenomic next-generation sequencing (mNGS) in pulmonary infections by comparing it with traditional culture methods in a Traditional Chinese Medicine (TCM) hospital setting.<br><br>METHODS: This retrospective cohort study enrolled 67 consecutively admitted patients with radiologically and clinically confirmed pulmonary infections from the Department of Respiratory Infectious Diseases at Xinchang Hospital of Traditional Chinese Medicine between December 2022 and September 2024. Clinical specimens included blood, bronchoalveolar lavage fluid (BALF), sputum, hydrothorax and cerebrospinal fluid (CSF). mNGS and conventional culture were performed to compare detection rates and microbial community profiles.<br><br>RESULTS: Among 67 cases, mNGS identified pathogens in 89.55% (60/67), compared to 20.90% (14/67) by traditional culture. Of 14 dual-positive cases, only 1 (1/14, 7.14%) showed complete concordance, while most exhibited discordance or partial genus-level overlap. mNGS further detected viral co-infections in 44.78% (30/67) and identified fastidious/non-culturable pathogens such as enterovirus, human herpesvirus type 1, and Mycobacterium tuberculosis. Patients with chronic diseases were more susceptible to EB virus infections.<br><br>CONCLUSION: mNGS significantly enhances pathogen detection in pulmonary infections, supports targeted antimicrobial therapy, and holds potential for contributing to clinical outcomes and reducing antibiotic resistance.},
}
@article {pmid41487392,
year = {2026},
author = {Guzmán-Fierro, V and Quiroz, M and Moscoso, K and Arriagada, C and Espinoza, C and Mansilla, J and Contreras, D and Campos, V and Gallardo-Rodríguez, JJ and Riveros, G and Roeckel, M},
title = {Aerobic granular sludge as a regenerative system for nutrient removal and metal recovery from landfill leachate.},
journal = {RSC advances},
volume = {16},
number = {2},
pages = {1121-1133},
pmid = {41487392},
issn = {2046-2069},
abstract = {Landfill leachate is a complex and variable wastewater rich in organic matter, ammonium, salts, and metals, with low biodegradability and highly fluctuating composition. Its management still largely relies on energy- and chemical-intensive treatment schemes, making the treatment of raw, undiluted landfill leachate particularly challenging. This study evaluates, at lab scale, the potential of aerobic granular sludge (AGS) for achieving simultaneous pollutant removal and metal recovery in a 2-L column sequencing batch reactor fed with raw, undiluted landfill leachate collected from an active municipal landfill site. The reactor was operated for 198 days without dilution or addition of co-substrates. This operation resulted in stable granulation and high removal efficiencies, 94% for chemical oxygen demand (COD) and 97% for total nitrogen. Cation analysis shows that assimilation reached 600.47 µmol g[-1] TS, with calcium and magnesium being the predominant cations. Quantitative analyses revealed near-equal contributions from biosorption (53%) and bioaccumulation (47%), with magnesium dominating biosorption and calcium prevailing in bioaccumulation. Then, a partial metal recovery was achieved by desorption with 0.1 M NaCl, without compromising the granule structure, as verified by FTIR and scanning electron microscopy (SEM). However, the desorption process reduced nitrification and denitrification activities by factors of 3.7 and 1.8, respectively, while heterotrophic activity increased by 2.4-fold. Metagenomic analysis revealed microbial shifts following desorption, favouring genera such as Paracoccus and Burkholderia, which are associated with heterotrophic metabolism. These results demonstrate the potential of AGS as a regenerative biosorbent for treating landfill leachate and recovering metals. This approach supports sustainable and circular strategies for managing landfill leachate and similar complex effluents.},
}
@article {pmid41486240,
year = {2026},
author = {Aghajani, S and Kerdraon, M and Wilson, J and Galinat, S and André-Miral, C and Cregut, M and Jouanneau, S and Thouand, G},
title = {Screening of exoenzymes for guar gum biodegradation in activated sludge and soil.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41486240},
issn = {1614-7499},
abstract = {Originally standardized biodegradation tests, designed for small molecules, are often considered inadequate for evaluating polymers, as they do not account for the crucial fragmentation step catalyzed by exoenzymes, which is essential for initiating the microbial degradation of polymers. In this study, the presence of EEs in the environment and their role in the biodegradation of guar gum, a WSP, were evaluated. A metagenomic shotgun approach assessed the abundance of genes encoding α-galactosidase and β-mannosidase in the Waste Water Treatment Plant (WWTP) and soil. Secondly, we employed sonication to release EEs, measured their activity, and evaluated the impact of their release on guar degradation using biodegradation tests. These findings indicated that genes encoding α-galactosidase and β-mannosidase were more abundant in the WWTP than in soil. A sonication protocol with a power density of 1 W/mL and a frequency of 20 kHz for 1 min (WWTP) and 2 min (soil) released EEs without significant cell lysis and significantly reduced the lag phase of guar-grafted acrylamide biodegradation from 8 to 5 days and decreased variability in native guar biodegradation by 10%. Our findings highlight the potential of WWTP and soil microbial communities to degrade guar gum by screening EEs and propose a new method for preparing the inoculum for WSPs biodegradation tests.},
}
@article {pmid41485666,
year = {2026},
author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X},
title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150042},
doi = {10.1016/j.ijbiomac.2025.150042},
pmid = {41485666},
issn = {1879-0003},
abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.},
}
@article {pmid41485494,
year = {2026},
author = {Miyachi, H and Shibata, R and Javornik Cregeen, SJ and Surathu, A and Sijaric, M and Espinola, JA and Sullivan, AF and Mansbach, JM and Camargo, CA and Zhu, Z},
title = {Interactions between host genetics and gut microbiome influence susceptibility to childhood asthma and lung function.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.12.1005},
pmid = {41485494},
issn = {1097-6825},
abstract = {BACKGROUND: The gut microbiome is thought to influence risk of childhood allergic diseases; however, data on species-level links to childhood asthma and lung function are limited, and the role of host genetics in the gut-lung axis remains unclear.<br><br>METHODS: In a multicenter cross-sectional study of children with a history of bronchiolitis, from the 35[th] Multicenter Airway Research Collaboration, we performed shotgun metagenomic profiling of stool samples at age 6 years and examined associations of gut microbiome with prevalent asthma and lung function. We also calculated polygenic risk scores (PRS) of asthma and lung function to investigate the interaction between host genetics and gut microbiome on these traits.<br><br>RESULTS: In the 300 children included for this study, three bacterial species (e.g., Bacteroides vulgatus, Eisenbergiella massiliensis, Butyricimonas virosa) were differentially associated with FEV1, and four bacterial species were differentially associated with FEV1/FVC (e.g., Bifidobacterium longum) (MaAsLin: FDR<0.25). Furthermore, host genetics-gut microbiome interaction analysis showed association of B.vulgatus (FDR=0.037) and Bacteroides uniformis (FDR=0.037) with FEV1/FVC among children with high FEV1/FVC PRS. Additionally, Ruminococcus bromii (FDR=0.067) and Alistipes indistinctus (FDR=0.13) were suggested to have protective associations with asthma, specifically in children with high asthma PRS, indicating that host genetics can modulate the effect of gut microbiome on these respiratory outcomes.<br><br>CONCLUSION: By applying the metagenomic approach to a multicenter cohort of children with a history of bronchiolitis during infancy, this study suggests potential interplay of host genetics with gut microbiome, and their integrated relationship with childhood asthma and lung function.},
}
@article {pmid41485293,
year = {2025},
author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H},
title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157744},
doi = {10.1016/j.phymed.2025.157744},
pmid = {41485293},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.<br><br>PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).<br><br>METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.<br><br>RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-&#x3ba;B-AP-1 axis and TGF-&#x3b2; receptor signaling, thereby suppressing NF-&#x3ba;B-driven inflammation and Smad2-mediated fibrosis.<br><br>CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.},
}
@article {pmid41485252,
year = {2026},
author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M},
title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.},
journal = {International immunopharmacology},
volume = {171},
number = {},
pages = {116155},
doi = {10.1016/j.intimp.2025.116155},
pmid = {41485252},
issn = {1878-1705},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.},
}
@article {pmid41484966,
year = {2026},
author = {Fu, R and Liang, XJ and Yang, WM and Li, R and Shi, YR and Guo, L and Yu, H and Chen, YH and Wang, HN},
title = {Gut microbial signatures in schizophrenia: exploring archaea, fungi, and bacteria.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-025-07721-3},
pmid = {41484966},
issn = {1471-244X},
support = {LHJJ24YF06//Interdisciplinary Integration Project of Xijing hospital/ ; 82201679//National Natural Science Foundation of China/ ; 82330043//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Gut microbial, mainly bacterial dysbiosis, has been demonstrated in patients with schizophrenia (SCH). However, the signatures and differences of minority gut microbiota in SCH, such as archaea and fungi, have been poorly addressed.<br><br>METHODS: We obtained stool samples from 61 SCH patients and 69 healthy controls (HC), and analyzed the compositional and functional alterations of gut archaea, fungi, and bacteria using metagenomic shotgun sequencing (MSS). Additionally, we developed potential biomarkers to distinguish SCH from HC.<br><br>RESULTS: SCH patients showed significantly lower archaeal &#x3b1;-diversity compared with that of HC. Whereas there were significant differences between SCH and HC in &#x3b2;-diversity at the species level of archaea, fungi and bacteria. Meanwhile, the functional differences between the two groups were concentrated in glucose, lipid and amino acid metabolic pathways. Furthermore, we established potential diagnostic archaeal (9 species, AUC&#x2009;=&#x2009;0.73), fungal (8 species, AUC&#x2009;=&#x2009;0.69), and bacterial (22 species, AUC&#x2009;=&#x2009;0.74) microbiomes for differentiating SCH patients from HC.<br><br>CONCLUSIONS: This study describes a more comprehensive understanding of abnormal gut microbiome in SCH and might provide candidate targets for the development of a microbe-based diagnosis for SCH.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2000032118, registration date: 2020/04/20.},
}
@article {pmid41484564,
year = {2026},
author = {Tang, LX and Yang, ZF and Yang, YS and Li, LH and Phurbu, D and Zheng, YY and Zhu, JY and Zhu, D and Lv, ZH and Xie, KQ and Hu, W and Yin, YR},
title = {[Not Available].},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-02000-6},
pmid = {41484564},
issn = {2191-0855},
support = {No. 202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; NSFC, Nos. 32560004 and 32570003//National Natural Science Foundation of China/ ; No. 230212528080//Xingdian Talent Support Program of Yunnan Province/ ; Nos. 2024YNLCYXZX0081 and YWLCYXZX2023300075//Yunnan Provincial Clinical Medical Center for Emergency Traumatic Dis-eases/ ; No. XZ202501ZY0019//Science and Technology Projects of the Xizang Autonomous Region, China/ ; },
abstract = {Uricase, a key enzyme in purine metabolism, is widely used for uric acid detection and for treating gout and hyperuricemia. To obtain a uricase with both high activity and thermal stability, we cloned and heterologously expressed a novel uricase gene (tc1-uox2) from the Tengchong hot spring metagenome and combined enzymatic characterization with molecular dynamics simulations. TC1-Uox2 exhibited optimal catalytic activity at 35 °C and pH 8.0. It showed remarkable thermal stability, retaining over 40% residual activity after 16 h at 40 °C and maintaining over 80% activity for 14 h at physiological temperature (37 °C). In vitro uric acid-lowering assays demonstrated that 1 µg/mL TC1-Uox2 reduced serum uric acid to below 360 µM within 20 min in whole-blood samples from six hyperuricemic patients. Comparative molecular dynamics simulations with rasburicase indicated that, based on RMSF, radius of gyration (Rg), and hydrogen-bond counts, TC1-Uox2 adopts a more compact overall structure. Free energy landscape (FEL) analysis further revealed that TC1-Uox2 occupies deeper and narrower energy basins, consistent with greater conformational rigidity and thermodynamic stability. These findings elucidate the structural basis of its enhanced thermostability. In summary, TC1-Uox2 is a high-activity, high-stability uricase candidate that represents a promising enzyme target for biotherapeutic intervention in hyperuricemia and illustrates the translational potential of extreme-environment metagenomics for metabolic disease applications.},
}
@article {pmid41484024,
year = {2025},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.<br><br>METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n&#xa0;=&#xa0;103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1&#xa0;% vs 7.7&#xa0;%; p&#xa0;<&#xa0;0.001), greater time in range (67.0&#xa0;% vs 59.4&#xa0;%; p-trend&#xa0;=&#xa0;0.03), and higher HDL cholesterol (1.62 vs 1.39&#xa0;mmol/L; p&#xa0;=&#xa0;0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.<br><br>CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}
@article {pmid41483288,
year = {2026},
author = {Lema, NK and Gemeda, MT and Woldesemayat, AA},
title = {Uncovering resistomes in hospital and pharmaceutical industry wastes: insights from shotgun metagenomic profiling.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41483288},
issn = {1618-1905},
}
@article {pmid41482808,
year = {2026},
author = {Ip, YCA and Allan, EA and Hirsch, SL and Kelly, RP},
title = {Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70091},
pmid = {41482808},
issn = {1755-0998},
support = {GR042390//OceanKind/ ; GR016745//David and Lucile Packard Foundation/ ; },
mesh = {*Workflow ; Animals ; *DNA, Environmental/isolation &amp; purification/genetics ; *Fishes/genetics/classification ; *Metagenomics/methods/economics ; Time Factors ; Sensitivity and Specificity ; Computational Biology/methods ; Biodiversity ; Resource-Limited Settings ; },
abstract = {Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges and improve accessibility, we directly compared multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 48 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed to assess where time and resource savings are possible without compromising detection. Workflows using the Qiagen Blood and Tissue (BT) extraction kit and amplification using the MiFish-U primer set provided the highest sensitivity, detecting ≥ 12 of 15 species by ~3-5 h and reaching the 15-OTU plateau at ~8-10 h with Oxford Nanopore's high accuracy (HAC) basecalling model. Chelex, an alternative lower-cost extraction method, showed partial recovery only (≤ 9 OTUs by 61 h) even with extended sequencing, and did not recover all 15 OTUs. DirectPCR and QuickExtract offered field-friendly extraction alternatives that achieved comparable recovery in ~10-12 h, though their cost-effectiveness varied. While the MarVer1 primer was designed to broaden vertebrate detection, it recovered the same fish species as MiFish-U, though with fewer total reads. Real-time sequencing trials (0-61 h) revealed that high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating sequencing time can be reduced without sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated demultiplexing but discarded more reads than an alternative, ONTbarcoder2.3, which retained low-abundance taxa at the cost of manual curation. Rather than identifying a single 'best' workflow, this study provides a transparent decision framework for prioritising cost, speed, and sensitivity in eDNA applications, supporting scalable, cost-effective eDNA monitoring in resource-limited settings.},
}
@article {pmid41482538,
year = {2026},
author = {Trigodet, F and Sachdeva, R and Banfield, JF and Eren, AM},
title = {Troubleshooting common errors in assemblies of long-read metagenomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41482538},
issn = {1546-1696},
abstract = {Assessing the accuracy of long-read assemblies, especially from complex environmental metagenomes that include underrepresented organisms, is challenging. Here we benchmark four state-of-the-art long-read assembly software programs, HiCanu, hifiasm-meta, metaFlye and metaMDBG, on 21 PacBio HiFi metagenomes spanning mock communities, gut microbiomes and ocean samples. By quantifying read clipping events, in which long reads are systematically split during mapping to maximize the agreement with assembled contigs, we identify where assemblies diverge from their source reads. Our analyses reveal that long-read metagenome assemblies can include >40 errors per 100 million base pairs of assembled contigs, including multi-domain chimeras, prematurely circularized sequences, haplotyping errors, excessive repeats and phantom sequences. We provide an open-source tool and a reproducible workflow for rigorous evaluation of assembly errors, charting a path toward more reliable genome recovery from long-read metagenomes.},
}
@article {pmid41482458,
year = {2026},
author = {Zhou, CB and Zhao, LC and Qin, Y and Yu, J and Li, W and Feng, Q and Tong, X and Abuduaini, R and Lu, SY and Tang, H and Zhang, YX and Cui, Y and Xiao, L and Song, LH and Ni, LK and Wu, K and Zhong, H and Jiang, YC and Zou, Y and Leng, XX and Wang, M and Zhao, WY and Wang, CJ and Liu, Q and Zhang, JQ and Hu, C and Chen, YX and Yao, YF and Zhu, S and Fang, JY},
title = {Streptococcus anginosus-derived methionine promotes gastric cancer progression.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336966},
pmid = {41482458},
issn = {1468-3288},
abstract = {BACKGROUND: Streptococcus anginosus has been linked with an increasing risk of gastric cancer (GC) and recognised as a signature for GC screening.<br><br>OBJECTIVE: To investigate the promotional effect of S. anginosus in terms of its metabolic interactions with the host.<br><br>DESIGN: We used the functional profiles of shotgun metagenomic sequencing from stools to detect bioactive molecules relevant to S. anginosus. In vivo and in vitro experiments were used to validate the facilitation of S. anginosus to GC progression. S. anginosus clinical strains were isolated and cultivated from cancerous tissues to verify its promotion of GC via methionine production. S. anginosus &#x394;metE mutant strains were constructed to confirm the critical role of metE in methionine biosynthesis.<br><br>RESULTS: We verified S. anginosus facilitated GC progression in vivo and in vitro. Our functional analysis of metagenomes revealed a significant enrichment of bacterial methionine biosynthesis pathways in GC patients with high S. anginosus abundance. Methionine, identified here as one of the primary microbial metabolites derived from S. anginosus, contributed to GC progression in humans and mice. S. anginosus strains from cancerous tissues were found to promote GC via methionine production. We further observed a higher abundance and prevalence of metE gene in cancer stool metagenomes. By constructing an S. anginosus &#x394;metE mutant strain, we confirmed the critical role of metE in methionine biosynthesis.<br><br>CONCLUSION: Our results elucidate the role of S. anginosus-derived methionine in GC progression, shedding light on intricate metabolic interplay between S. anginosus and host.},
}
@article {pmid41482085,
year = {2025},
author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J},
title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121142},
doi = {10.1016/j.jep.2025.121142},
pmid = {41482085},
issn = {1872-7573},
abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.<br><br>AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.<br><br>MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of 4-hydroxyphenylacetic acid (4-HPA) was investigated through cell viability assays, immunofluorescence staining, and western blot analysis in vitro.<br><br>RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota. Furthermore, the therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.<br><br>CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.},
}
@article {pmid41481471,
year = {2026},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2518978123},
doi = {10.1073/pnas.2518978123},
pmid = {41481471},
issn = {1091-6490},
support = {IOS-1558044//NSF (NSF)/ ; P41GM136463//HHS | NIH (NIH)/ ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 21HLSRM06//Canadian Space Agency (CSA)/ ; },
mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.},
}
@article {pmid41481285,
year = {2026},
author = {Zhu, J and Huang, Z and Lin, Y and Zhu, J and Min, R and Wan, Z and Chen, Y and Zhu, J and Xing, L and Li, S and Olovo, CV and Wang, X and Li, G and Zhang, P},
title = {The potential immunological mechanisms of gut microbiota dysbiosis caused by antibiotics exacerbate the lethality of influenza viruses.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609451},
doi = {10.1080/19490976.2025.2609451},
pmid = {41481285},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/immunology/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; *Influenza A virus/drug effects/pathogenicity/immunology ; Lung/immunology/virology/pathology/drug effects ; Humans ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Antibiotics are not recommended to treat influenza A virus (IAV). However, antibiotic misuse for IAV persists worldwide. How to scientifically use antibiotics for IAV-infected patients remains a considerable challenge.<br><br>RESULTS: Here, we investigated the impact of antibiotics on viral pathogenicity, pulmonary-intestinal antiviral immunity, and antiviral drug efficacy. Our findings indicated that antibiotic intervention exacerbated IAV-caused mortality and lung injury in mice, manifested as increased mortality rates, shortened survival time, aggravated pulmonary injury, and excessive inflammatory responses. Furthermore, antibiotic pretreatment significantly diminished the efficacy of antivirals. Metagenomic sequencing revealed that antibiotics reduced the diversity and abundance of beneficial gut microbiota, including Lactobacillus and Bifidobacterium, while promoting the proliferation of pathogenic bacteria such as Klebsiella pneumoniae and Escherichia coli. Mechanistically, antibiotic intervention exacerbated IAV-caused excessive inflammatory responses by the blockage of pulmonary-intestinal antiviral immune pathways, which were caused by the upregulation of PKR, RIG-I, ISG15, and TRIM25 levels while downregulating IPS-1 mRNA levels. However, it is noteworthy that the combination of antibiotics and antiviral drugs effectively offset the adverse effects of antibiotic pretreatment on influenza mortality by upregulating IPS-1 levels and partially restoring pulmonary-intestinal immune homeostasis.<br><br>CONCLUSIONS: Pulmonary-intestinal immune homeostasis imbalance caused by antibiotic misuse can not only markedly exacerbate the lethality of IAV, but also significantly attenuate the efficacy of antiviral drugs. A mechanistic study confirmed that gut microbes dysbiosis caused by antibiotic pretreatment exacerbates the homeostasis imbalance of host antiviral immunity by blocking the RIG/MDA5/IPS-1 antiviral signaling pathway. However, combination therapy with antibiotics and antivirals effectively reversed the fatal outcome exacerbated by antibiotic pretreatment. Collectively, our findings not only provide a scientific explanation from the perspective of antiviral immunity as to why antibiotics should not be arbitrarily used to treat viral infections but also lay the scientific foundation for the rational clinical use of antivirals and antibiotics for treating influenza.},
}
@article {pmid41481221,
year = {2026},
author = {Sun, S and Ning, Z and Xu, H and Peng, S and Gao, C and Hu, X},
title = {Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios-a retrospective study from a single center.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2608531},
doi = {10.1080/07853890.2025.2608531},
pmid = {41481221},
issn = {1365-2060},
mesh = {Humans ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Sensitivity and Specificity ; Blood Culture ; *Communicable Diseases/diagnosis/blood ; Coinfection/diagnosis/blood/microbiology ; },
abstract = {BACKGROUND: Plasma cell-free DNA metagenomic next-generation sequencing (mNGS) is a non-invasive comprehensive method for the etiological diagnosis of various infectious diseases. However, research on the early diagnosis and real-world clinical impact of plasma mNGS in patients with suspected infection are still limited.<br><br>MATERIALS AND METHODS: This study retrospectively included 140 patients with suspected infections who underwent early plasma mNGS and conventional culture testing. Referring to the clinical diagnosis of infectious diseases, the diagnostic performance of plasma mNGS and culture tests was compared, and the application scenarios and clinical effects of plasma mNGS were evaluated.<br><br>RESULTS: The positive rate of plasma mNGS was significantly higher than that of culture methods (55.71% vs 25.10%, p&#x2009;<&#x2009;0.001) and blood cultures (55.71% vs 12.86%, p&#x2009;<&#x2009;0.001). Regarding clinical diagnosis, the sensitivity of plasma mNGS was significantly higher than that of culture (58.27% vs 37.80%, p&#x2009;=&#x2009;0.002). The combination of mNGS and culture achieved a higher detection sensitivity (69.29%), especially in patients with multi-site co-infections (73.68%) and blood infections (73.17%). Plasma mNGS demonstrated higher sensitivity in patients with procalcitonin (PCT) index > 5&#x2009;ng/ml or human neutrophil lipocalin (HNL) index > 200&#x2009;ng/ml. In terms of treatment, a total of 69 patients (54.33%) benefited from plasma mNGS.<br><br>CONCLUSION: This study highlights the significant improvement in pathogen detection performance by combining conventional culture with plasma mNGS detection, especially in patients with multi-site co-infections and blood infections. Early use of plasma mNGS as an adjunct to culture can better guide clinicians to initiate appropriate anti-infective therapy.},
}
@article {pmid41480976,
year = {2026},
author = {Rao, C and Su, X and Xia, Y and Li, N and Wan, Y and Lyu, H and Song, T and Dong, W and Shen, X},
title = {From Physical Architecture to Ecosystem Function: Tillage Exerts Indirect Control on Nitrogen Transformation by Restructuring Preferential Flow Paths.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12351},
pmid = {41480976},
issn = {1520-5851},
abstract = {How long-term tillage drives nitrogen (N) function succession by degrading vadose zone preferential flow paths remains unclear. This study investigated croplands across multiple tillage chronosequences by integrating dye tracing, [15]N isotope tracing, and metagenomic techniques. The study shows that tillage-induced degradation of preferential flow structures homogenizes the vadose zone and reshapes N-cycling communities, shifting denitrifiers from nirK- to nirS-dominated assemblages. Consistent with this community turnover, gross nitrification rates in shallow preferential paths are 30.8% higher than in the adjacent matrix in short-term tillage, whereas in deep layers matrix denitrification and DNRA rates exceed those in preferential paths by 37.9 and 76.1%, and anammox appears only in the matrix at medium- and long-term tillage, indicating a concentration of reductive N processes in the matrix. Path analysis further shows that tillage-driven alterations in hydraulic properties (path coefficient = -0.91, p < 0.01), together with these community and process-rate shifts, redirect the dominant N pathway from hotspot-driven nitrification in preferential channels to matrix-driven reductive N loss, converting a nitrate-leaching-prone system into one with higher gaseous emission potential. This establishes a mechanistic link linking soil hydraulic degradation to N functional succession and supports targeted, stage-dependent farmland nitrogen management.},
}
@article {pmid41480659,
year = {2026},
author = {Balbino, KP and Kravchychyn, ACP and Cândido, FG and Dias, MME and Mendes, TAO and Oliveira, LL and Castro, LCV and Bressan, J and de la Garza, AL and Milagro, FI and Zulet, MA and Hermsdorff, HHM},
title = {Precision nutrition in weight loss and neuroendocrine control of people with obesity: The study protocol of a factorial randomised controlled trial (GenON Programme).},
journal = {Diabetes, obesity &amp; metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70414},
pmid = {41480659},
issn = {1463-1326},
support = {444037/2023-3//National Council for Scientific and Technological Development - CNPq/ Brazilian Ministry of Health - MoH, Brazilian National Program of Genomics and Precision Health - Genomas Brasil/ ; Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {AIMS: Precision nutrition, guided by genetic testing, has emerged as a promising approach for managing obesity. However, robust clinical trials testing its effectiveness in real-world dietary interventions remain scarce. The GenOn Programme aims to evaluate whether tailoring nutritional care based on genetic risk for obesity enhances weight loss, satiety control, and metabolic outcomes in adults with overweight and obesity.<br><br>MATERIALS AND METHODS: The GenOn Programme is an 18-week, 2&#x2009;&#xd7;&#x2009;2 factorial, randomised controlled trial including 120 adults classified as high or low genetic risk for obesity (variants: FTO rs9939609 and rs1121980; MC4R rs1782313; LEP rs7799039). Participants are randomised to standard or satiety-focused dietary counselling. Both groups receive five calorie-restricted (-500&#x2009;kcal/day), nutritionally balanced meal plans. The satiety arm additionally includes a high-protein breakfast, daily granola supplementation and behavioural strategies. Assessments at baseline, Week 12, and Week 18 include weight loss, body composition, satiety perception, quality of life, cardiometabolic markers, (epi)genetics, inflammation, neuroendocrine regulation, and metagenomics.<br><br>RESULTS AND CONCLUSIONS: The GenOn Programme is a randomised controlled trial to test a precision nutrition approach for overweight and obesity, integrating genetics, dietary strategies, and behavioural support. Findings may inform dietitians and healthcare systems on the clinical value of genetically guided nutritional care to improve outcomes in the treatment of overweight and obesity.},
}
@article {pmid41480317,
year = {2025},
author = {Zakharzhevskaya, NB and Erdes, SI and Belousova, EA and Samolygo, IS and Manina, MA and Kondrashova, PV and Lomakina, EY and Kardonsky, DA and Vorobyeva, EA and Shagaleeva, OY and Silantyev, AA and Kazakova, VD and Kashatnikova, DA and Kalachnuk, TN and Kolesnikova, IV and Chaplin, AV and Markelova, MI and Grigoryeva, TV and Olekhnovich, EI and Veselovsky, VA and Morozov, MD and Zoruk, PY and Boldyreva, DI and Vanyushkina, AA and Efimov, BA},
title = {Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients.},
journal = {World journal of gastroenterology},
volume = {31},
number = {48},
pages = {112653},
pmid = {41480317},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolomics/methods ; *Colitis, Ulcerative/microbiology/diagnosis/metabolism ; *Crohn Disease/microbiology/diagnosis/metabolism ; Feces/microbiology ; Child ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Aged ; Biomarkers/metabolism/analysis ; Age Factors ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: The gut microbiota displays pronounced compositional differences between pediatric and adult populations, both under normal conditions and during the development of inflammatory bowel disease (IBD). These structural variations are accompanied by substantial changes in microbial metabolic activity.<br><br>AIM: To identify novel early diagnostic biomarkers of IBD, we performed an integrated multi-omics analysis that included assessing microbial community structure and profiling microbial metabolic activity in pediatric and adult cohorts with ulcerative colitis (UC) and Crohn's disease (CD).<br><br>METHODS: The study cohort consisted of two distinct age groups with confirmed IBD diagnoses: Adult patients (aged 45 to 70) and pediatric patients (aged 5 to 15), each diagnosed with either CD or UC. 16S rRNA gene sequencing was performed using the MinION&#x2122; Mk1B platform, with data acquisition carried out via MinKNOW software version 22.12.7 (Oxford Nanopore Technologies). Stool samples were analyzed using a Shimadzu QP2010 Ultra GC/MS system equipped with a Shimadzu HS-20 headspace extractor.<br><br>RESULTS: Comparative analysis revealed significant age-related differences in the abundance of Bacteroidota, with pediatric IBD patients showing a lower prevalence compared to adults. Microbial profiling identified Streptococcus salivarius and Escherichia coli as potential biomarkers for assessing IBD risk in children. Furthermore, metagenomic analysis uncovered five microbial signatures with diagnostic potential for CD: Ralstonia insidiosa, Stenotrophomonas maltophilia, Erysipelatoclostridium ramosum, Blautia spp., and Coprococcus comes. Using comprehensive metabolomic profiling, we developed and validated novel risk prediction algorithms for pediatric IBD. The CD risk stratification model identifies high-risk patients based on two key biomarkers: An elevated IBD risk coefficient score and reduced levels of 1H-indole-3-methyl. The UC risk prediction model incorporates three metabolic biomarkers indicative of increased disease risk: An elevated risk coefficient score, increased acetate levels, decreased pentanoic acid, and altered excretion of p-cresol (4-methylphenol).<br><br>CONCLUSION: Functional metabolomics holds transformative potential for IBD diagnostics across all age groups, with especially significant implications for pediatric patients. The distinct metabolic and metagenetic profiles observed in the pediatric cohort may represent primary alterations in IBD, providing valuable insights for exploring novel mechanisms underlying disease pathogenesis.},
}
@article {pmid41480270,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Venter, SN and Bosch, R and Konstantinidis, KT and Rodriguez-R, LM and Rossello-Mora, R},
title = {Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf228},
pmid = {41480270},
issn = {2730-6151},
abstract = {An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.},
}
@article {pmid41480265,
year = {2025},
author = {Ren, G and Gubry-Rangin, C and Wang, W and Liu, R and Liu, J and Liu, J and Zhang, XH and Liu, J},
title = {Purifying selection and low recombination facilitated sequential colonization of benthic and pelagic coastal ocean by ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf234},
pmid = {41480265},
issn = {2730-6151},
abstract = {The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.},
}
@article {pmid41480263,
year = {2025},
author = {Ma, M and Wang, M and Liang, Y and Guo, Y and Zhang, H and Cao, L and Fu, L and Hu, G and Li, C and Mock, T and Li, C},
title = {Microbial communities and metabolic functions vary with spatial heterogeneity in cold-seep carbonates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf232},
pmid = {41480263},
issn = {2730-6151},
abstract = {Cold-seep carbonates, formed through interactions among methane, fluid chemistry, and microbial chemosynthesis, represent biodiversity hotspots in the deep sea. Spatial heterogeneity within these carbonates arises from variations in methane flux, yet the microbial contributions to this heterogeneity remain underexplored. Here we combined remotely operated vehicle-based in situ measurements, X-ray imaging, metagenomics, qPCR, and [13]C-CH4 stable-isotope labeling to investigate microbial communities across carbonate habitats in the South China Sea. We found that methane flux linked to carbonate structural properties, shapes microbial metabolic interactions, notably anaerobic methane oxidation coupled with aragonite and FeS precipitation. These processes may contribute to self-sealing carbonate features, potentially reducing methane permeability and influencing geochemical gradients and geomorphology. Our findings reveal that microbiomes and their feedbacks play a significant role in shaping habitat-scale spatial heterogeneity of cold-seep carbonates, improving our understanding of methane cycling and carbonate ecosystem dynamics.},
}
@article {pmid41480114,
year = {2025},
author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A},
title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727830},
pmid = {41480114},
issn = {1664-302X},
abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.<br><br>METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess &#x3b1;- and &#x3b2;-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.<br><br>RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.<br><br>DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.},
}
@article {pmid41480112,
year = {2025},
author = {Fu, J and Bu, G and Aimaier, S and Yang, Y and Bao, Z and Wulasihan, M},
title = {Sex-specific association between gut Faecalibacterium prausnitzii and hypertension in male individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683587},
pmid = {41480112},
issn = {1664-302X},
abstract = {OBJECTIVE: While gut microbiota (GM) dysbiosis has been implicated in hypertension, the sexassociated microbial signatures and their underlying mechanisms remain poorly understood, particularly in populations living in unique geographical and climatic conditions.<br><br>DESIGN: Through an integrated approach combining 16S rRNA sequencing, shotgun metagenomics, and serum metabolomics, we systematically investigated the sex-associated characteristics of the gut microbiota in hypertension among a cohort of 200 participants from Xinjiang.<br><br>METHODS: An initial cohort analysis identified Faecalibacterium as a male-associated biomarker for hypertension. Subsequent species-level characterization revealed that Faecalibacterium prausnitzii (F. prausnitzii) showed significant negative correlations with systolic blood pressure (SBP). This male-specific association was consistently observed across both 16S rRNA sequencing and shotgun metagenomic datasets. Then, our integrated analysis suggested a potential pathway through which F. prausnitzii may be linked to systolic blood pressure in male individuals, with N-phenylacetylglutamine (PAGln) identified as a potential mediating metabolite.<br><br>CONCLUSION: Our study establishes a microbe-metabolite-clinical trait axis in the pathophysiology of sex-associated hypertension and significantly advances our understanding of sex-driven host-microbe interactions.},
}
@article {pmid41479870,
year = {2025},
author = {Ghosh, N and Sinha, K},
title = {Guardians within: Cross-talk between the gut microbiome and host immune system.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {111245},
pmid = {41479870},
issn = {2150-5330},
abstract = {The gut microbiome, a complex ecosystem of trillions of microorganisms, plays a crucial role in immune system regulation and overall health. This review explores the intricate cross-talk between the gut microbiota and the host immune system, emphasizing how microbial communities shape immune cell differentiation, modulate inflammatory responses, and contribute to immune homeostasis. Key interactions between innate and adaptive immune cells - including macrophages, dendritic cells, natural killer cells, innate Lymphoid cells, T cells, and B cells - and gut microbiota-derived metabolites such as short-chain fatty acids are discussed. The role of commensal bacteria in neonatal immune system development, mucosal barrier integrity, and systemic immunity is highlighted, along with implications for autoimmune diseases, inflammatory conditions, and cancer immunotherapy. Recent advances in metagenomics, metabolomics, and single-cell sequencing have provided deeper insights into the microbiota-immune axis, opening new avenues for microbiome-based therapeutic strategies. Understanding these interactions paves the way for novel interventions targeting immune-mediated diseases and optimizing health through microbiome modulation.},
}
@article {pmid41479581,
year = {2025},
author = {Komatsu, H},
title = {Comparison of three pediatric studies investigating acute hepatitis of unknown etiology.},
journal = {World journal of virology},
volume = {14},
number = {4},
pages = {110435},
pmid = {41479581},
issn = {2220-3249},
abstract = {Between 2021 and 2023, approximately 400 pediatric cases of acute hepatitis of unknown etiology (AHUE) were reported in European countries and the United States. In 2023, three pediatric studies revealed that adeno-associated virus serotype 2 (AAV-2) infection was associated with AHUE. This article presents a summary and comparison of the results of metagenomic sequencing, viral whole-genome sequencing, virus-specific real-time polymerase chain reaction (PCR) and histological analysis of the liver, all of which were among the common investigative methods used in the three pediatric studies. All three pediatric studies revealed 80% or greater rates of positivity for AAV-2 in cases of AHUE according to metagenomic sequencing. Moreover, on the basis of PCR results, two studies revealed high AAV-2 positivity rates (96.4% and 81.2%) among cases of AHUE. These findings suggest that AAV-2 is a pathogen in AHUE. Coinfection with AAV-2 and one or more helper viruses (human adenovirus, human herpesvirus 6B, Epstein-Barr virus, etc.), high viral loads of AAV-2 in blood, anti-AAV-2 IgM and human leukocyte antigen typing could be candidate diagnostic criteria for AHUE. AAV-2 infection should be incorporated into clinical guidelines for the management of acute liver failure. Cidofovir can be administered if coinfection with AAV-2 and HAdV is detected.},
}
@article {pmid41478956,
year = {2026},
author = {Halford, C and Moragues-Solanas, L and Weller, SA and Gilmour, M},
title = {Whole Genome Amplification of Microbial DNA from Host-Depleted Clinical Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {175-186},
pmid = {41478956},
issn = {1940-6029},
mesh = {Humans ; *Metagenomics/methods ; *Nucleic Acid Amplification Techniques/methods ; *DNA, Bacterial/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Clinical metagenomics (CMg) involves the untargeted sequencing of the genetic content of samples collected from patients and is a highly promising method for the diagnosis of infectious disease. Depending on the sample type, CMg can be reliant on the removal of the host genetic material from the sample to support detection of microbial pathogens, and this selective process (or an otherwise low abundance of microbial cells in the sample) may result in concentrations of DNA too low for productive sequencing. Whole genome amplification (WGA), the nonselective amplification of the total DNA of a sample, can be applied to significantly increase the concentration of DNA and enable CMg sequencing. This chapter describes the methods for the amplification of microbial DNA extracted from host-depleted wound swab samples using the GenomiPhi[™] V3 Ready-To-Go[™] (Cytiva) DNA WGA kit and host-depleted whole blood samples using the REPLI-g[®] Single-Cell WGA kit (Qiagen). This is followed by the de-branching and bead-based clean-up of the amplified DNA, resulting in highly concentrated DNA ready for CMg DNA sequencing.},
}
@article {pmid41478955,
year = {2026},
author = {Cruz-Flores, R and Cáceres-Martínez, J and Dhar, AK},
title = {Laser Microdissection and Near Single-Cell Whole Genome Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {165-173},
pmid = {41478955},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Laser Capture Microdissection/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; *Nucleic Acid Amplification Techniques/methods ; *Genome, Viral ; Paraffin Embedding ; Tissue Fixation ; Genomics/methods ; DNA, Viral/genetics/isolation &amp; purification ; },
abstract = {Laser microdissection (LMD) and whole genome amplification (WGA) are powerful techniques that integrate molecular and histological approaches to enable the precise selection of a minimal number of virus-infected cells-down to near single-cell resolution-and the subsequent generation of whole viral genomes with minimal host DNA interference. This chapter presents a detailed protocol for LMD and near single-cell WGA, specifically optimized for the recovery and sequencing of viral genomes from formalin-fixed paraffin-embedded (FFPE) tissues. The method allows for the targeted isolation of infected cells, thereby reducing host genomic background and enhancing the detection of pathogen-specific signals for downstream next-generation sequencing (NGS). The protocol includes steps for tissue section preparation, cell isolation via LMD, DNA extraction using the PicoPure DNA Extraction Kit, and unbiased genome amplification using the SeqPlex DNA Amplification Kit-ensuring high-quality nucleic acid recovery suitable for NGS workflows.},
}
@article {pmid41318438,
year = {2025},
author = {Liu, J and Wu, J and Zhang, W and Huang, H and Liao, D},
title = {Disseminated Talaromyces marneffei infection mimicking tuberculosis in an HIV-negative adult with anti-IFN-γ autoantibodies: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {1},
pmid = {41318438},
issn = {1471-2334},
support = {2024J0112//the Nature Science Foundation of Fujian Province of China/ ; },
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic fungus causing life-threatening disseminated infections in immunocompromised individuals. While classically associated with HIV, TM is increasingly reported in HIV-negative patients, often misdiagnosed due to nonspecific manifestations.<br><br>CASE PRESENTATION: A 38-year-old HIV-negative Chinese woman with a history of thyroid cancer presented with a three-month history of fever, cough, weight loss, and subcutaneous masses. Imaging revealed diffuse pulmonary nodules and osteolytic bone destruction. She was initially misdiagnosed with tuberculosis and received anti-TB therapy without improvement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified TM, which was later confirmed by fungal culture. Anti&#x2013;interferon-gamma autoantibodies (anti&#x2013;IFN-&#x3b3; auto-Abs) were markedly elevated (111.72 ng/mL). She was treated with liposomal amphotericin B(L-AmB) followed by itraconazole, achieving temporary remission. One month post-discharge, TM recurred with new Sweet syndrome&#x2013;like skin lesions. Immunomodulatory therapy combined with antifungals led to disease control.<br><br>CONCLUSION: This case highlights three key clinical insights: (1) TM can closely mimic tuberculosis, especially in HIV-negative individuals; (2) mNGS is a valuable diagnostic tool when conventional tests fail; and (3) Anti&#x2013;IFN-&#x3b3; auto-Abs may underlie recurrent or refractory TM infections. Clinicians in endemic regions should consider TM and evaluate immune status early in atypical or treatment-resistant cases.},
}
@article {pmid41316171,
year = {2025},
author = {Meldrum, OW and Tiew, PY and Xu, H and Low, DY and Ivan, FX and Narayana, JK and Jaggi, TK and Ching, J and Chotirmall, SH},
title = {Integrated multi-omics profiling for risk stratification in Asians with COPD.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {2},
pmid = {41316171},
issn = {1465-993X},
support = {(#020458-00001//LKCMedicine-ICL Fellowship/ ; MOH-001636//National Research Foundation Singapore under its Open Fund-Large Collaborative Grant and administered by the Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; MOH-001855//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Award (CSA) Investigator (INV) category/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; },
abstract = {BACKGROUND: Comorbidity-based risk stratification in Chronic Obstructive Pulmonary Disease (COPD) incompletely captures inherent biological heterogeneity, particularly in Asian populations that demonstrate high-risk clinical phenotypes including prior pulmonary tuberculosis. We investigated whether integrated sputum multi-omics could improve risk stratification in an Asian COPD cohort.<br><br>METHODS: We conducted a prospective, multicenter assessment of N&#x2009;=&#x2009;56 Asians with established COPD, classified as high- (N&#x2009;=&#x2009;25; cardiovascular or ex-tuberculosis) or low-risk (N&#x2009;=&#x2009;31; diabetic or low-comorbidity) based on established co-morbidity phenotyping. Sputum was subjected to mucus analysis (MUC5AC, MUC5B, mucus solids, rheology), metabo-lipidomics (LC-MS/MS) and microbiome assessment (shotgun metagenomics). Multivariate statistics was employed to integrate datasets.<br><br>RESULTS: High-risk Asian COPD demonstrates abnormal mucus biochemistry characterized by elevated MUC5AC; extensive metabo-lipidomic alterations characterized by dysregulated tryptophan-kynurenine metabolism and lipid remodeling with enrichment of lysophosphatidylcholines and triacylglycerols. Microbial networks are disrupted in high-risk patients, typified by antagonistic interactions driven by K. pneumoniae, H. influenzae and Neisseria spp. Integrative assessment combining all datasets partitioned the cohort into two clusters: SNF 1 (N&#x2009;=&#x2009;34) and SNF 2 (N&#x2009;=&#x2009;22), the former representing an unfavorable group characterized by exacerbations, hospitalizations, mucus dysfunction, microbial pathogens and dysregulated metabo-lipidomic pathways. Remarkably, 42% (N&#x2009;=&#x2009;13 of 31) of the originally classified low risk COPD exhibited the unfavorable SNF 1 endotype, distinguished by more severe exacerbations (hospitalizations), K. pneumoniae and elevated hypoxanthine, creatine, spermine and phosphatidylcholines.<br><br>CONCLUSION: Integrative multi-omics profiling of Asian COPD significantly refines clinical risk stratification identifying a novel &#x2018;high-risk&#x2019; biological endotype. Substantial proportions of clinically low-risk COPD exhibit this endotype, suggesting that clinical and co-morbidity profiling in Asians with COPD should be supplemented by molecular assessment to ensure accurate risk stratification.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-025-03440-1.},
}
@article {pmid41478953,
year = {2026},
author = {Lozano-Escobar, ED and Mateo-Cáceres, V and Mayoral-Campos, C and Redrejo-Rodríguez, M},
title = {Assessing Amplification Quality and Bias in MDA Methods Through Comparative Analysis of Short-Read Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {131-148},
pmid = {41478953},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA Copy Number Variations ; *Nucleic Acid Amplification Techniques/methods/standards ; *Sequence Analysis, DNA/methods ; Genomics/methods ; Metagenome ; },
abstract = {Although high-throughput sequencing methods have greatly improved over the last few years, direct sequencing remains unfeasible when DNA quantity or quality is limited. In such instances, various whole genome or metagenome amplification (WGA) techniques can generate sufficient DNA for multiple analyses, albeit with some amplification bias. Competent WGA analysis is typically evaluated by sequence coverage, assessed through two key parameters: depth, referring to the number of reads containing each nucleotide, and breadth, indicating the proportion of nucleotides in the consensus sequence relative to the original sequence length at the obtained depth. Adequate coverage is essential for detailed genomic analysis and the detection of population variants, copy number variations (CNVs), and structural variants (SVs). This chapter outlines a pipeline for analyzing Illumina sequencing data of amplified samples compared to non-amplified samples to assess the performance of various WGA methods, starting from raw sequences.},
}
@article {pmid41478678,
year = {2026},
author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L},
title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105001},
doi = {10.1016/j.fm.2025.105001},
pmid = {41478678},
issn = {1095-9998},
mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation &amp; purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation &amp; purification/drug effects ; Shellfish/microbiology ; Phylogeny ; },
abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.},
}
@article {pmid41478427,
year = {2025},
author = {Zhou, Z and Xu, M and Gao, C and Zheng, C and Bao, K and Ma, J},
title = {Metagenomic insights into N2O emission pathways shaped by arsenic and hydrological regimes in mangrove soils: An incubation study.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123658},
doi = {10.1016/j.envres.2025.123658},
pmid = {41478427},
issn = {1096-0953},
abstract = {Mangrove wetlands are characterized by an abundant and complex nitrogen cycling (N-cycling) process during periodic tidal flooding, and increasing arsenic (As) concentration profoundly influences microbial ecosystems and nitrogen (N) transformation. However, the combined impacts of As and hydrology on nitrous oxide (N2O) emissions remain unclear. Here, a soil microcosm experiment was conducted under two hydrological regimes (non-flooded and flooded) and with three As addition levels (50, 100, and 200 mg kg[-1]) to examine their effects on N2O fluxes and N transformation. The results demonstrated that As addition significantly enhanced N2O uptake, reducing fluxes by 1.29-26.47 % and 3.18-10.04 % relative to the control (CK) under non-flooded and flooded conditions, respectively. Notably, the N2O uptake flux under flooded conditions was 3.01 times that of non-flooded conditions on average. Furthermore, influencing mechanisms on N2O emission differ significantly between hydrological regimes. In non-flooded treatments, As primarily decreased NO3[-]-N availability and increased NH4[+]-N retention via upregulating nirBD and nrfAH genes to enhance the DNRA pathway, which reduced the production of N2O. Meanwhile, As promoted N2O reduction mainly through the upregulation of the nosZ gene, resulting in more N2O uptake. However, As predominantly existed as As(III) in flooded treatments, which stimulated the expression of As-resistance genes. This response helped alleviate As toxicity on microorganisms. Additionally, the enhanced decomposition of SOC served as the major energy source for microorganisms, maintaining and even increasing the abundance of partial N-cycling functional genes. Meanwhile, under nitrate-limited conditions, one possible explanation for the observed N2O uptake is that its reduction was stimulated because N2O could serve as an alternative terminal electron acceptor. The altered C and N availability under As contamination also shifted the microbial nitrogen transformation pathways toward processes that produce less N2O. These findings provided valuable insights about N-cycling and adaptations of N functional microorganisms in heavy metal-stressed mangrove wetland ecosystems.},
}
@article {pmid41478169,
year = {2025},
author = {Wang, W and Zhang, S and Wang, Y and Ge, J and Li, L},
title = {Metagenomic and cytotoxicity insights into the migration behavior and pathogenic potential of multi-medium microorganisms in a wastewater treatment plant.},
journal = {Water research},
volume = {292},
number = {},
pages = {125285},
doi = {10.1016/j.watres.2025.125285},
pmid = {41478169},
issn = {1879-2448},
abstract = {As important interphases between the human society and natural water environments, wastewater treatment plants (WWTPs) accumulate a variety of human activity-related microorganisms. The characteristics of potential pathogenic microorganisms associated with WWTPs have gradually become a research hotspot. In this study, the distribution characteristics and migration patterns of potential pathogenic genera in different processes, media and seasons were investigated via the metagenomic analysis of samples regularly collected at a typical WWTP in North China. The results obtained 112 pathogenic bacteria and 33 pathogenic fungi in the wastewater, sludge, and bioaerosol samples. Resistance mechanisms were dominated by antibiotic efflux with proportion of 62.63-63.53%. Functional genes encoding offensive virulence factors (VFs) including adherence, secretion system, toxin, invasion, and actin-based motility were the most common category in all the WWTP samples. Network analysis revealed the presence of core antibiotic resistance genes (including mtrA, bcrA, oleC, MexB, PmrE) and core VFs (including Type IV pili (VF0082), HIS-I (VF0334), LOS (CFV494), and Alginate (VF0091)) on multiple microbes, which increased the survival rate of microorganisms even under adverse conditions and enhanced the invasion potential to cause diseases. Additionally, cell exposure experiments confirmed the ability of Pseudomonas aeruginosa to induce inflammatory responses in Beas-2B cells. Based on these findings, which offer the insight of a comprehensive understanding of the potential pathogenicity of microorganisms in WWTPs, it is recommended to improve regulation of effluents from WWTPs a nd the implementation of measures to reduce the risk posed by airborne pathogenic microorganisms.},
}
@article {pmid41478124,
year = {2025},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}
@article {pmid41478064,
year = {2025},
author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H},
title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1270},
number = {},
pages = {124905},
doi = {10.1016/j.jchromb.2025.124905},
pmid = {41478064},
issn = {1873-376X},
abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.},
}
@article {pmid41477534,
year = {2026},
author = {Vallejos, G and Kim, C and Holroyd, KB and Thakur, KT},
title = {Evaluating the Clinical Impact of Metagenomic Next-Generation Sequencing in CNS Infections: A Diagnostic Pathway and Resource Utilization Modeling Study.},
journal = {Open forum infectious diseases},
volume = {13},
number = {1},
pages = {ofaf743},
pmid = {41477534},
issn = {2328-8957},
abstract = {BACKGROUND: Diagnosing meningitis and encephalitis remains challenging due to nonspecific clinical presentations and the limitations of traditional microbiological methods. Metagenomic next-generation sequencing (mNGS) offers a broad approach to detect pathogens, but its real-world impact on clinical decision-making remains undefined.<br><br>METHODS: We used a cohort of patients with confirmed central nervous system infections and autoimmune encephalitis (AE) who underwent traditional microbiological cerebrospinal fluid testing at Columbia University Irving Medical Center. Using published sensitivity and specificity data for mNGS, we applied Bayes' theorem to calculate different etiology-specific pretest probabilities and model the potential impact in the diagnostic workflows including the number of lumbar punctures (LPs), additional etiologic tests potentially avoided, and time to diagnosis.<br><br>RESULTS: The cohort includes 54 patients in the infectious cohort and 29 patients with confirmed autoimmune encephalitis. In a modeled scenario, utilizing an mNGS test, such as Delve Detect, in patients with DNA viral infections (n = 23) could lead to a reduction of up to 88 microbiological tests, 145 days to diagnosis, and 2 LPs in total. For bacterial infections (n = 16), estimated impact included a reduction of 30 microbiological tests, 144 days to diagnosis, and 12 LPs (Table 1). Although fungal, RNA viral and parasitic infections were less common, with adjusted positive predictive values of 92.8%, 89.5%, and 84.6%, respectively. In the autoimmune cohort, a total of 2 LPs, 126 microbiological tests, and 297 days to diagnosis could have been avoided through the use of mNGS.<br><br>CONCLUSIONS: Our analysis suggests that an mNGS test, such as Delve Detect, could potentially streamline diagnostic and treatment pathways in meningitis and encephalitis of infectious or autoimmune origin.},
}
@article {pmid41477211,
year = {2025},
author = {Mankiewicz-Boczek, J and Font-Nájera, A and Gin, KY and Graham, JL and Strapagiel, D and Gorney, RM and Kok, JWK and Te, SH and Kluska, M and Skóra, M and Seweryn, M and López-Hun, F},
title = {Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1655370},
pmid = {41477211},
issn = {1664-302X},
abstract = {Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis-dominated blooms, despite the increasing prevalence of filamentous genera (Aphanizomenon and Planktothrix). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis, Snowella, and Aphanizomenon had the broadest range of cyanotoxin synthetase genes (mcyE, cyrJ, anaF and sxtA). Microcystis blooms correlated with increased Roseomonas, while Planktothrix co-occurred with Flavobacterium - both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen - (ureB, glnA, narB, and narHZ) and phosphorus-cycling genes (phoBHPR and ppk1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon. These findings suggest that Aphanizomenon-dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.},
}
@article {pmid41477025,
year = {2025},
author = {Miao, H and Wang, Z and Chen, S and Wang, J and Ma, H and Liu, Y and Yang, H and Guo, Z and Wang, J and Cui, P},
title = {Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy.},
journal = {eGastroenterology},
volume = {3},
number = {4},
pages = {e100253},
pmid = {41477025},
issn = {2976-7296},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease with complex aetiology and limited treatment options. Antimicrobial peptides (AMPs), as endogenous immune effectors, have recently emerged as promising therapeutic agents in UC. However, systematic identification and functional evaluation of AMPs remain underexplored. We aimed to discover novel AMPs with potential therapeutic efficacy in UC by leveraging machine learning-based prediction and validating their impact in an experimental colitis model.<br><br>METHODS: We established a machine learning-driven pipeline to predict candidate AMPs based on their structural and functional features. Top-ranked peptides were synthesised and subjected to in vitro antibacterial assays and proteolytic stability tests. Their therapeutic potential was evaluated using a dextran sulfate sodium (DSS)-induced colitis mouse model, assessing clinical indicators, histopathology, inflammatory markers and gut microbiota alterations. Metagenomic and metabolomic analyses provided insights into microbial community dynamics and metabolic pathways. To probe the role of gut microbes in AMP-mediated gut homeostasis, we conducted Akkermansia (A.) muciniphila replenishment experiments.<br><br>RESULTS: Several AMPs identified by machine learning exhibited potent antimicrobial activity and resistance to proteolytic degradation. In vivo, AMP administration ameliorated DSS-induced colitis symptoms, including body weight loss, Disease Activity Index and histological damage. Treatment also modulated the gut microbiome, increasing the abundance of A. muciniphila and restoring microbial balance. Functional metagenomic profiling revealed enrichment of genes involved in mucosal barrier protection and immunoregulation. These findings were supported by improved inflammatory cytokine profiles and enhanced epithelial integrity.<br><br>CONCLUSIONS: Our findings demonstrate that machine learning-guided discovery of AMPs is a viable approach to identify promising therapeutic agents for UC. By integrating multi-omics analyses, we reveal potential microbiota-mediated mechanisms underlying AMP efficacy. These insights provide a strong foundation for advancing AMP-based strategies in UC management.},
}
@article {pmid41476341,
year = {2025},
author = {Njage, PMK and Becsei, &#xc1; and Marques, ARP and Muchiri, BW and Pedersen, JLM and Otani, S and Avot, BJP and Pruden, A and Calarco, J and Harwood, V and Meschke, JS and Gonzalez, R and Sozzi, E and Sobsey, M and McNamara, P and Beck, N and Clark, K and Ballash, G and Mollenkopf, D and Wittum, T and Smith, B and Maile-Moskowitz, A and Kang, S and Capone, D and Aarestrup, FM},
title = {Sociodemographic and Health Factors Are Associated with Antimicrobial Resistance across Eight States in the United States.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c07425},
pmid = {41476341},
issn = {1520-5851},
abstract = {Recent studies suggest that country-level socioeconomic factors may explain antimicrobial resistance (AMR) patterns better than antimicrobial usage (AMU), but it remains unclear whether this holds for sociodemographic and health variation within countries. We used metagenomic analysis of untreated sewage to cross-sectionally characterize the bacterial resistome as a proxy for AMR at 44 wastewater treatment plants across eight USA states between 2019 and 2020. We examined associations between AMR with site-specific sociodemographic and health indicators and AMU. Spatial autocorrelation analyses were used to identify clusters of AMR. Gradient-boosted multivariate regression trees were applied to evaluate individual and joint predictor effects on AMR. Outpatient AMU explained negligible variation in AMR, whereas predictors related to economy, income, preventive health care, access to health care, social welfare, housing, and racial/ethnic composition showed the strongest associations. These relationships were observed across individual resistance classes and their combinations and predicted AMR nonlinearly, with thresholds where AMR shows sharp increases (risk factors) or decreases (protective factors). Significant interannual differences in resistome and bacteriome composition were observed between 2019 and 2020. Although causal inference is limited, the findings suggest that local-level indicators of health, economic conditions, well-being, and development may play an important role in shaping AMR within countries.},
}
@article {pmid41476181,
year = {2025},
author = {Fedi, S and Ghezzi, D and Firrincieli, A and Lopo, E and Romeo, A and Sauro, F and Cappelletti, M},
title = {Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29105-z},
pmid = {41476181},
issn = {2045-2322},
}
@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67711-7},
pmid = {41476057},
issn = {2041-1723},
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}
@article {pmid41475602,
year = {2025},
author = {Zhou, L and Zhang, M and Qiu, Y and Zhao, B and Li, H and Zhuang, WQ},
title = {'Protector' DNRA bacteria, shielding anammox systems from perfluorooctanoic acid by mitigating nitrite accumulation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133898},
doi = {10.1016/j.biortech.2025.133898},
pmid = {41475602},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process is integral to nitrogen removal in wastewater treatment, but its effectiveness can be compromised by contaminants such as perfluorooctanoic acid (PFOA). This study revealed the protective mechanism of dissimilatory nitrate reduction to ammonium (DNRA) in protecting anammox bacteria from PFOA-induced toxicity in a lab-scale anaerobic membrane bioreactor (anammox-AnMBR), which operated for over 100 days. The system was exposed to stepwise PFOA increases (0.25, 0.5, and 0.75 mg/L). Nitrogen removal efficiency and extracellular polymeric substance (EPS) production were monitored. Microbial community dynamics were analyzed by metagenomic sequencing. Notably, increasing PFOA concentrations corresponded to stable NO2[-] levels and fluctuating NH4[+], suggesting a biphasic response to PFOA toxicity by the DNRA and anammox communities. Results indicate that DNRA bacteria were more tolerant to PFOA, even at high concentrations, than anammox bacteria. Metagenomic analysis further demonstrated the acute toxicity of high PFOA concentrations to anammox. The abundances of anammox functional genes (hzs, encoding hydrazine synthase; hdh, encoding hydrazine dehydrogenase) showed initial increases followed by declines at elevated PFOA concentrations. Concurrently, the increase in EPS (polysaccharides: 33.3 to 111.1 mg/g VSS; proteins: 3.0 to 247.6 mg/g VSS) indicated defense responses.},
}
@article {pmid41475601,
year = {2025},
author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W},
title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133911},
doi = {10.1016/j.biortech.2025.133911},
pmid = {41475601},
issn = {1873-2976},
abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.},
}
@article {pmid41475238,
year = {2025},
author = {Xin, H and Chen, S and Li, X and Chen, Z and Fan, Q and Luo, H and Liu, G and Mai, W},
title = {High-level chloramphenicol degradation in mariculture wastewater via cathodic nitro-reduction in a single-chamber bioelectrochemical system.},
journal = {Water research},
volume = {291},
number = {},
pages = {125174},
doi = {10.1016/j.watres.2025.125174},
pmid = {41475238},
issn = {1879-2448},
abstract = {The aim of this study was to investigate the mechanism of high-level chloramphenicol (CAP) degradation in mariculture wastewater using a single chamber bioelectrochemical system (BES). The reactor was assembled with carbon-brush electrodes and operated with sea mud as inoculum. Nearly complete removal of 200 mg/L CAP was achieved within 36 h when 2 g/L glucose was supplied as a co-substrate. With 200 mg/L CAP as the sole carbon source, BES at the close circuit achieved 28 ± 3% higher CAP removal than that at the open circuit within 72 h. CAP removal declined from 100 ± 5% to 45 ± 4% as the initial concentration increased from 200 to 600 mg/L within 36 h. High CAP concentration markedly inhibited sulfate-reducing bacteria (SRB), reducing the relative abundance of Desulfobulbus from 28.7% to < 0.5%, and decreasing sulfate removal from 90 ± 5% to < 56 ± 3% compared with the control. Nitro-reduction of CAP at the cathodic biofilm was determined as the predominant pathway among the three degradation routes in the BES. Metagenomic analysis revealed that 200 mg/L CAP significantly inhibited both multidrug efflux pump genes and key operons involved in dissimilatory sulfate reduction in the cathodic biofilm. Our results could be useful for eliminating high concentrations of antibiotic contaminants from seawater.},
}
@article {pmid41475234,
year = {2025},
author = {Wang, N and Lv, K and Guo, S and Peng, D},
title = {Functional imbalance between Thauera and anammox governs PD/A pathway stability under contrasting reactor modes.},
journal = {Water research},
volume = {291},
number = {},
pages = {125201},
doi = {10.1016/j.watres.2025.125201},
pmid = {41475234},
issn = {1879-2448},
abstract = {Partial denitrification coupled with anammox (PD/A) is a promising energy-efficient alternative for mainstream nitrogen removal, yet its stability under different reactor modes remains unclear. This study systematically compared sequencing batch (RS) and continuous-flow (RC) PD/A systems using performance monitoring, activity assays, and metagenomic analyses. RC maintained superior long-term stability, achieving >80% nitrogen removal with anammox contributing above 90%, whereas RS remained less stable (∼65% NRE, ∼75% anammox contribution) and relied more on complete denitrification. Activity assays revealed that PD activity in RS was 5.03 times that of anammox, favoring complete denitrification. In contrast, RC maintained balanced activities, with PD activity being 0.89 times that of anammox, supporting cooperative PD/A interactions. Metagenomic analysis further revealed that Thauera-associated Nir/Nor/Nos genes were markedly enriched in RS, indicating a stronger potential for complete denitrification. These findings demonstrate that reactor mode regulates PD/A interactions through distinct stabilization mechanisms, with continuous-flow operation enhancing microbial cooperation and system resilience. This study provides mechanistic insights and practical guidance for the stable implementation of mainstream PD/A processes.},
}
@article {pmid41475142,
year = {2025},
author = {Gallego-Cartagena, E and Morillas, H and Maguregui, M},
title = {Biodeterioration of built heritage in the context of climate change and atmospheric pollution: Toward transdisciplinary conservation strategies.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181313},
doi = {10.1016/j.scitotenv.2025.181313},
pmid = {41475142},
issn = {1879-1026},
abstract = {The built heritage -encompassing monuments, historic buildings and sculptural ensembles- is increasingly threatened by the synergistic impacts of climate change, atmospheric pollution and biological activity. This review critically analyses current understanding of the mechanisms driving the biodeterioration of built heritage, focusing on calcareous materials (e.g., limestone, marble and lime-based mortars), which are both widespread in built heritage and highly susceptible to degradation. We examine how environmental drivers -such as elevated humidity, temperature fluctuations, and pollutant deposition (SOₓ, NOₓ, particulate matter)-trigger complex physicochemical and biochemical reactions that compromise structural stability and aesthetic integrity. The review explores the metabolic strategies of biodeteriative organisms (fungi, algae, cyanobacteria), the interactions of pollutants and mineral substrates, and the consequent formation of salts, black crusts and corrosion products. We highlight the role of biomonitoring as a methodological and interpretive bridge linking atmospheric pollution to biodeterioration processes. In addition, we discuss emerging interdisciplinary methodologies - including functional metagenomics, microbial network analysis, and metabolomic profiling -and introduce the Function-Based Biodegradation Risk Assessment model, extended into a Multi-Level Risk Assessment Framework that connects microbial functionality, material diagnostics, and climate modeling. We contend that safeguarding built heritage in a changing climate requires transitioning from static, material-centred diagnostics to integrated, predictive frameworks that link microbial ecology, materials science, and climate dynamics, providing the basis for adaptive and anticipatory conservation strategies.},
}
@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Child, Preschool ; *Nutritional Status ; Case-Control Studies ; Feces/microbiology ; Saliva/microbiology ; Malaysia ; Female ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.<br><br>METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.<br><br>CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}
@article {pmid41474524,
year = {2025},
author = {Luo, S and Li, Z and Peng, Y and Xie, X and Zeng, Y and Dai, L and Zhang, X},
title = {Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {21},
pmid = {41474524},
issn = {1573-0972},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; 2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/genetics ; *Crohn Disease/microbiology/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.},
}
@article {pmid41474055,
year = {2025},
author = {Mehar, K and K, KP and Sen, AP and Paliwal, RK and M, BK and Kalidhas, AM and Mohapatra, TK and Samrat, A and Jayabal, R},
title = {Next-Generation Eco-Omics: Integrating Microbial Function Into Predictive Ecosystem Models.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70121},
pmid = {41474055},
issn = {1470-8744},
abstract = {Microorganisms drive essential ecosystem functions by mediating carbon, nitrogen, sulfur, and phosphorus transformations that regulate productivity and shape climate feedbacks. Rapid methodological advances now allow precise linkage of microbial identity, in situ activity, and ecosystem processes across spatial and temporal scales. High-resolution approaches-including long-read metagenomics and Hi-C-generate near-complete metagenome-assembled genomes (MAGs) from diverse environments, enabling reconstruction of microbial and viral-host interaction networks. Activity-resolved tools such as quantitative stable isotope probing (qSIP) and bioorthogonal non-canonical amino acid tagging (BONCAT), combined with fluorescence-activated cell sorting (FACS), yield taxon-specific growth and substrate assimilation rates within hours. Single-cell isotope techniques, including Raman-SIP and nanoSIMS, deliver nanometer-scale metabolic insights. Spatial meta-omics platforms, such as MetaFISH and MALDI-MSI, map metabolites alongside microbial identities with micrometer-level precision. Meanwhile, autonomous sequencing systems, including environmental sample processors and nanopore adaptive sampling, enable real-time (<24 h) ecological surveillance. Integrating these multimodal datasets into trait-based frameworks has reduced uncertainty in carbon flux predictions by nearly 20%. This review synthesizes these innovations, outlines optimized analytical pipelines, and proposes a framework for embedding eco-omics into predictive ecosystem and climate models, supporting evidence-driven management aligned with Climate Action and Life on Land.},
}
@article {pmid41473771,
year = {2025},
author = {Mao, X and Hu, X and Fang, J},
title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1737234},
pmid = {41473771},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; },
abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.},
}
@article {pmid41473686,
year = {2025},
author = {Yao, X and Zou, X and Cao, B},
title = {The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e00022},
pmid = {41473686},
issn = {2641-6573},
abstract = {The human respiratory virome is an underexplored component of the microbiome that includes diverse DNA and RNA viruses such as eukaryotic viruses, bacteriophages, and archaeal viruses. Recent advances in metagenomics have revealed the complexity and dynamic nature of the human respiratory virome, which interacts closely with the host and the bacterial microbiome to influence respiratory health and disease. In healthy individuals, the virome is characterized by low biomass and high temporal variability, with Anelloviruses predominant in the upper airways, whereas Streptococcus phages and herpesviruses are most commonly detected in the lower airways. Common respiratory viruses, such as respiratory syncytial virus, human rhinovirus, and influenza A virus, can persist after acute infection and modulate host immunity. The respiratory virome also plays a significant role in chronic respiratory diseases. Despite its importance, research on the respiratory virome is hampered by technical challenges, including low viral abundance and limited reference databases. This review summarizes current understanding of the composition and determinants of the respiratory virome in healthy individuals, describes its interactions with the host and respiratory microbiota, including the potential modulatory roles of bacteriophages, outlines virome alterations in respiratory diseases, examines methodological challenges, and highlights potential clinical applications and future research directions.},
}
@article {pmid41473253,
year = {2025},
author = {Wagner, ES and Oliphant, K and D'Souza, M and Cruz-Ayala, W and Azzam, RK and Andrews, B and Claud, EC},
title = {Fecal Microbiome and Bile Acid Profiles Differ in Preterm Infants with Parenteral Nutrition-associated Cholestasis.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {12},
pages = {1036-1045},
pmid = {41473253},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: Parenteral nutrition (PN)-associated cholestasis (PNAC) is frequently diagnosed in premature infants; however, not all PN-exposed infants develop PNAC. We propose that, in premature infants receiving PN and varying amounts of enteral feeds, differences in the gut microbiome and fecal bile acid content are associated with PNAC development. This study aimed to examine the fecal microbiome and bile acid content of premature infants on PN to determine if there is a relationship with the development of PNAC.<br><br>METHODS: Twenty-two preterm infants had serial bilirubin measurements and fecal samples collected during their neonatal intensive care unit admission. Fecal samples underwent 16S rRNA gene sequencing and bile acid analysis. Binomial regression, adjusting for postmenstrual age with feed amount as a moderator, was used to assess the impact of the fecal microbiome and bile acids on PNAC development.<br><br>RESULTS: Cholestatic patients (n = 11) had greater PN and antibiotic exposure (p = 0.020; p = 0.010) and longer neonatal intensive care unit stays (p = 0.0038) than non-cholestatic patients. Microbiome richness was higher in non-cholestatic infants (p < 2E-16), with no difference in &#x3b2; diversity (p = 1.0). Cholestatic infants had a significantly higher abundance of Proteobacteria and Fusobacteriota and a lower abundance of Bacteroidota (p < 2E-16). Akkermansia was abundant in all infants on low feeds; as feed volume increased, Akkermansia abundance significantly increased in non-cholestatic infants (p < 2E-16). Bile acid analysis demonstrated significantly lower deoxycholic acid concentrations in cholestatic infants (p < 2E-16). Metagenomic analysis revealed an increase in Proteobacteria requiring augmented stress responses in non-cholestatic infants.<br><br>CONCLUSIONS: This is the first study to directly explore the relationship between PNAC susceptibility, the microbiome, and fecal bile acids in preterm infants. The microbiome and bile acid patterns identified here may inform the development of targeted therapeutics for this vulnerable population.},
}
@article {pmid41472855,
year = {2025},
author = {Wu, D and Wang, AJ and Bu, DC and Sun, YY and Li, CH and Hong, YM and Zhang, S and Chen, SY and Zhou, JA and Zhang, TY and Yu, MH and Ma, YJ and Wang, XL and Xu, J and He, W and Heeschen, C and Chen, JF and Mao, WJ and Ding, H and Wu, WJ and Zhao, Y and Wang, H and Liu, NN},
title = {The interplay between tissue-resident microbiome and host proteins by integrated multi-omics during progression of colorectal adenoma to carcinoma.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70090},
pmid = {41472855},
issn = {2770-596X},
abstract = {The intratumoral microbiome is an emerging hallmark of cancer, yet its multi-kingdom host-microbiome ecosystem in colorectal cancer (CRC) remains poorly characterized. Here, we conducted an integrated analysis using deep shotgun metagenomics and proteomics on 185 tissue samples, including adenoma (A), paired tumor (T), and para-tumor (P). We identified 4057 bacterial, 61 fungal, 108 archaeal, and 374 viral species in tissues and revealed distinct intratumor microbiota dysbiosis, indicating a CRC-specific multi-kingdom microbial ecosystem. Proteomic profiling uncovered four CRC subtypes (C1-C4), each with unique clinical prognoses and molecular signatures. We further discovered that host-microbiome interactions are dynamically reorganized during carcinogenesis, where different microbial taxa converge on common host pathways through distinct proteins. Leveraging this interplay, we identified 14 multi-kingdom microbial and 8 protein markers that strongly distinguished A from T samples (area under the receiver operating characteristic curve (AUROC) = 0.962), with external validation in two independent datasets (AUROC = 0.920 and 0.735). Moreover, we constructed an early- versus advanced-stage classifier using 8 microbial and 4 protein markers, which demonstrated high diagnostic accuracy (AUROC = 0.926) and was validated externally (AUROC = 0.659-0.744). Functional validation in patient-derived organoids and murine allograft models confirmed that enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum promoted tumor growth by activating Wnt/β-catenin and NF-κB signaling pathways, corroborating the functional potential of these biomarkers. Together, these findings reveal dynamic host-microbiome interactions at the protein level, tracing the transition from adenoma to carcinoma and offering potential diagnostic and therapeutic targets for CRC.},
}
@article {pmid41472852,
year = {2025},
author = {Liu, J and Xing, W and Zhang, X and Xu, N and Xu, R and Gong, J and Zhang, J and Yang, F and Gao, S and Hou, Y and Shan, Y and Liu, B and Yuan, Q and Wang, A and Ren, N and Huang, C},
title = {Metagenomics and digital cell modeling facilitate targeted high-throughput sorting of anaerobic hydrogen-producing microorganisms.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70082},
pmid = {41472852},
issn = {2770-596X},
abstract = {This study proposes a novel strategy that prioritizes functional recognition, followed by targeted high-throughput sorting, to enable the comprehensive, rapid, and efficient acquisition of target microorganisms. Using metagenomic sequencing and binning analysis, we identified 215 potential anaerobic hydrogen-producing strains from 12 large-scale biogas samples. Digital cell models were subsequently constructed from metagenome-assembled genomes, which guided the design of 14 selective culture media for enriching these hydrogen-producing bacteria. Flow cytometry-based high-throughput sorting successfully isolated 81 potential anaerobic hydrogen-producing strains, achieving a target acquisition rate above 37% and a survival rate exceeding 70%. This method holds broad potential for the discovery and sorting of functional microorganisms across diverse environments and may ultimately facilitate the development of synthetic microbiomes for industrial applications.},
}
@article {pmid41472849,
year = {2025},
author = {Xiao, Z and Ding, K and Guo, X and Zhao, Y and Li, X and Jiang, D and Zhu, D and Chen, Q and Jong, MC and Graham, DW and Li, G and Zhu, YG},
title = {Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil-plant continua.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70094},
pmid = {41472849},
issn = {2770-596X},
abstract = {Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.},
}
@article {pmid41472846,
year = {2025},
author = {Wang, G and Zhao, L and Shi, Y and Qu, F and Ding, Y and Liu, W and Liu, C and Luo, G and Li, M and Bai, X and Li, L and Wang, L and Wong, CC and Ho, YP and Yu, J},
title = {High-throughput generic single-entity sequencing using droplet microfluidics.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70087},
pmid = {41472846},
issn = {2770-596X},
abstract = {Single-cell sequencing has revolutionized our understanding of cellular heterogeneity by providing a micro-level perspective in the past decade. While heterogeneity is fundamental to diverse biological communities, existing platforms are primarily designed for eukaryotic cells, leaving significant gaps in the study of other single biological entities, such as viruses and bacteria. Current methodologies for single-entity sequencing remain limited by low throughput, inefficient lysis, and highly fragmented genomes. Here, we present the Generic Single-Entity Sequencing (GSE-Seq), a versatile and high-throughput framework that overcomes key limitations in single-entity sequencing through an integrated workflow. GSE-Seq combines (1) one-step generation of massive barcodes, (2) degradable hydrogel-based in situ sample processing and whole genome amplification, (3) integrated in-droplet library preparation, and (4) long-read sequencing. We applied GSE-Seq to profile viral communities from human fecal and marine sediment samples, generating thousands of high-quality single-entity genomes and revealing that most are novel. GSE-Seq identified not only dsDNA and ssDNA viruses, but also hard-to-detect giant viruses and crAssphages. GSE-Seq of bacterial genomes also revealed putative novel bacterial species, validating the versatility of this platform across different microbial kingdoms. Collectively, GSE-Seq represents a robust framework that addresses persistent challenges in high-throughput profiling for generic applications and holds immense promise for single-cell deconvolution of diverse biological entities.},
}
@article {pmid41472810,
year = {2025},
author = {Lan, B and Liang, Y and Zhou, Z and Liu, J},
title = {Gut microbiome dysbiosis implicates the gut-bone axis in Modic changes: a metagenomic case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702357},
pmid = {41472810},
issn = {1664-302X},
abstract = {INTRODUCTION: Modic changes (MCs) are vertebral endplate lesions strongly associated with discogenic low back pain (LBP), though their pathogenesis remains poorly understood. Emerging evidence implicates gut microbial dysbiosis in systemic inflammation and musculoskeletal disorders, yet its potential role in MCs has not been investigated. This study aimed to characterize the gut microbiome in patients with MCs and identify microbial and metabolic features linked to disease severity.<br><br>METHODS: In a case-control study, shotgun metagenomic sequencing was performed on fecal samples from 31 patients with MCs (16 Type 1, 15 Type 2) and 25 age- and sex-matched healthy controls. Microbial community structure was assessed via alpha and beta diversity analyses. Differential taxa and predictive biomarkers were identified using linear discriminant analysis effect size (LEfSe) and Random Forest modeling. Functional potential was evaluated via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Associations between microbial features and clinical markers (C-reactive protein [CRP], Pfirrmann grade) were also examined.<br><br>RESULTS: Patients with MCs showed significantly reduced gut microbial alpha diversity compared to controls (Chao1 index: p =&#x202f;0.005; Shannon index: p =&#x202f;0.034; Simpson index: p =&#x202f;0.042), with the most pronounced reduction in Type 1 MCs. Beta diversity analysis revealed distinct microbial communities between groups (PERMANOVA, p =&#x202f;0.001). Key discriminative taxa included unclassified_Parabacteroides (AUC&#x202f;=&#x202f;0.895) and Bacteroides uniformis (AUC&#x202f;=&#x202f;0.889). Metabolic pathway analysis identified 52 differentially abundant pathways, with significant enrichment of quorum sensing (p <&#x202f;0.001) and glycerolipid metabolism (p <&#x202f;0.001) in MC patients, both strongly correlated with elevated CRP and higher Pfirrmann grade (p <&#x202f;0.001).<br><br>DISCUSSION: Gut microbial dysbiosis is associated with MCs, marked by reduced diversity, specific bacterial biomarkers, and altered metabolic pathways related to inflammation and tissue degeneration. These results suggest a potential role of the gut-bone axis in MC pathogenesis and highlight novel targets for diagnostic and therapeutic strategies in LBP.},
}
@article {pmid41472461,
year = {2025},
author = {Xu, ST and Qian, ZY and Tao, Y},
title = {Chinese Expert Consensus on the Application of Metagenomic Sequencing Technology in Ocular Infectious Diseases: A Delphi Method.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {12},
pages = {1550-1557},
doi = {10.3967/bes2025.156},
pmid = {41472461},
issn = {2214-0190},
}
@article {pmid41472301,
year = {2025},
author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW},
title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472301},
issn = {1999-4915},
mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; },
abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.},
}
@article {pmid41472294,
year = {2025},
author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ},
title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472294},
issn = {1999-4915},
support = {0//Gyeongkuk National University/ ; },
mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; },
abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.},
}
@article {pmid41472225,
year = {2025},
author = {Dos Santos, MM and Salles, TS and de Campos, GM and Brcko, IC and Lima, ARJ and Sampaio, SC and Elias, MC and Giovanetti, M and Slavov, SN},
title = {Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121554},
pmid = {41472225},
issn = {1999-4915},
support = {17/23205-8, 23/12155-0, 21/11944-6, 23/07688-0//FAPESP/ ; 403075/2023-8, 305111/2022-1//CNPq/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/virology/diagnosis/etiology ; *Viruses/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Virus Diseases/virology/diagnosis ; Acute Disease ; Genome, Viral ; },
abstract = {Acute respiratory infections (ARIs) remain a leading cause of global morbidity and mortality, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. Despite the availability of traditional diagnostic tools, including viral culture and highly elaborated PCR respiratory panels, many cases of ARI remain without an identified etiological agent. This is due to the vast diversity of viral agents that can be involved in cases of ARI, which represents a major limitation of the targeted diagnosis. In this context, viral metagenomics has emerged as a powerful, unbiased approach for detecting both known and novel pathogens directly from clinical samples. This review highlights the application of metagenomic next-generation sequencing for the investigation of etiological causes of ARIs, emphasizing its relevance in complex cases-particularly among immunocompromised patients-where standard methods might fail. We highlight the main viruses involved in respiratory infections, the strengths and limitations of metagenomic next-generation sequencing approaches, their role in genomic surveillance of respiratory viruses, and their potential to build public health responses to potentially emerging respiratory threats. Ultimately, integrating viral metagenomics into clinical and surveillance frameworks could enhance the early detection and control of respiratory viral diseases worldwide.},
}
@article {pmid41472209,
year = {2025},
author = {Galeeva, J and Kuzmichenko, P and Manolov, A and Lukashev, A and Ilina, E},
title = {Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121538},
pmid = {41472209},
issn = {1999-4915},
support = {075-15-2025-530//Russian Ministry of Education and Science/ ; },
mesh = {*Viruses/genetics/classification/isolation &amp; purification ; *Computational Biology/methods ; *Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Humans ; },
abstract = {The exponential growth of viral metagenomic data has created an urgent need for accurate and scalable tools for virus discovery, yet the extreme diversity, rapid evolution, and limited reference databases for viruses pose unique computational challenges that traditional sequence comparison methods struggle to address. This systematic review, conducted in accordance with PRISMA 2020, examines current trends and methodological advances in virus discovery tools from 1990 to 2025. As virus discovery is a broad and multi-dimensional topic, this review focuses on the first-line tools used to analyze the results of high-throughput sequencing. The review was conducted using the PubMed database with a snowballing approach, with over 54 key studies selected for the analysis. These studies encompass the following approaches: alignment-based methods, rapid similarity estimation techniques, profile hidden Markov model methods, combination pipelines, k-mer-based approaches, and machine learning-based methods. The transition from alignment-based to machine learning methods has dramatically improved the detection of divergent viruses, yet challenges remain in interpreting model decisions and handling incomplete viral genomes. This review summarizes current knowledge and potential future directions for the development of virus detection capabilities.},
}
@article {pmid41472203,
year = {2025},
author = {Lapshina, VK and Guskova, NI and Stetsenko, IF and Luong, MT and Tran, TV and Matsvay, AD and Shipulin, GA and Yudin, SM and Skvortsova, VI},
title = {Characterizing the Bat Virome of Vietnam: A Systematic Review of Viral Diversity and Zoonotic Potential.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121532},
pmid = {41472203},
issn = {1999-4915},
support = {388-00084-24-00//Federal Medical Biological Agency/ ; },
mesh = {*Chiroptera/virology ; Vietnam/epidemiology ; Animals ; *Virome ; *Zoonoses/virology/epidemiology ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; Disease Reservoirs/virology ; Biodiversity ; Viral Zoonoses/virology ; Genetic Variation ; },
abstract = {Bats have been identified as reservoir hosts for an exceptional diversity of viruses, including multiple taxa of high zoonotic concern. Over a hundred bat species inhabit Vietnam, which, combined with significant biodiversity, carry high risk of zoonotic spillover due to dense human-animal interfaces, extensive wildlife trade, and proximity to recent outbreak epicenters. This review systematically synthesizes data on the bat virome in Vietnam and neighboring Southeast Asian countries, assessing viral diversity, host species involvement, and zoonotic potential. By prioritizing virus groups with established zoonotic capacity and pandemic potential, the systematic search identified studies reporting viruses from 32 families across 13 bat families. Based on the WHO 2024 risk classification, seven of these viral families were categorized as high-risk, three as medium-risk, and twelve as low-risk. The comparatively higher viral diversity reported in neighboring countries suggests that the current study likely represents an underestimation of the true virome present in Vietnamese bat populations. We emphasize the urgent need for expanded virological studies integrating metagenomic sequencing, serological surveys, and ecological modeling to improve early detection of emerging threats, as the comparatively higher viral diversity reported in neighboring countries suggests existing research likely represents an underestimation of the true virome present in Vietnamese bat populations. Strengthening regional collaboration is critical for establishing proactive pandemic prevention strategies in this high-risk zoonotic hotspot.},
}
@article {pmid41472198,
year = {2025},
author = {Koutsakos, M and Parry, RH and Wille, M},
title = {Mounting Evidence for an Expanded Host Range of Influenza B Viruses.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121528},
pmid = {41472198},
issn = {1999-4915},
mesh = {Animals ; *Influenza B virus/physiology/genetics/classification ; *Host Specificity ; Humans ; *Orthomyxoviridae Infections/virology/veterinary ; Influenza, Human/virology ; Phylogeny ; },
abstract = {Influenza B viruses (IBV) belong to the family of Orthomyxoviridae and circulate annually in humans causing respiratory illness. Although they are considered an exclusively human pathogen, there is evidence of IBV infections in animals, including wildlife, companion animals and livestock. In addition, metagenomic studies have identified novel orthomyxoviruses in amphibians and fish that appear related to IBV, suggesting influenza viruses, including IBV, have been associated with vertebrates across their evolutionary history. In this review, we summarise our current knowledge of potential IBV and IBV-like infections in animals. These collectively suggest that the ecology of IBV extends beyond humans and warrants further investigations.},
}
@article {pmid41472072,
year = {2025},
author = {Cheng, H and Chong, H and Yuan, M and Ren, C and Wang, J and Zhao, F},
title = {Soil Microbial Life History Strategies Drive Microbial Carbon Use Efficiency Following Afforestation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472072},
issn = {2076-2607},
support = {42277322, 31570440//National Natural Science Foundation of China/ ; },
abstract = {Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation remains, however, a major scientific challenge. In particular, there are major uncertainties about the role of microbial traits in driving CUE. Here, we compared sites along a 45-year afforestation chronosequence and combined the novel [18]O-H2O tracer method with metagenomic analysis to quantify CUE and explore the mechanisms underlying microbe-mediated C dynamics. The results showed that soil microbial CUE significantly increased following afforestation and showed a positive relationship with SOC, which suggested that microbial CUE could promote C accumulation in afforested ecosystems. We further found the critical role of microbial traits in the regulation of CUE through altering microbial life history strategies: microbial CUE was positively and significantly correlated with resource acquisition (A) genes, but showed a negative and significant correlation with stress tolerance (S) strategy genes. These results suggested that soil microbes reduce investment in S strategies and shift to A and high yield (Y) strategies, thereby increasing CUE. This knowledge is important because it advances our understanding of the microbial physiological and evolutionary tradeoffs mediating soil C cycling in the context of human-induced land use change.},
}
@article {pmid41472057,
year = {2025},
author = {Yamaguchi, J and Orf, GS and Malinauskas, J and Mata, M and Weiss, SL and Forberg, K and Meyer, TV and Wiebe, PO and Mowerman, I and Piotrowski, SJ and Glownia, D and Rodgers, MA and Hackett, J and Suputtamongkol, Y and Phoompoung, P and Gomathi, S and Pradeep, A and Solomon, SS and Bbosa, N and Kaleebu, P and Ahouidi, AD and Mboup, S and Sequeira, AF and Tojo, A and Cloherty, GA and Berg, MG},
title = {teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472057},
issn = {2076-2607},
support = {N/A//Abbott Laboratories/ ; },
abstract = {Probe-based capture represents a highly sensitive and cost-effective approach for overcoming host background and enriching viruses in metagenomic NGS (mNGS) libraries. Using clinical specimens collected globally from patients with fever or respiratory illness, we generated mNGS libraries by random priming and Nextera XT tagmentation, followed by target enrichment (teNGS) with Comprehensive Viral Research Panel (CVRP) probes. Capture pool sizes and total reads were optimized, and libraries were initially sequenced separately. Using only 3-4% of reads required for standard mNGS, teNGS achieved increased sensitivity, 100-10,000× increases in depth, and >50% genome coverage for pathogens with titers ≥ 1000 cp/mL. Application to >2000 clinical specimens from various matrices and to contrived samples containing viruses absent from the CVRP probe set enabled detection of diverse viral families and established a minimum 65% nucleotide identity for hybridization, respectively. To save time and resources, teNGS and mNGS libraries were then combined into one sequencing run: teamNGS. In addition to streamlining the workflow, teamNGS also improved genome recovery. Coupling methods maintain the sensitivity and coverage for viruses achieved by enrichment alone while also ensuring comprehensive recovery of non-viral microbes. teamNGS has the potential to improve patient management and lower the rates of unnecessary testing and antibiotic use.},
}
@article {pmid41472033,
year = {2025},
author = {Gladkov, GV and Kimeklis, AK and Orlova, OV and Lisina, TO and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE},
title = {Taxonomic and Metagenomic Survey of a Peat-Based Straw Degrading Biofertilizer.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472033},
issn = {2076-2607},
support = {23-16-00147//Russian Science Foundation/ ; },
abstract = {The mobilization of complex microbial communities from natural resources can be a valuable alternative to the use of single-species biofertilizers when it comes to the decomposition of plant residues. However, the functioning and interaction of microorganisms within these communities remain largely unexplored. Our task was to investigate the cellulose-degrading community using the biofertilizer BAGS (peat-based compost with straw) as an example and define its active component. For this, we monitored the succession of the biofertilizer's taxonomic composition during two consecutive rounds of its six-month composting process, varying in the applied mineral fertilization. The amount of added nitrogen significantly affected the performance of the biofertilizer, contributing to its high cellulolytic activity. Based on the network analysis, the biofertilizer's mature phase was determined, and its characteristic ASVs (amplicon sequence variants) were described. Metagenomic analysis of this phase revealed MAGs (metagenome-assembled genomes) corresponding to these ASVs, which contained genes for cellulose and aromatics degradation, as well as genes for nitrogen and sulfur pathways, including anaerobic nitrate reduction and thiosulfate oxidation. Thus, we propose that the cellulose-decomposing bacterial component of BAGS, associated with the mature phase, occupied different trophic niches, not limited to cellulose degradation, which should be considered when designing natural or artificial microbial systems for the decomposition of plant residues.},
}
@article {pmid41472032,
year = {2025},
author = {Li, M and Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z},
title = {Gut Microbiome and Metabolome Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472032},
issn = {2076-2607},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; BK20241934//Natural Science Foundation of Jiangsu Province/ ; 32172686//National Natural Science Foundation of China/ ; },
abstract = {Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome-metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial-metabolite networks, exemplified by the Faecalimonas-LysoPS (16:0/0:0) and UBA737-Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial-metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle.},
}
@article {pmid41472029,
year = {2025},
author = {Dhakal, R and Guo, W and Vieira, RAM and Guan, L and Neves, ALA},
title = {Advances in Lignocellulose-Degrading Enzyme Discovery from Anaerobic Rumen Fungi.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472029},
issn = {2076-2607},
abstract = {Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further characterization. Anaerobic rumen fungi play a pivotal role in lignocellulose degradation due to their unique enzymatic capabilities. This review explores the enzymatic systems of rumen anaerobic fungi, highlighting their ability to produce a diverse array of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. These enzymes facilitate the breakdown of complex plant polymers, making anaerobic fungi essential contributors to fiber degradation in the rumen ecosystem and valuable resources for biotechnological applications. This review summarizes the structural and functional diversity of fungal CAZymes, and the mechanical disruption of plant cell walls by fungal rhizoidal networks is discussed, showcasing the ability of fungi to enhance substrate accessibility and facilitate microbial colonization. Recent studies using genomic, transcriptomic, and biochemical approaches have uncovered several novel CAZymes in anaerobic fungi, including multifunctional xylanases, β-glucosidases, and esterases. These findings highlight the continued expansion of fungal enzyme repertoires and their potential for biotechnology and feed applications. Continued research in this field will enhance our understanding of microbial ecology and enzyme function, paving the way for applications that address global challenges in energy, food security, and environmental sustainability.},
}
@article {pmid41472016,
year = {2025},
author = {Li, H and Yang, K and Liu, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Effects of Long-Term Heavy Metal Exposure on Oral Microbial Antibiotic Resistance Genes of Residents in the Mining and Smelting Area.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472016},
issn = {2076-2607},
support = {lzujbky-2023-34//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Growing evidence highlights the role of heavy metals in driving the co-selection of an-tibiotic resistance genes (ARGs), and the human oral cavity is an important reservoir of ARGs. This cross-sectional study investigated the effects of heavy metal exposure on human oral microbiota and ARGs, collecting buccal mucosal and blood samples from residents in a heavy metal-contaminated area (Baiyin City) and a non-contaminated area (Yuzhong County, Lanzhou City). The results showed heavy metal exposure is associated with altered alpha and beta diversity of bacteria and ARGs in human oral cavities, with bacterial compositional shifts being the main factor in ARG variation. Metagenomic analysis revealed heavy metal exposure is linked to modifying the interactions in the bacterial community and between ARGs and metal resistance genes (MRGs), shown by simplified topological structures in bacterial and resistome networks, along with enhanced positive correlations among nodes. Neisseria, Haemophilus, Morococcus, Streptococcus, Staphylococcus, and Mycobacteroides as potential hosts for resistance genes in human oral cavity. Furthermore, blood metal quantification revealed distinct associations with resistance patterns. This study demonstrates significant associations between environmental heavy metal exposure and the oral resistome and emphasizes the role of bacterial community composition.},
}
@article {pmid41472002,
year = {2025},
author = {Cheng, H and Yuan, M and Ren, C and Zhao, F and Wang, J},
title = {Soil Nitrogen Mineralization Is Driven by Functional Microbiomes Across a North-South Forest in China.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472002},
issn = {2076-2607},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; },
abstract = {Nitrogen (N) mineralization is a complex microbial-driven process that controls the supply of N for plants and microbes. The relative contribution of different microbial N-cycling species/genes to the variation in N mineralization rate (NMR) across contrasting forest biomes was unclear. Here, we investigate the linkages between soil metagenomes and N mineralization rates across 10 contrasting forest biomes (covering temperate, subtropical, and tropical forests) along a 3425 km north-south forest in China. We found that the NMR was higher in subtropical forests, and the variation in NMR can be explained by climate and soil environments, particularly for soil substrate NH4[+]. Similar to NMR, microbial N-cycling genes/species were also higher in subtropical forests, suggesting that the higher microbial N-cycling traits in warm regions may drive higher NMR. We also quantified the contribution of microbial N-cycling gene pathways to NMR across forest biomes and found that the microbial N-denitrification pathway (genes like norZ, narG, nirK, and norB) and nitrification pathway (genes like nxr) explained more variation in NMR than other pathways, such as N ammonification. Collectively, our work demonstrates the importance of microbial N-cycling traits to explain soil N mineralization rates across forest biomes and suggests that this information can be used to help improve the management of the N cycle in forests across biomes.},
}
@article {pmid41471973,
year = {2025},
author = {Pang, Z and Guo, J and Xu, H and Li, Y and Chen, C and Zhang, G and Lu, A and Shao, X and Kan, H},
title = {Inter-Row Grassing Reshapes Nitrogen Cycling in Peach Orchards by Influencing Microbial Pathways in the Rhizosphere.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471973},
issn = {2076-2607},
support = {KJCX20230220//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; KJCX20240319//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; KJCX 20230305//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; },
abstract = {Traditional clean tillage in peach orchards leads to soil degradation and nitrogen (N) loss. While inter-row grassing can optimize N cycling, the specific rhizosphere microbial mechanisms involved have not been fully understood. This study investigated how different inter-row grassing modes influence N availability through microbial communities in a peach orchard. The experiment included a monoculture of Trifolium repens L. (Tr), a monoculture of Lolium perenne L. (Pr), their mixture (TPr), and clean tillage (CK). By combining soil physicochemical analyses, metagenomic sequencing, functional gene quantification, and multivariate statistics, the study systematically examined the impacts of inter-row grassing modes on soil N cycling. The results showed that inter-row grassing modes played a significant role in reshaping N processes. Pr enhanced mineralization and nitrification, increasing inorganic N through specific genes (amoA, hao). Tr, on the other hand, promoted diazotrophs (Bradyrhizobium) and dissimilatory nitrate-reducing bacteria, enhancing biological N fixation and retention. TPr combined these benefits, leading to enhanced nitrification, increased labile carbon, and elevated enzyme activities, creating a complex microbe-gene network that mediated nitrification and denitrification. Overall, inter-row grassing modulates rhizosphere functions by enhancing N cycling through a "carbon input-microbial regulation" mechanism, offering an effective strategy for improving N use efficiency and promoting sustainable orchard management.},
}
@article {pmid41471959,
year = {2025},
author = {Wang, C and Yu, Y and Feng, W and Xu, Y and Deng, T and Cai, W and Liang, W and Wang, H},
title = {The Microbial Community Succession Drives Stage-Specific Carbon Metabolic Shifts During Agaricus bisporus Fermentation: Multi-Omics Reveals CAZymes Dynamics and Lignocellulose Degradation Mechanisms.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471959},
issn = {2076-2607},
support = {No. 2021C02073-9//Zhejiang Science and Technology Major Program on Agriculture New Variety Breeding/ ; },
abstract = {This study integrates metagenomic and metabolomic data to systematically analyze the microbial community succession and carbon source metabolism transitions during the third fermentation cycle of Agaricus bisporus, with the aim of optimizing fermentation efficiency and lignocellulose degradation strategies. Principal Coordinate Analysis (PcoA) based on Bray-Curtis dissimilarity reveals significant microbial community separation across the stages of the first mushroom fruiting cycle. The overall pattern of "stage-specific differentiation" is consistent with the "cellulose hydrolysis" turn to the degradation of complex polysaccharides via carbohydrate-active enzymes (CAZymes). In the microbial network analysis showed that different microbe group controlled the stage-specific differentiation. These findings highlight a phase-dependent metabolic shift during the fermentation process: the early stages of fruiting rely more on cellulose-degrading microbes and their enzymatic systems, while later stages are driven by the degradation of complex polysaccharides and lignin derivatives, with Planctomycetota leading the degradation. This provides new mechanistic insights into agricultural waste resource utilization and the directional regulation of fermentation processes.},
}
@article {pmid41471954,
year = {2025},
author = {Cui, G and Cui, J and Zhang, M and Zhang, B and Huang, Y and Wang, Y and Feng, W and Zhou, J and Liu, Y and Li, T},
title = {Study on the Source and Microbial Mechanisms Influencing Heavy Metals and Nutrients in a Subtropical Deep-Water Reservoir.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471954},
issn = {2076-2607},
support = {42403018//National Natural Science Foundation of China/ ; },
abstract = {Reservoirs are hotspots for the coupling of nutrients and heavy metals, and they substantially modify the compositions and spatiotemporal distributions of microorganisms in fluvial systems. However, relatively few studies have been performed that investigate the microbial mechanisms driving interactions among heavy metals and nutrients in reservoirs. The Goupitan Reservoir, a seasonal stratified reservoir located within the Wujiang River catchment, was chosen as the research subject. The temporal and spatial variations in heavy metals and nutrients, and the metagenomic composition of the reservoir water were analyzed in January, April, July, and October 2019. The results revealed that As, Ni, Co, and Mn were derived primarily from mine wastewater, whereas Zn, Pb, Cd, and Cr were related to domestic and agricultural wastewater discharge. The study area was dominated by Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes, with the proportion of dominant phyla reaching 90%. Decreases in the dissolved oxygen (DO) concentration and pH in the bottom water during July and October were conducive to increases in the abundance of the anaerobic bacterial groups Planctomycetes and Acidobacteria. The functional genes norBC and nosZ associated with denitrification (DNF), the key gene nrfAH involved in the dissimilatory nitrate reduction to ammonium (DNRA) process, the functional genes aprAB and dsrAB responsible for sulfate reduction/sulfide oxidation, as well as the thiosulfate oxidation complex enzyme system SOX, all exhibit high abundance in hypoxic water bodies and peak in the redoxcline, highlighting the significance of related nitrogen (N) and sulfur (S) metabolic processes. In addition, the concentrations of heavy metals significantly affected the spatial differentiation of the planktonic bacterial community structure, with Mn, Co, Fe, Ni, As, and Cu making relatively high individual contributions (p < 0.01). This study is important for elucidating the sources and microbiological mechanisms influencing heavy metals and nutrients in seasonally stratified subtropical reservoirs.},
}
@article {pmid41471939,
year = {2025},
author = {Luo, Z and Zhou, Y and Wang, X and He, L and Jia, T},
title = {Effects of Endophytic Fungi and Arbuscular Mycorrhizal Fungi on Microbial Community Function and Metabolic Pathways in the Rhizosphere Soil of Festuca rubra.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471939},
issn = {2076-2607},
abstract = {Numerous studies have shown that there are many uncertainties associated with the interactions of nitrogen with plants and microorganisms. In particular, the effects of symbioses between plants and various microorganisms on soil microbial community function remain unclear. Metagenomic sequencing was used to explore the changes in microbial community composition, function and metabolic pathways in rhizosphere soil and the associated influencing factors under different nitrogen levels caused by arbuscular mycorrhizal fungi (AMF) inoculation of F. rubra infected with endophytic fungi and nonendophytic fungi. Plant nutrient allocation (aboveground/belowground), soil pH, and enzymatic activities significantly modulated the functional profiles of the bacterial, fungal, and archaeal communities within these rhizospheres. Soil β-glucosidase activity had the greatest effect on the cluster of orthologous groups of proteins (COG) function of the rhizosphere soil bacterial community, and soil L-leucine aminopeptidase had the greatest effect on the COG function of the rhizosphere soil fungal and archaeal communities. The contributions of AMF colonization to the kyoto encyclopedia of genes and genomes (KEGG) functions of bacteria and archaea in the rhizosphere soil were greater than those of F. rubra infection with endophytic fungi, and AMF colonization improved the metabolic pathways, secondary metabolite biosynthesis, microbial metabolism, amino acid biosynthesis and carbon metabolism of bacterial and archaeal communities in the rhizosphere soil of F. rubra. The effects of endophytic fungi and AMFs on the function and metabolic pathways of symbiotic rhizosphere soil microbial communities were heterogeneous. This study revealed that considering both biotic and abiotic factors is essential for predicting the maintenance of soil ecosystem function by plant-fungal symbionts.},
}
@article {pmid41471929,
year = {2025},
author = {Han, D and Zhao, R and Yang, X and Wang, T and Li, Z and Zhu, M and Yang, Q and Qu, Y and Chen, X and Chen, Z},
title = {Comparative Analysis of Environmental and Host-Associated Microbiome in Odorrana schmackeri (Auran: Ranidae): Insights into Tissue-Specific Colonization and Microbial Adaptation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471929},
issn = {2076-2607},
support = {ZC (Grant no. 32270440), XHC (Grant no. U21A20192) and YFQ (32171498)//National Natural Science Foundation of China/ ; },
abstract = {Amphibian microbial communities are known to be shaped by host physiology and environmental factors, yet the relative roles of sexual dimorphism and tissue specialization remain poorly understood. Using 16S rRNA gene sequencing, we compared the gastrointestinal and integumentary microbiomes of a monomorphic Chinese frog population, Odorrana schmackeri, inhabiting identical montane streams. Our results showed distinct phylogenetic stratification between niches: Proteobacteria dominated both environmental microbiota and O. schmackeri gut and skin microbiotas but with differential sub-phylum specialization. The soil microbiota was dominated by unclassified_Vicinamibacteraceae, the water microbiota was Limnohabitans-dominated, the skin microbiota was dominated by Bordetella, and the gut microbiota was led by Acinetobacter. Alpha diversity analysis revealed significant tissue- and environmental-based divergences but no sexual differentiation, a pattern confirmed by beta diversity assessments showing stronger microbial community separation by tissue and environmental compartmentalization than by sex. Functional metagenomic prediction indicated convergent enrichment of metabolic pathways across host-associated and environmental communities. These results suggest that microbial community structure in O. schmackeri is principally governed by tissue-specific ecological selection pressures rather than host sexual characteristics. Our findings enhance understanding of microbiome assembly rules in vertebrate ectotherms and identify potential connections between microbiota in different ecological niches.},
}
@article {pmid41471911,
year = {2025},
author = {Zhang, Z and Islam, MS and Noman, M and Hao, Z and Chai, R and Qiu, H and Wang, J and Cai, Y and Wang, Y and Wang, J},
title = {Enhanced Mesophilic Degradation of Rice Straw by Microbial Consortium SXJG15 Through Coordinated Enzymatic Activity and Community Reshaping.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471911},
issn = {2076-2607},
support = {2023C02018//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; 2023SNJF033//"Three Agriculture and Nine organizations" Science and Technology Cooperation Program of Zhejiang Province/ ; },
abstract = {The sustainable utilization of rice straw is challenged by its recalcitrant lignocellulosic structure, especially under low-to-moderate field temperatures. In this study, a novel microbial consortium (SXJG15) mainly containing Sphingobacterium, Azospirillum, and Pseudomonas was enriched from overwintering rice stubble in Zhejiang, China, and evaluated for its rice straw degradation efficiency at 25 °C. Over an 18-day cultivation period, SXJG15 achieved a 52.5% degradation of total rice straw, including 60.2% cellulose, 76.3% hemicellulose, and 40.7% lignin. High extracellular enzymatic activities, including cellulases (up to 80.3 U/mL) and xylanases (up to 324.8 U/mL), were observed during the biodegradation process. 16S rRNA gene sequencing and metagenomics analyses revealed a succession of dominant taxa, including Sphingobacterium, Azospirillum, and Cellulomonas. Further, CAZy annotation indicated that the SXJG15 enzyme system was rich in glycoside hydrolases (42.7%) and glycosyltransferases (34.2%), demonstrating its high potential for lignocellulose degradation. This study uniquely demonstrates the mesophilic (moderate temperature 25 °C) efficiency of SXJG15 in lignocellulose breakdown, provides new insights into the microbial mechanisms of straw decomposition, and lays a foundation for bioenergy and soil fertility applications for developing a sustainable agriculture system.},
}
@article {pmid41471909,
year = {2025},
author = {Cui, Y and Wang, S and Zhao, W and Du, Y and Wang, L and Han, B and Zhang, M and Xu, X and Wang, S and Ma, X and Xu, X and Zhao, Y and Liu, S and Wang, Y and Tuo, H},
title = {Shared Gut Microbial and Functional Signatures Linking Parkinson's Disease and Type 2 Diabetes Revealed by Function-Anchored Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471909},
issn = {2076-2607},
support = {82071257, 82371254//National Natural Science Foundation of China/ ; JX2023YJ021//Tongzhou District, Beijing Medical and Health Industry Development Project/ ; tsqn202306029//Taishan Young Scholars/ ; },
abstract = {Parkinson's disease (PD) and type 2 diabetes mellitus (T2DM) exhibit increasing comorbidity, yet the shared contribution of gut microbiota remains unclear. To investigate parallel microbial and functional alterations underlying PD, T2DM, and PD with diabetes (PDDM), we performed fecal metagenomic sequencing in 156 PD, 41 T2DM, and 44 PD with diabetes (PDDM) patients and 83 healthy controls (HC). PD and T2DM showed highly concordant microbial shifts, with 22 genera and 91 species consistently altered across disease groups compared with HC. Functional enrichment highlighted common perturbations in taurine and hypotaurine metabolism, retinol metabolism, the hypoxia-inducible factor-1 (HIF-1) pathway, and xenobiotic degradation, implicating disrupted oxidative stress responses, neuro-metabolic regulation, and detoxification. Key taxa, including Limosilactobacillus fermentum, Lactobacillus porci, and Lactobacillus delbrueckii, were increased and showed moderate positive correlations (|ρ| ≥ 0.3) with antioxidant/retinol-HIF-1, taurine-hypotaurine, and xenobiotic degradation pathways. Bifidobacterium breve (unadjusted analysis) was increased in PD and further enriched in PDDM, correlating with multiple beneficial pathways. Bifidobacterium simiarum (covariate-adjusted analyses) showed the broadest positive pathway associations, while selected Bacteroides species (e.g., B. acidifaciens) exhibited negative correlations with insulin-resistance pathways and positive correlations with steroid hormone biosynthesis. By contrast, Butyricimonas vaginalis showed negative correlations with HIF-1 and insulin signaling and with cytochrome P450-related drug metabolism. These findings provide the first systematic evidence of parallel taxonomic and functional dysbiosis in PD and T2DM, supporting gut microbiota as a shared mediator and potential therapeutic target in comorbidity.},
}
@article {pmid41471883,
year = {2025},
author = {Ji, J and Jiang, X and Song, P and Yang, Q and Sun, M and Dong, Z and Lu, Y and Dou, S and Dong, L},
title = {Multi-Omics Insights into Microbial Interactions and Fermented Food Quality.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471883},
issn = {2076-2607},
support = {2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS2023037//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; },
abstract = {The quality, flavor, and functional attributes of fermented foods are intrinsically shaped by the composition and metabolic dynamics of their microbial communities. This systematic review explores the structural organization, successional patterns, and mechanistic roles of these communities in influencing food quality, with a specific focus on core functional groups-including lactic acid bacteria (LAB), yeasts, and molds-and their interplay through key metabolic pathways. By integrating multi-omics approaches, such as metagenomics and metabolomics, we elucidate the underlying relationships between microbial activity and the formation of volatile flavor compounds, nutritional metabolites, and bioactive substances. These insights offer a scientific basis for the targeted regulation and functional enhancement of fermented food products.},
}
@article {pmid41471878,
year = {2025},
author = {Qi, X and Han, Z and Meng, J and Zhao, H and Zhou, M and Wang, M and Kang, S and Shi, Q and Li, H and Lu, F and Zhao, H},
title = {Integrated Metagenomic and Lipidomic Profiling Reveals Dysregulation of Facial Skin Microbiome in Moderate Acne Vulgaris.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471878},
issn = {2076-2607},
support = {32402248//the National Natural Science Foundation of China/ ; No. 24JCQNJC00880//the Natural Science Foundation of Tianjin/ ; },
abstract = {Acne vulgaris is a prevalent chronic inflammatory dermatosis primarily affecting the pilosebaceous units. Current therapeutic approaches often exhibit limited efficacy and high recurrence rates. To investigate the microbiome-related mechanisms of acne vulgaris, facial skin samples from 19 patients with moderate acne and 20 healthy individuals were analyzed using an integrated metagenomic and lipidomic profiling strategy. Metagenomic analysis revealed a significant reduction in microbial diversity (Chao index) in acne-affected skin compared to healthy controls (p < 0.001). The relative abundance of Staphylococcus, particularly Staphylococcus epidermidis, was significantly elevated in acne group (p < 0.05), while Cutibacterium acnes levels remained unchanged. Carbon metabolism pathways were enriched in the acne group (p < 0.05), predominantly driven by Cutibacterium, whereas other enriched metabolic pathways, such as ABC transporters and glycine, serine, and threonine metabolism (p < 0.05), showed a greater contribution from Staphylococcus. Virulence factors enriched in acne samples were primarily offensive in nature and largely attributed to Staphylococcus. Moreover, acne-associated microbiome exhibited a significantly higher prevalence of resistance genes against fluoroquinolones, fosfomycin, and triclosan (p < 0.05). Untargeted lipidomic analysis demonstrated significantly elevated total serum and triglyceride levels, along with a reduction in fatty acid chain length and a higher degree of saturation compared to the healthy group (p < 0.01). Specific triglycerides significantly enriched in the acne group, such as TG (15:0_14:0_16:0) + NH4, exhibited a significant positive correlation with Staphylococcus. This correlation is associated with elevated clinical erythema and melanin indices, suggesting that Staphylococcus is implicated in the development of acne-related inflammation. Additionally, Thermus exhibits negative correlations with acne-associated lipids and inflammatory parameters, potentially exerting a protective role. These findings suggest that Cutibacterium and Staphylococcus play differential yet synergistic roles in acne pathogenesis. The observed skin microbiome dysbiosis and lipid metabolic alterations provide novel insights into the pathophysiology of acne vulgaris, which may inform the development of targeted therapeutic strategies.},
}
@article {pmid41471876,
year = {2025},
author = {Wang, Y and Gong, L and Gao, Z and Dong, D and Li, X},
title = {Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471876},
issn = {2076-2607},
support = {42176114//National Natural Science Foundation of China/ ; ZR2023MD100//the Shandong Provincial Natural Science Foundation/ ; CAS-TAX-24-30//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.},
}
@article {pmid41471869,
year = {2025},
author = {Brouwir, L and KleinJan, H and Balent, C and Quabron, G and Salmerón, I and Venditti, S and Gritten, F},
title = {Fate and Removal of Antibiotics and Antibiotic Resistance Genes in a Rural Wastewater Treatment Plant: A Microbial Perspective of Nature-Based Versus Advanced Technologies.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471869},
issn = {2076-2607},
abstract = {Antibiotics (ATBs), antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) present an increasing threat/challenge to our environment and human health, resulting in increasingly strict wastewater management regulations through the revised Urban Wastewater Treatment Directive (UWWTD, 2024/3019/EU). This study evaluates a vertical-flow constructed wetland (CW) as a nature-based solution for removing ATBs, ARB, and ARGs from urban wastewater. The CW operated alongside two conventional quaternary treatments: granular activated carbon (GAC) and ozonation combined with GAC (O3 + GAC). Hydraulic conditions were kept stable across seasonal variations. Three antibiotics were quantified (through LC-MS/MS) in parallel to ARGs (through qPCR and metagenomics) and bacterial profiling (metabarcoding and plate counts). Results indicate that under the conditions tested (rural environment; UWWTP 13.000 p.e.), the CW achieves effective and stable removal of ATBs and ARGs. This study highlights the potential of nature-based solutions to match advanced quaternary treatments in removal performance and operational reliability, offering a sustainable and cost-effective means to reduce the spread of ATBs and ARGs via wastewater.},
}
@article {pmid41471853,
year = {2025},
author = {Tkaczyk, M},
title = {Biofilm as a Key Element in the Bacterial Pathogenesis of Forest Trees: A Review of Mechanisms and Ecological Implications.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471853},
issn = {2076-2607},
abstract = {Bacterial diseases of forest trees represent an increasing threat to ecosystem health and the sustainability and resilience of forest management, particularly under changing climate conditions. One of the key yet still insufficiently understood adaptive mechanisms of pathogens is biofilm formation-a structured community of bacterial cells embedded in a matrix of extracellular polymeric substances (EPS), which provides protection against stress factors, biocides, and the host's defensive responses such as antimicrobial compounds or immune reactions. This paper presents a comprehensive review of current knowledge on the role of biofilms in the bacterial pathogenesis of forest trees, covering their formation mechanisms, molecular regulation, and ecological significance. Four key stages of biofilm development are discussed-adhesion, microcolony formation, EPS production, and dispersion-along with the roles of quorum sensing systems and c-di-GMP-based signaling in regulating these processes. Examples of major tree pathogens are presented, including Pseudomonas syringae, Erwinia amylovora, Xylella fastidiosa, the Brenneria-Gibbsiella complex associated with Acute Oak Decline (AOD) and Lonsdalea populi. Biofilm formation is shown to play a crucial role in the colonization of xylem, leaf surfaces, and tissues undergoing necrosis, where biofilms may stabilize decomposition zones and support saprophytic-pathogenic transitions. In the applied section, the concept of "biofilm-targeted control" is discussed, encompassing both chemical and biological strategies for disrupting biofilm structure-from quorum-sensing inhibitors and EPS-degrading enzymes to the use of biosurfactants and antagonistic microorganisms. The need for in situ research in forest environments and the adaptation of advanced imaging (CLSM, micro-CT) and metagenomic analyses to tree systems is also emphasized. This review concludes that biofilms are not merely a physiological form of bacterial organization but a complex adaptive system essential for the survival and virulence of pathogens in forest ecosystems. Understanding their functions is fundamental for developing sustainable and ecologically safe phytosanitary strategies for forest protection.},
}
@article {pmid41471192,
year = {2025},
author = {Liu, P and Wang, D and Zhang, F and Wang, T and Han, J and Zou, Q},
title = {Seasonal Metagenomic Survey of Pathogenic Microorganisms in Non-Human Primates in Mayanghe National Nature Reserve, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121237},
pmid = {41471192},
issn = {2076-0817},
mesh = {Animals ; Seasons ; China ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Understanding the diversity of pathogenic microorganisms in wild primates is essential for assessing their health and zoonotic risks. In this study, metagenomic sequencing was applied to investigate the composition and seasonal dynamics of potential pathogenic microorganisms in the feces of François' langurs. A total of 77 potential pathogenic taxa were identified, mainly belonging to Bacillota and Pseudomonadota. The most abundant genera were Streptococcus, Staphylococcus, Salmonella, Listeria, and Pseudomonas, while dominant species included Staphylococcus aureus, Streptococcus pneumoniae, Salmonella enterica, Listeria monocytogenes, and Escherichia coli. Significant seasonal differences were detected in both α- and β-diversity indices, with higher microbial diversity in spring and distinct community structures across seasons. Several genera and species, including Vibrio, Chlamydia, Mycobacteroides, Vibrio cholerae, Yersinia enterocolitica, Chlamydia trachomatis, and Mycobacteroides abscessus, showed marked seasonal fluctuations. The findings reveal that the pathogenic microbial community of François' langurs is strongly shaped by seasonal environmental factors. The detection of multiple zoonotic pathogens suggests a potential risk of cross-species transmission, providing valuable baseline data for primate disease ecology and conservation health management.},
}
@article {pmid41471117,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Yoon, Y and Tajdozian, H and Ahmed, I and Atashi, A and Jeong, G and Suh, HS and You, J and Sung, C and Kim, M and Seo, H and Song, HY},
title = {Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121603},
pmid = {41471117},
issn = {1999-4923},
support = {No. RS-2023-00219563//Ministry of Science and ICT/ ; Bio Workforce Training Program//Ministry of Trade, Industry, and Energy/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
abstract = {Background/Objectives: Traditionally consumed fermented foods and lactic acid bacteria (LAB)-based products have primarily been investigated for their nutritional and health-promoting benefits as dietary supplements. More recently, research has advanced toward exploring their therapeutic potential in pharmaceutical development. However, reliance on conventional LAB strains despite their established safety and efficacy has led to saturation at the strain level, underscoring the need for next-generation probiotics (NGPs) with novel therapeutic potential. In this context, we identified Flavonifractor plautii from human feces as a candidate NGP and investigated its effects on the human gut microbiota. Methods: Whole-genome sequencing revealed distinct genetic features that supported its uniqueness, and the strain was designated PMC93. A human gut microbial ecosystem simulator was used to administer F. plautii daily for one week, after which microbial community changes were evaluated using 16S rRNA gene-based metagenomic sequencing. Results: The administration did not induce significant changes in alpha or beta diversity, suggesting that F. plautii does not disrupt overall bacterial community structure, thereby supporting its microbial community safety. Taxonomic analysis demonstrated a significant increase in the Firmicutes-to-Proteobacteria ratio (NGP F/P index). The improvement surpassed that of conventional LAB treatments and was consistently maintained under supplementation with commonly encountered pharmaceutical compounds and nutrients. The shift was associated with an increase in short-chain fatty acid (SCFA)-producing beneficial taxa and a decrease in pro-inflammatory and potentially pathogenic groups. Functional outcomes, including elevated SCFA levels and downregulation of inflammation-related gene expression, further corroborated these compositional changes. The strain also demonstrated safety in in vivo models. Conclusions: Collectively, these findings suggest that strain PMC93 is a promising NGP candidate with substantial therapeutic potential for microbiota-associated health and disease modulation, particularly due to its ability to enhance the NGP F/P index.},
}
@article {pmid41470606,
year = {2025},
author = {Karpova, D and Belkina, D and Porotikova, E and Yurchenko, E and Vinogradova, S},
title = {Metagenomic Study of the Grapevine Decline Detected a Cocktail of Fungi Associated with Grapevine Trunk Diseases.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41470606},
issn = {2223-7747},
support = {23-16-00232//Russian Science Foundation/ ; 00000//Ministry of Education and Science of Russian Federation/ ; },
abstract = {This study analyzed the microbiome of three varieties differing in genotype and technical purpose: Cristal, Riesling, and Avgustin, all exhibiting decline symptoms of unknown etiology. A total of 92 symptomatic and asymptomatic grapevines were analyzed using ITS and 16S rRNA amplicon sequencing and molecular genetic methods. Phytoplasmas and the pathogenic bacteria Xylella fastidiosa and Xylophilus ampelinus were not present in the samples. The decline symptoms were associated with a cocktail of fungal pathogens that cause grapevine trunk diseases. In particular, the analysis revealed the causative agents of Botryosphaeria dieback (Sphaeropsis spp. and Botryosphaeria spp.), fungi associated with the Esca complex (Phaeomoniella spp., Phaeoacremonium spp., Inonotus spp., Seimatosporium spp., Stereum spp., and Cadophora spp.), and the causative agents of Phomopsis dieback (Diaporthe spp.). The symptoms of decline may be increased by several facultative grapevine pathogens that have been identified in microbiome (genera Stemphylium, Alternaria, Aspergillus, Penicillium, Talaromyces, and Fusarium). The metagenomic data of the grapevine microbiome provides opportunities for developing disease control strategies, which is important for the sustainable management of vineyards.},
}
@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12369-1},
pmid = {41469598},
issn = {1471-2334},
}
@article {pmid41469026,
year = {2025},
author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW},
title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00771},
pmid = {41469026},
issn = {2373-8227},
abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.},
}
@article {pmid41468749,
year = {2025},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
doi = {10.1016/j.psj.2025.106308},
pmid = {41468749},
issn = {1525-3171},
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}
@article {pmid41468674,
year = {2025},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}
@article {pmid41468660,
year = {2025},
author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111600},
doi = {10.1016/j.ijfoodmicro.2025.111600},
pmid = {41468660},
issn = {1879-3460},
abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.},
}
@article {pmid41467811,
year = {2025},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303325},
doi = {10.1128/spectrum.03033-25},
pmid = {41467811},
issn = {2165-0497},
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.<br><br>IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}
@article {pmid41467786,
year = {2025},
author = {McParland, EL and Wittmers, F and Bolaños, LM and Carlson, CA and Curry, R and Giovannoni, SJ and Michelsen, M and Parsons, RJ and Kido Soule, MC and Swarr, GJ and Temperton, B and Vergin, K and Worden, AZ and Longnecker, K and Kujawinski, EB},
title = {Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0154025},
doi = {10.1128/msystems.01540-25},
pmid = {41467786},
issn = {2379-5077},
abstract = {Hundreds of thousands of individual microbe-molecule interactions regulate the flux, transformation, and fate of carbon stored in the climatically important reservoir of marine dissolved organic matter (DOM). While marine microbial communities have been characterized at high resolution for over a decade, observations of the molecules cycled by the microbial-chemical network at similar resolution are limited. In addition, bulk characterizations of DOM can mask the complex network of interactions comprised of rich chemical diversities. Here, we present a three-year, depth-resolved, molecular time-series of DOM and prokaryoplankton at the Bermuda Atlantic Time-series Study (BATS) site. Both time-series exhibited seasonality that was compositionally distinct and primarily endemic to one sampling depth. We also putatively identified four exometabolites (gonyol, glucose-6-sulfate, succinate, and trehalose) that exhibit seasonal accumulation. We hypothesize these patterns result from environmental conditions that alter community composition on a seasonal timescale and thus shift the relative proportions of microbial functions that produce and consume the substrates. Critically, we observed the interannual composition of seasonal DOM molecules to be more stable than the taxonomy of the microbial community. This points to an important role of functional redundancy in regulating DOM composition. We tested this observation by querying metagenomes for pathways that utilize metabolic by-products putatively identified in the DOM time-series. We find that core microbial metabolisms, either those required by all or by a subset of marine microbes, are important predictors of DOM composition. The molecular-level characterization of DOM herein highlights the potential imprint of microbial activity on seasonal DOM composition.IMPORTANCEMarine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth's climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.},
}
@article {pmid41467315,
year = {2025},
author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y},
title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {1},
pages = {},
doi = {10.1093/jleuko/qiaf169},
pmid = {41467315},
issn = {1938-3673},
support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; },
mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; },
abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.},
}
@article {pmid41467083,
year = {2022},
author = {Kulohoma, BW and Ng'eno, I},
title = {NOMAD: metagenomic characterisation of the viral pathogen composition in outbreaks of non-malaria acute febrile illness cases.},
journal = {Open research Africa},
volume = {5},
number = {},
pages = {24},
doi = {10.12688/openresafrica.13406.2},
pmid = {41467083},
issn = {2752-6925},
abstract = {The clinical importance of non-malaria febrile acute illness (NM-AFI) in patients with a negative parasitological test has become apparent, with the progressive reduction in malaria transmission in endemic regions. Bacterial pathogens, for example Streptococcus pneumoniae and Haemophilus influenzae, which contribute disproportionally to febrile illness, are now preventable by vaccines. However, there are no vaccines, and little is known about viral NM-AFI prevalence, proliferation, virulence, and transmission chains between hosts. Although the predominant viral causes of NM-AFI are established, it is unclear if there are other NM-AFI associated emerging infectious viral pathogens that previously remained undetectable by conventional diagnostic strategies, for example severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Presumptive broad-spectrum antibiotic prescriptions to aparasitaemic patients not only drive drug resistance, but also lead to poor treatment outcomes. We hypothesized that insights on NM-AFI etiology, and consequently case management, could be improved by exploiting viral sequence diversity to identify viral pathogens present within metagenomics samples. We exploited simulated and existing infectious disease (Ebola, hepatitis C, chikungunya, and mosquito-borne arboviruses) metagenomic datasets to determine the composition of viral pathogens present, by implementing profile Hidden Markov Models derived from Swiss-Prot viral reference sequences for accurate pathogen detection and classification. Our analysis identified a combination of sequences from multiple viral etiological agents within the same disease sample. This approach provides a granular perspective of multiple viral etiological agents present within a single intra-host disease episode. It highlights prevalent viral strains that can subsequently be routinely detected using directed diagnostic tests to improve disease surveillance in endemic regions.},
}
@article {pmid41467046,
year = {2025},
author = {Sharma, S and Gupta, N and Kaur, S and Kumawat, KC and Chakkal, AS},
title = {Soil microbial resources: Unlocking sustainable strategies for crop productivity and soil health.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100468},
pmid = {41467046},
issn = {2666-5174},
abstract = {Using efficient rhizospheric microbes as bio-inoculants is a key factor in promoting agricultural sustainability, as these microbes have been shown to enhance plant growth promotion and crop productivity. Soil microbial communities offer numerous benefits to crops, including improved nutrient uptake efficiency, phytohormone production, improved soil structure, nutrient balance, enhanced plant and soil health, protection against soil borne phyto-pathogens and increased plant resilience to abiotic and biotic stresses. These characteristics of rhizospheric microbes have attracted researcher's attention, as using these microbes individually or in consortia has enhanced soil fertility as well as soil heatlh in a eco-friendly manner. Further, the utilization of multi-omics techniques for exploring the hidden potential of beneficial plant growth promoting microbes is one of the novel approaches that can result in the generation of new biological formulations under changing climatic conditions. This review is therefore focused on the diversity of microbes, their contributions for plant growth promotion and yield with advances in techniques for screening and development of efficient bio-inoculant with a special emphasis on promoting sustainable agriculture practices.},
}
@article {pmid41467044,
year = {2025},
author = {Fernandes, P and Cano-Díaz, C and Pinto, R and Mourão, I and Brito, LM and Moura, L},
title = {The composition and structure of bacterial and fungal communities in kiwifruit are influenced by photoselective nets.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100424},
pmid = {41467044},
issn = {2666-5174},
abstract = {Photoselective nets in agriculture are typically designed to modify the light spectrum, intensity, and microclimate around crops, influencing plant growth, productivity, and quality. However, knowledge regarding their impact on the microbiota of plants and fruits remains limited. This study assessed the impact of pearl, grey, and yellow photoselective nets on the microbial communities present on kiwifruit surfaces using amplicon high-throughput sequencing of ITS and 16S metagenomic DNA. Kiwifruit pathogens associated with postharvest rot, such as Alternaria, Didymella, and Cladosporium, were significantly more prevalent on kiwis grown without nets. Additionally, different net types influenced microbial diversity, richness, and network structure. Pearl nets promoted bacterial richness and fungal diversity, while yellow nets enhanced overall diversity and resilience in both microbial communities. Grey nets resulted in evenness in fungal communities but led to less robust bacterial networks. Kiwifruit yield increased under photoselective nets compared to outside. At harvest, fruit dry matter, firmness, pH, total soluble solids, and titratable acidity were similar across treatments. However, fruits under yellow and grey nets showed significantly lower firmness compared to other treatments. Understanding these effects may contribute to optimizing fruit production and shelf-life management.},
}
@article {pmid41466423,
year = {2025},
author = {Chen, L and Tang, C and Hu, D and Yu, S and Liao, P},
title = {Brevilin a reverses colitis of inflammatory bowel disease via modulation of TNF-α signaling and microbiome dysregulation.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00792-3},
pmid = {41466423},
issn = {1757-4749},
support = {2024000003-09//Middle-aged Backbone Talents in the Province/ ; },
abstract = {BACKGROUND: Brevilin A (Br) has shown potential in modulating inflammatory bowel disease (IBD). Our study aims to explore its mechanism of anti-inflammatory action.<br><br>METHODS: Colitis was induced in C57BL/6 mice with dextran sulfate sodium (DSS), followed by treatment with or without Br(20&#xa0;mg/kg). Fecal microbiota and metabolites were profiled by metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Furthermore, to delineate the essential role of the gut microbiota, we employed antibiotic-treated (microbiota-depleted) mice in our investigation of Br's mechanism of action.<br><br>RESULTS: Br significantly alleviated DSS-induced colitis and modulated the gut microbiota profile. Specifically, Br enriched beneficial bacteria such as Lactobacillus, while suppressing pathogenic bacteria including Escherichia coli and Clostridium perfringens. Metabolomic analysis revealed that Br significantly altered bacterial metabolites, including 7-Oxolithocholic Acid, Kudinoside A, Veratrine, and Soyasaponin. These metabolites were linked to key pathways such as GPCR signaling, DNA damage response, aminoacyl-tRNA biosynthesis, riboflavin metabolism, and central carbon metabolism in cancer. Transcriptomic profiling indicated that Br inhibited the TNF-&#x3b1; signaling pathway, and this inhibition was confirmed as TNF-&#x3b1; overexpression reversed its anti-inflammatory effects. Furthermore, the therapeutic effects of Br were partially recapitulated in microbiota-depleted mice through fecal microbiota transplantation from Br-treated donors.<br><br>CONCLUSION: Br's ability to regulate gut microbiota and metabolites, improve gut barrier function, and eliminate inflammation by inhibiting TNF-&#x3b1; highlights its potential as a novel therapeutic medicine for IBD. Future research should focus on further exploring its mechanisms and clinical applications.},
}
@article {pmid41466385,
year = {2025},
author = {Zhao, L and Li, M and Wang, Y and Chen, L},
title = {Combined effects of sound and temperature on the composition and function of bacterial and fungal communities in loess.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {803},
pmid = {41466385},
issn = {1471-2180},
support = {31920250052; 22YF7FA172; Z2101707; 31560120//the Fundamental Research Funds for the Central Universities; the Key Research and Development Program of Gansu Province; Talent Introduction Program of Northwest Minzu University; National Natural Science Foundation of China/ ; },
mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Temperature ; *Soil Microbiology ; China ; *Sound ; Biodiversity ; *Mycobiome ; Metagenomics ; Phylogeny ; Soil/chemistry ; *Microbiota ; },
abstract = {In Northwest China, the dominant soil type is loess, which is highly susceptible to various environmental factors. Of these, limited research has focused on the impacts of sound disturbance and temperature fluctuations on the microbial communities in loess. An orthogonal experiment was conducted by varying sound intensity (70 dB, 90 dB, 110 dB), sound duration (2 h, 4 h, 6 h), and temperature (- 5 °C, 15 °C, 35 °C). Metagenomic sequencing was then applied to investigate the effects of sound and temperature on the composition and function of bacterial and fungal communities in loess. Our results show that under the combined effects of sound and temperature, the dominant phyla and genera of bacteria and fungi have different responses and preferences to temperature and sound decibels. Alpha diversity analysis revealed that the Shannon index of the bacterial community differed significantly under the 90 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). For the fungal community, both the Simpson and Shannon indices showed significant differences under the 70 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). Notably, the richness of rare fungal taxa and overall species richness in the loess fungal community were significantly enhanced at 90 dB compared with the control and other treatment groups, while these indices were significantly reduced at 110 dB. In the loess microbial treatment groups subjected to the combined effects of sound and temperature, the gene abundance of CAZy family genes was lowest under high decibel (110 dB) sound stimulation. Among the six enzyme-encoding gene categories within the CAZy family, the highest number of annotated species was observed in Group A (2 h, 70 dB, - 5 °C), whereas the lowest was recorded in Group C (6 h, 110 dB, - 5 °C). Among the metabolic pathway functional genes annotated in the KEGG database, the abundance of metabolic genes in Group C (6 h, 110 dB, - 5 °C) was significantly lower than that in other treatment groups.},
}
@article {pmid41466331,
year = {2025},
author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X},
title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {259},
pmid = {41466331},
issn = {2049-2618},
support = {2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; *Bacteria/classification/genetics/isolation &amp; purification ; Farms ; },
abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.<br><br>RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.<br><br>CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.},
}
@article {pmid41466328,
year = {2025},
author = {Thirumaran, S and George, C and Kortheerakul, C and Khunthong, N and Bhunjun, CS and Phukhamsakda, C and Chan, KG and Chang, Y and Tan, EJ and Daroch, M and Hyde, KD and Goh, KM and Waditee-Sirisattha, R and Pointing, SB},
title = {Fungi dominate eukaryotic microbial assemblages in hot spring biofilms of East and Southeast Asia.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {156},
pmid = {41466328},
issn = {2524-6372},
support = {MOE-T2EP30123-0007//Ministry of Education - Singapore/ ; },
abstract = {Terrestrial hot springs are globally distributed extreme environments, and these systems have long served as natural laboratories for studying microbial life under thermal stress. While much of the research to date has focused on thermophilic bacteria and archaea, there is a growing appreciation for the diversity and ecological significance of eukaryotic microorganisms in these habitats. In this study, we used metagenomic sequencing to assess inter-domain microbial diversity in biofilms from 47 circumneutral hot springs across East and Southeast Asia, with a specific focus on resolving eukaryotic taxa and their ecology. Whilst all biofilm communities were dominated by bacteria, the microbial eukaryotes represented approximately 10% of the taxonomic diversity and accounted for 1.3% of overall taxa abundance, indicating a small but significant presence. We provide the first comprehensive inter-domain checklist of over 14,500 microbial taxa in hot springs. Patterns in diversity were significantly correlated with temperature, hydrogen sulfide, and pH in hot springs. Fungi emerged as the most abundant and prevalent eukaryotic group, indicating an important role as eukaryotic saprotrophs, with Ascomycota yeasts comprising the most individually abundant taxa. Among other microbial eukaryotic phyla, the photosynthetic Chlorophyta and Bacillariophyta were most abundant. Predatory/grazing microbial eukaryotes were relatively less diverse and abundant. Network co-occurrence analysis was used to indicate extensive and specific biotic interactions between eukaryotes and bacteria in biofilms. We further employed metatranscriptomics to identify putatively active taxa, revealing that most detected eukaryotes were transcriptionally active. While fungi accounted for most transcripts, the highest RNA:DNA ratios were observed among predatory and photosynthetic taxa, suggesting elevated activity in these functional groups. Overall, our findings highlight the diversity, interactions, and activity of eukaryotes in Southeast Asian hot spring biofilms, underscoring their potential importance in shaping microbial community structure and function in extreme environments.},
}
@article {pmid41466105,
year = {2025},
author = {Zhang, H and Shen, C and Lei, W and Wang, J and Liu, J and Qiu, Z},
title = {Pilot Clinical Trial of Fecal Microbiota Transplantation for Constipation in Parkinson's Disease.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2509029},
doi = {10.4014/jmb.2509.09029},
pmid = {41466105},
issn = {1738-8872},
mesh = {Humans ; *Constipation/therapy/etiology/microbiology ; *Fecal Microbiota Transplantation/methods ; *Parkinson Disease/complications/therapy/microbiology ; Aged ; Pilot Projects ; Middle Aged ; Male ; Gastrointestinal Microbiome ; Female ; Prospective Studies ; Feces/microbiology ; Treatment Outcome ; Dysbiosis/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {The purpose of this study was to evaluate the safety and efficacy of fecal microbiota transplantation in patients with constipation due to parkinson's disease. Gut dysbiosis has long been associated with parkinson's and recent studies have shown that FMT can restore the normal flora of the gut. Therefore, this clinical trial aimed to test the therapeutic efficacy of FMT in 5 patients aged 55 to 71 diagnosed with PD who presented with constipation. The study was conducted as an open label, prospective trial and consisted of FMT performed every 3 days via nasojejunal tube placement followed by 8 weeks of patient follow-up to evaluate response to drug therapy and to assess neurological function using UPDRS-III OFF scores, and improvement in constipation assessed with Wexner scores. Samples taken before and after FMT were collected for shotgun metagenomic sequencing to analyze the composition of the microbial communities present in patients. Untargeted non-targeted metabolomic studies were performed to investigate the impact of FMT on metabolome changes due to FMT. The results indicate an improvement in constipation and neurological functioning following FMT, and significant alteration of the gut microbiota. Significant increases in Bifidobacteria bifidus, Alistipes shahi, Anaerotruncus coli, and uncharacterized Flavonifractor were found post-treatment compared to the baseline. Many of the other strains present prior to treatment, including Acinetobacter sp. and Proteobacteria sp., had significantly decreased after the FMT. The metabolomic studies found shifts in metabolic pathways involved with unsaturated fatty acid synthesis and amino acid metabolism due to FMT. FMT may be an effective treatment option for constipation and neurological symptoms associated with PD.},
}
@article {pmid41466004,
year = {2025},
author = {Li, S and Zhang, M},
title = {Mycobacterium chelonae infection treated with combined medication and surgical therapy: A case report.},
journal = {Medicine},
volume = {104},
number = {52},
pages = {e46692},
pmid = {41466004},
issn = {1536-5964},
mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/therapy/drug therapy/etiology/diagnosis/surgery ; *Mycobacterium chelonae/isolation &amp; purification ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Female ; Levofloxacin/administration &amp; dosage/therapeutic use ; Rifampin/administration &amp; dosage/therapeutic use ; *Skin Diseases, Bacterial/therapy ; Combined Modality Therapy ; Drug Therapy, Combination ; *Cosmetic Techniques/adverse effects ; Adult ; },
abstract = {RATIONALE: The misuse of antibiotics and immunosuppressive agents has led to an increase in the incidence of infections caused by opportunistic pathogens, and even rare microbial infections such as Mycobacterium chelonae (MC) have emerged. Currently, there are very few reported cases of MC infection globally, and clinical experience in treating this disease is limited. This case report focuses on the treatment methods for infections caused by this bacterium, aiming to accumulate experience for clinicians in the diagnosis and treatment of this condition.<br><br>PATIENT CONCERNS: This study reports a case of MC infection that occurred following an invasive cosmetic injection treatment. Due to the progression of the condition, medical intervention was required. The patient underwent combined medication and surgical therapy, and the treatment outcomes were subsequently tracked.<br><br>DIAGNOSES: Histopathological examination of the skin lesion, fungal culture, and metagenomic detection of the infectious pathogen suggested MC infection.<br><br>INTERVENTIONS: The patient underwent excision of the skin lesion, along with intravenous infusion of levofloxacin hydrochloride and sodium chloride injection at a dose of 0.4&#x2009;g once daily and oral administration of rifampicin capsules at a dose of 0.45&#x2009;g once daily. Complete lesion resolution was achieved at 1 month postoperatively.<br><br>OUTCOMES: At the 1-month postoperative follow-up, the patient's rash had healed completely.<br><br>LESSONS: This case fills a gap in domestic and international reports of MC infection following cosmetic filler injections. By employing metagenomic next-generation sequencing, the pathogen was rapidly identified within a short timeframe, significantly reducing the diagnostic delay associated with conventional bacterial culture and identification methods. Early radical lesion excision combined with a dual-antibiotic regimen (levofloxacin-rifampin) achieved complete resolution within 1 month, establishing a replicable treatment paradigm for cutaneous MC infections. Further multicenter prospective studies are warranted to optimize surgical margins and antimicrobial treatment duration.},
}
@article {pmid41465859,
year = {2025},
author = {Angelova, B and Boteva, S and Traykov, I and Tsvetkov, M and Kenarova, A},
title = {Bacterial Community Composition and Structure in the Littoral of Rila Mountains Glacial Lakes.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465859},
issn = {2075-1729},
support = {KP-06-M71/2//The Bulgarian National Science Fund/ ; },
abstract = {High-mountain lakes are biodiversity hotspots sensitive to increasing regional and global climate warming. However, their microbial communities remain insufficiently characterized due to their remoteness and limited accessibility. This study aimed to determine how seasonal environmental parameters shape the composition, structure and diversity of littoral bacterial communities in three glacial lakes in Rila Mountains (Bulgaria). Water samples were collected during ice-free periods in 2023 and 2024, and bacterial taxonomic composition was analysed by Next-generation sequencing. A total of 1158 bacterial OTUs were identified encompassing 18 phyla and 165 families. Actinomycetota, Pseudomonadota, and Bacteroidota were dominant at the phylum level, and Sporichthyaceae, Comamonadaceae, Chitinophagaceae and Mycobacteriaceae were most abundant among the families. Community richness and diversity peaked in June, immediately after ice melting, particularly in the highest-altitude lake (Sulzata Lake), and declined during the warm season (August), when the relative abundances of Sporichthyaceae and Mycobacteriaceae (Actinomycetota) increased. Seasonal restructuring occurred across phyla and families even in a single taxon, with water temperature and organic carbon availability identified as the main environmental drivers. The findings have improved our understanding of temperature-driven bacterial responses. They have also highlighted the vulnerability of cold-adapted taxa to regional climate warming which may contribute to more effective biodiversity conservation strategies for these unique ecosystems.},
}
@article {pmid41465696,
year = {2025},
author = {Jin, JX and Wang, Y and Zhang, GF and Ye, ZC and Liu, B and Yao, DD and Jiang, ZC and He, YF},
title = {Diversity and Functional Analysis of Gut Microbiota in the Adult of Lissorhoptrus oryzophilus (Coleoptera: Curculionidae) by Metagenome Sequencing.},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465696},
issn = {2075-4450},
abstract = {The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus.},
}
@article {pmid41465567,
year = {2025},
author = {Zhao, H and Wang, H and Zhao, X and Song, Y and Liang, D and Ma, Y and Xu, Z},
title = {Bifidobacterium adolescentis Strengthens Gut Barrier in Post-Voyage Functional Constipation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465567},
issn = {1422-0067},
support = {2024QN019//University-level research project of the Naval Medical University/ ; },
mesh = {*Constipation/microbiology/therapy/etiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Bifidobacterium adolescentis/physiology ; *Probiotics ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Humans ; Gastrointestinal Motility ; },
abstract = {Prolonged periods of sailing may contribute to the development of functional constipation, which can significantly impair an individual's work efficiency. Currently, the efficacy of Bifidobacteria in treating functional constipation is gaining recognition. However, since the therapeutic effects of Bifidobacteria are strain-specific, further research is required on strains isolated from pre-voyage fecal samples. This study examines the role of gut microbiota in post-stroke constipation, aiming to identify specific microbial biomarkers for the development of targeted therapeutic strategies. B. adolescentis was identified through metagenomic analysis and subsequently isolated for validation. In the experimental group (EG), C57BL/6J mice received fecal suspension treatment following a 12-day navigation period, which was subsequently followed by a 12-day oral administration of B. adolescentis. After treatment, EG significantly improved fecal volume, intestinal motility, and goblet cells; reversed microbial ecological imbalance; reduced pathogens (E. coli and Klebsiella) by restoring arginine/bile acid metabolism, decreasing Tauro-ursodeoxycholic acid (TUDCA) content, 5-Hydroxytryptamine 4 Receptor (5-HT4R)/Slc8a1 signaling, and Ca[2+] signaling pathway; and restoring beneficial species (B. adolescentis, Pseudomonas aeruginosa). This study provides new insights into probiotics in improving human intestinal health.},
}
@article {pmid41462122,
year = {2025},
author = {Chang, Z and Chen, J and Chen, J and Zhu, Y and Zhang, Y and Liu, J and Deng, J and Wu, H and Bin, L and Lin, H and Liang, Y and Li, Q and Sun, B and Zeng, G},
title = {Precision diagnosis of preoperative infection in urolithiasis: integrating targeted next-generation sequencing for enhanced accuracy-a multicenter cohort study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1767},
pmid = {41462122},
issn = {1471-2334},
abstract = {BACKGROUND: Preoperative infection in urolithiasis patients poses significant risks for surgical complications. Traditional urine culture methods have limitations in detection speed and accuracy, necessitating more precise and rapid diagnostic approaches for preoperative infection assessment.<br><br>METHODS: This multicenter cohort study evaluated urolithiasis patients with suspected preoperative infections (discovery cohort: n&#x2009;=&#x2009;114; validation cohort: n&#x2009;=&#x2009;64), comparing the diagnostic performance of traditional urine culture, metagenomic next-generation sequencing (mNGS), and targeted next-generation sequencing (tNGS).<br><br>RESULTS: In urolithiasis patients with suspected preoperative infections, both NGS methods demonstrated 100% sensitivity and negative predictive values (NPV) for pathogen detection, with tNGS showing superior specificity and positive predictive values (PPV) compared to mNGS. tNGS significantly reduced detection time (13&#xa0;h vs. 48&#x2013;72&#xa0;h for traditional culture). mNGS detected 43 distinct pathogens while tNGS identified 42, both revealing previously undetected microorganisms including viruses and fungi. Among culture-positive cases, Escherichia coli (E. coli) was the predominant pathogen with higher prevalence in female patients. In polymicrobial infection patterns, tNGS identified bacterial-viral combinations as the dominant pattern (50.79%), followed by bacterial-mycoplasma/chlamydia (17.46%), and bacterial-viral-fungal (12.70%) combinations. These findings were validated in the second cohort, where bacterial-viral co-infections remained predominant (73.68%). Both NGS methods maintained 100% concordance with culture-positive results in clear and turbid urine samples, with tNGS demonstrating fewer false positives.<br><br>CONCLUSIONS: For urolithiasis patients with suspected preoperative infections, tNGS emerges as a superior diagnostic tool due to its higher specificity, faster turnaround time, and ability to detect complex pathogen patterns. While mNGS offers advantages in broad-spectrum screening, tNGS provides a more practical approach for precise preoperative infection assessment, potentially improving surgical timing decisions and patient outcomes.<br><br>CLINICAL TRIAL: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12119-3.},
}
@article {pmid41266970,
year = {2025},
author = {Jin, L and Xu, Q and Miao, C and Zhan, J and Zhang, Y and Li, M and Cheng, J and Liu, P and Yang, Y and Zhou, H and Hu, Z and Li, F and Wu, C},
title = {Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1745},
pmid = {41266970},
issn = {1471-2229},
support = {110202102033//the Key Grant of China National Tobacco Corporation, China/ ; },
abstract = {UNLABELLED: Aging in crops like tea and tobacco involves the production of secondary metabolites, with symbiotic microbes playing a key role. However, their dynamic changes and correlation with metabolites during aging remain poorly understood. This study investigates changes in microbial communities, aroma compounds, and protein expression during tobacco leaf aging using artificial accelerated aging techniques, which combine GC-MS, metagenomics, and metaproteomics methods. We identified 62 aroma compounds with distinct change patterns and observed significant changes in the structure of symbiotic bacteria. Type one, represented by Wolbachia_endosymbiont_of_Diaphorina_citri, increased in abundance from the fourth month, correlating with compounds like 2-Furaldehyde. Type two, represented by Sphingomonas_sp_LK11, showed a bimodal abundance pattern, correlating with compounds like Tabanone. Metaproteomics revealed that protein functions were initially limited to cytoskeleton organization but diversified from the fourth month. Fungi also displayed two distinct clustering patterns, Rhizopus and Mortierella elongata were abundant early on, while Colletotrichum asianum and Trichophyton violaceum appeared later. Rhizopus and other fungi exhibited a significant positive correlation with 24 aroma compounds, including 5-Methylfuran-2(5 H)-one. Linderina pennispora and other fungi showed a significant positive correlation with 28 aroma compounds, including 2-Furaldehyde. The dynamic changes in microbial community structure during aging are closely related to the generation of aroma compounds. Overall, temporal shifts in microbial communities were closely linked to aroma formation. One set of microorganisms, such as Wolbachia_endosymbiont_of_Diaphorina_citri and Linderina pennispora, is positively correlated with 2-Furaldehyde, Isophorone, and 2-Methylbenzofuran. Another set, including Sphingomonas_sp_LK11 and Rhizopus, exhibits a positive correlation with 5-Methylfuran-2(5 H)-one and 1,2-Cyclohexanedione. These findings provide new insights into the biological mechanisms of tobacco leaf aging, and offer new research directions for the development and innovation of future tobacco products.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07765-3.},
}
@article {pmid41467004,
year = {2025},
author = {Xu, LX and Wang, F and Yao, Y and Yao, M and Kuzyakov, Y and Yu, GH and Liu, CQ},
title = {Key role of microbial necromass and iron minerals in retaining micronutrients and facilitating biological nitrogen fixation in paddy soils.},
journal = {Fundamental research},
volume = {5},
number = {6},
pages = {2612-2621},
pmid = {41467004},
issn = {2667-3258},
abstract = {Paddy fields, as the largest anthropogenic wetlands on Earth, face a high risk of micronutrient loss through surface runoff and leaching due to their frequent irrigation-drainage cycles, as well as removal with crop harvest. While micronutrient's losses largely impede biological nitrogen fixation (BNF) in soils, agricultural practices and mechanisms that retain micronutrients and thus increase BNF in paddy soils remain underexplored. Here we showed that the long-term (40 years) application of fertilizers increased the contents of microbial necromass in paddy soils by 20%-43% compared to the unfertilized control. In particular, long-term organic fertilizations increased poorly crystalline minerals through intensifying mineral weathering, which further contributed to the increased stable carbon burials in paddy soils. Synchrotron radiation based spectromicroscopy analysis provided direct evidence demonstrating a differential control of hydroxyl functional groups from mineral surfaces on C functional groups at the submicron scale in paddy soils. Notably, microbial necromass and short-range ordered minerals had a strong correlation with the content and bioavailability of micronutrients in paddy soils, indicating their key roles in the retention of micronutrients. Metagenomic sequencing analysis further indicated that the content and bioavailability of micronutrients were strongly correlated with the abundance of the key N-fixing genera (i.e., Azospirillum and Bradyrhizobium). Unexpectedly, structural equation modeling (SEM) identified that microbial necromass exerted the strongest control on N-fixing genera, highlighting an underappreciated role of microbial necromass as a reservoir of micronutrients. Based on micronutrient's bioavailability and metagenomic sequencing, we conclude that micronutrients are the key factor for BNF in paddy soils, offering significant implications for managing BNF in paddy soils.},
}
@article {pmid41465246,
year = {2025},
author = {Sokolova, EA and Smirnova, NV and Fedorets, VA and Khlistun, IV and Mishukova, OV and Tromenschleger, IN and Savenkov, OA and Saprikin, OI and Rogaev, EI and Buyanova, MD and Filippova, IM and Mayorova, TM and Glukhova, MA and Ivanovna, MM and Manakhov, AD and Voronina, EN},
title = {Microbial Consortium Application Under Temperature Stress: Effects on the Rhizosphere Microbiome and Plant Growth.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262411814},
pmid = {41465246},
issn = {1422-0067},
support = {075-15-2025-473//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019-2030)/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Microbiota ; *Microbial Consortia ; *Stress, Physiological ; *Plant Development ; Crops, Agricultural/growth &amp; development/microbiology ; Temperature ; Bacteria/genetics ; Triticum/growth &amp; development/microbiology ; Fagopyrum/growth &amp; development/microbiology ; },
abstract = {The aim of the present study was to investigate the effect of a synthetic microbial consortium (SMC) containing five functionally different bacterial strains (Rahnella aquatilis, Rothia endophytica, Stenotrophomonas indicatrix, Burkholderia contaminans, Lelliotia amnigena) on the growth and development of three agricultural crops (wheat, buckwheat, and rapeseed) on two soil types (chernozem and gray forest soil) under field conditions. The experiment was conducted from June to September 2024 under extreme field conditions, with temperatures reaching 43.8 °C. This study evaluates SMC efficacy under severe abiotic stress, reflecting increasingly common climate extremes. Metagenomic data analysis showed that the introduced strains did not establish stable populations in the soil, possibly due to heat-induced bacterial mortality, though other factors including competition with indigenous microflora and lack of protective formulations may have also contributed. No statistically significant effects on plant morphometric parameters were observed. The extreme temperature and water stress conditions appear to have been the dominant limiting factors, overriding any potential benefits from microbial inoculation, as evidenced by the lack of response to mineral fertilizer application as well. Crop-specific effects were revealed: when cultivating rapeseed on chernozem, a significant increase in available phosphorus content was noted (from 278 ± 45 to 638 ± 92 mg/kg with SMC application, p < 0.001).},
}
@article {pmid41465102,
year = {2025},
author = {Neumann, GB and Korkuć, P and Rahmatalla, SA and Reißmann, M and Omer, EAM and Elzaki, S and Brockmann, GA},
title = {Surviving the Heat: Genetic Diversity and Adaptation in Sudanese Butana Cattle.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/genes16121429},
pmid = {41465102},
issn = {2073-4425},
mesh = {Animals ; Cattle/genetics ; *Genetic Variation ; *Adaptation, Physiological/genetics ; Sudan ; Selection, Genetic ; Breeding ; Hot Temperature ; *Heat-Shock Response/genetics ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Butana are native Sudanese Bos indicus cattle that are well adapted to arid environments and valued for their relatively high milk performance and resilience under harsh conditions. Despite their adaptive advantages, Butana cattle face the risk of genetic erosion due to low production performance and the absence of structured breeding programs underscoring the urgent need to conserve their unique genetic potential for climate-resilient livestock development.<br><br>METHODS: In this study, we analyzed whole-genome sequencing data from 40 Butana cattle to assess their genetic diversity, population structure, signatures of selection, and potential pathogen load.<br><br>RESULTS: Butana cattle exhibited high nucleotide diversity and low levels of inbreeding, indicating a stable gene pool shaped by natural selection rather than by intensive breeding. Signatures of selection and functional variant analysis revealed candidate genes involved in heat stress adaptation (COL6A5, HSPA1L, TUBA8, XPOT), metabolic processes (G6PD, FAM3A, SLC10A3), and immune regulation (IKBKG, IRAK3, IL18RAP). Enrichment analyses and RoH island mapping consistently highlighted immune and thermoregulatory pathways as key selection targets, distinguishing Butana from both the geographically neighbored Kenana cattle and the specialized dairy cattle breed Holstein. Furthermore, metagenomic screening of unmapped reads detected the tick-borne parasite Theileria annulata and the opportunistic pathogen Burkholderia cenocepacia in all animals, underscoring the importance of integrating pathogen surveillance into genomic studies.<br><br>CONCLUSIONS: Taken together, our findings highlight the distinct adaptive genomic profile of Butana cattle and reinforce their value in breeding programs aimed at improving climate resilience and disease resistance in livestock through the utilization of local breeds.},
}
@article {pmid41465030,
year = {2025},
author = {Kahraman Ilıkkan, &#xd6; and Bağdat, E&#x15e; and Yılmaz, R and Çetin, B and Çon, AH and Erten, H and Göksungur, MY and Şimşek, &#xd6;},
title = {Bridging Tradition and Innovation: A Systematic Review and Bibliometric Analysis of Turkish Fermented Foods.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/foods14244324},
pmid = {41465030},
issn = {2304-8158},
abstract = {BACKGROUND: Traditional fermented foods from Türkiye are integral components of the nation's culinary heritage, reflecting a remarkable diversity shaped by local practices and ecosystems. These products embody region-specific microbial communities, often conceptualized as a "microbial terroir," which influence their sensory qualities, nutritional value, and health-promoting properties.<br><br>METHODS: This study followed the PRISMA 2020 guidelines and included a systematic review and bibliometric analysis. A structured search was conducted in the Web of Science Core Collection (WoSCC) on 15 January 2025 using predefined keywords related to Turkish fermented foods and fermentation processes. Records were screened based on language (English or Turkish) and document type (articles, reviews, book chapters, and early access). A total of 1464 studies met the eligibility criteria, reflecting a 2.81% annual growth rate and a 12.7% international co-authorship rate. Bibliometric analysis was performed using the bibliometrix R package (RStudio 2024.12.1) and the biblioshiny interface.<br><br>RESULTS: The analysis revealed that the diversity of microbial consortia in Turkish fermented foods contributes to their distinctive characteristics, including enhanced nutritional profiles, probiotic potential, and food safety attributes. Emerging studies employing omics technologies-such as next-generation sequencing, metagenomics, and metabolomics-have expanded our understanding of fermentation ecosystems. Additionally, the growing integration of artificial intelligence supports predictive modeling and process optimization for advanced quality control.<br><br>CONCLUSION: This synthesis highlights the significant technological, nutritional, and cultural value of T&#xfc;rkiye's traditional fermented foods. Future directions should include omics-based translational research, indigenous starter culture development, and strengthened international collaborations to support sustainable and competitive functional food innovation.},
}
@article {pmid41463940,
year = {2025},
author = {Ospałek, W and Wlazło, &#x141; and Tajchman, K and Targońska-Karasek, M and Nowakowicz-Dębek, B},
title = {Cultivated Gut Microbiota of Roe Deer and Red Deer in Central Poland Forest.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243656},
pmid = {41463940},
issn = {2076-2615},
abstract = {The aim of this study was to compare, using culture methods, the microflora of the small and large intestines, distinguishing pathogenic bacteria, in free-living ruminants: roe deer (Capreolus capreolus) and red deer (Cervus elaphus). Intestinal samples from six individuals of each species were collected immediately after hunting under aseptic conditions. Aerobic and facultatively anaerobic bacteria, including Lactobacillus spp., Escherichia coli, Listeria spp., and Clostridium perfringens, were quantified using standard culture methods. Statistical analysis (ANOVA) revealed no significant differences (p > 0.05) between species in any of the microbial groups analyzed, although higher mean abundances were observed in red deer, particularly in the large intestine. The results indicate that interspecific variation in cultured microbiota may reflect individual and environmental factors rather than consistent taxonomic differences. Due to the high inter-individual variability and limited sample size, this study should be considered preliminary. The results demonstrate the predominance of viable aerobic and facultative anaerobic bacterial groups in culture-based analysis and provide reference data for future metagenomic studies. This study fills an important knowledge gap, as culture-dependent studies of the gut microbiota of wild cervids are still rare due to the logistical and ethical constraints associated with sampling wild animals.},
}
@article {pmid41463937,
year = {2025},
author = {Woś, K and Pachciński, K and Wacko, M and Koszła, O and Sołek, P and Czech, A},
title = {The Role of Swine Gut Microbiota and Its Metabolites in Maintaining Intestinal Barrier Integrity and Mitigating Stress via the Gut-Brain Axis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243653},
pmid = {41463937},
issn = {2076-2615},
abstract = {The gut-brain axis is a complex communication network linking the gastrointestinal tract and the central nervous system, in which the gut microbiota plays a pivotal role in regulating intestinal homeostasis, immune responses and neuroendocrine functions. This review summarizes current knowledge on the role of the porcine gut microbiota in the functioning of the gut-brain axis and examines nutritional strategies aimed at its modulation. Key production-related stressors, such as weaning, transport and handling, disrupt microbiota composition, increase intestinal permeability and activate the hypothalamic-pituitary-adrenal (HPA) axis, leading to heightened stress responses, impaired immunity and behavioral disturbances. Evidence indicates that supplementation with probiotics, prebiotics, or postbiotics stabilizes the gut microbiota, enhances the production of bioactive metabolites, supports intestinal barrier integrity and alleviates oxidative stress. Such interventions improve adaptation to environmental stress, animal welfare and performance, while potentially reducing the need for antibiotics. Maintaining a balanced gut microbiota is therefore essential for the proper functioning of the neuroendocrine and immune systems in pigs. An integrated approach utilizing omics technologies (metagenomics, metabolomics, proteomics) may further elucidate microbiota-brain interactions and support the development of sustainable and ethical swine production strategies.},
}
@article {pmid41463923,
year = {2025},
author = {Sakarnyte, L and Spinkyte, R and Merkeviciene, L and Siugzdiniene, R and Ruzauskas, M},
title = {Next-Generation Sequencing Insights into the Oral Microbiome and Antibiotic Resistance Genes in Grey Wolves (Canis lupus).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243639},
pmid = {41463923},
issn = {2076-2615},
abstract = {The oral microbiome of apex predators such as grey wolves (Canis lupus) is colonised by complex microbial communities and plays a crucial role in the health of wild mammals, but remains poorly understood. In this study, a single pooled sample mixed from oral samples of 17 wolves (Canis lupus) hunted in Lithuania was investigated for the determination of a variety of oral microbiota, providing the first metagenomic insight into wolf oral microbiomes in Baltic countries. The aim of this study was to identify the zoonotic and antimicrobial resistance potential of the oral microbiota. The results revealed diverse microbiomes associated with periodontal health as well as microbiomes related to the environment. Unique microbial taxa potentially reflect the nutritional and ecological interactions of carnivores. Shotgun metagenomic sequencing yielded a total of 18,726,406 raw reads, and following quality trimming and filtering, 86.01% of these (16,106,613) were retained. Among the total reads, 45.15% (8,455,255) were identified as host-derived and were removed. The most common oral bacterial genera were Pseudomonas (50%) and Psychrobacter (22.6%). Metagenomic reads for zoonotic pathogens, including Salmonella, Mycobacterium spp., Yersinia, Coxiella burnetii, Corynebacterium pseudotuberculosis, and others, were also detected, suggesting that grey wolves are potential natural reservoirs of zoonotic infections. Genes encoding antimicrobial resistance to many classes of antibiotics were also detected. This research contributes to understanding wolf dietary habits, oral health, the carriage and possible risk of transmitting AMR, and social interactions.},
}
@article {pmid41463847,
year = {2025},
author = {Moreira, G and Rodrigues, S and Gomes-Gonçalves, S and Silva, G and Amorim, I and Silva, E and Carmezim, S and Soeiro, V and Mesquita, JR},
title = {Highly Virulent Newcastle Disease Virus in Eurasian Collared Doves in the North of Portugal.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243563},
pmid = {41463847},
issn = {2076-2615},
abstract = {Newcastle disease (ND), caused by avian orthoavulavirus 1 (AOAV-1), poses a global threat to poultry and wild birds. In early 2025, an outbreak of pigeon paramyxovirus type 1 (PPMV-1, genotype VI AOAV-1) was detected in a wildlife rehabilitation centre in northern Portugal, affecting Streptopelia decaocto, Streptopelia risoria, and Columba livia. Birds showed acute neurological signs and died rapidly. Necropsy revealed brain and pulmonary congestion, splenomegaly, and cloacal lesions, while histopathology demonstrated hepatocellular necrosis, hemorrhage, and eosinophilic intracytoplasmic inclusions in hepatocytes and renal tubular cells. Matrix (M) gene PCR using standard primers was negative, but metagenomic sequencing identified genotype VI as being closely related to strains from Iran and Cyprus. Partial fusion (F) gene analysis revealed the velogenic RRQKRF motif. These findings confirm the circulation of highly virulent PPMV-1 in Portugal, highlight that standard, recommended primers may fail to detect some genetically diverse strains, and emphasize the role of Columbidae as reservoirs with potential transmission to domestic poultry.},
}
@article {pmid41463766,
year = {2025},
author = {Novakovic, J and Milosavljevic, I and Stepanova, M and Ramenskaya, G and Jeremic, N},
title = {Safe Meat, Smart Science: Biotechnology's Role in Antibiotic Residue Removal.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121264},
pmid = {41463766},
issn = {2079-6382},
abstract = {The widespread use of antibiotics in livestock farming has led to the persistent issue of antibiotic residues in meat products, raising significant concerns for food safety and public health. These residues can contribute to the emergence and spread of antimicrobial resistance (AMR), a growing global health threat recognized by the World Health Organization. While some regulatory bodies have imposed restrictions on non-therapeutic antibiotic use in animal agriculture, inconsistent global policies continue to hinder unified efforts to reduce AMR risks. This review explores the role of biotechnology in addressing this challenge by offering innovative tools for the detection, degradation, and removal of antibiotic residues from meat. Biotechnological approaches include the use of biosensors, high-throughput screening, enzymatic degradation, microbial bioremediation, genetically engineered bacteria, phage therapy, and phytoremediation. In addition, enabling technologies such as genomics, metagenomics, bioinformatics, and computational modeling support the rational design of targeted interventions. We further examine the integration of these biotechnological strategies within the broader "One Health" framework, which emphasizes the interconnectedness of human, animal, and environmental health. Case studies and recent applications demonstrate the potential of these methods to ensure safer meat production, reduce public health risks, and enhance consumer trust. By focusing on scalable, science-driven solutions, biotechnology offers a promising path toward mitigating antibiotic residues in the food supply and combating the long-term threat of AMR.},
}
@article {pmid41463765,
year = {2025},
author = {Saleem, N and Kumar, N and El-Omar, E and Willcox, M and Jiang, XT},
title = {Harnessing Machine Learning Approaches for the Identification, Characterization, and Optimization of Novel Antimicrobial Peptides.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121263},
pmid = {41463765},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) has become a major health crisis worldwide, and it is expected to surpass cancer as one of the leading causes of death by 2050. Conventional antibiotics are struggling to keep pace with the rapidly evolving resistance trends, underscoring the urgent need for novel antimicrobial therapeutic strategies. Antimicrobial peptides (AMPs) function through diverse, often membrane-disrupting mechanisms that can address the latest challenges to resistance. However, the identification, prediction, and optimization of novel AMPs can be impeded by several issues, including extensive sequence spaces, context-dependent activity, and the higher costs associated with wet laboratory screenings. Recent developments in artificial intelligence (AI) have enabled large-scale mining of genomes, metagenomes, and quantitative species-resolved activity prediction, i.e., MIC, and de novo AMPs designed with integrated stability and toxicity filters. The current review has synthesized and highlighted progress across different discriminative models, such as classical machine learning and deep learning models and transformer embeddings, alongside graphs and geometric encoders, structure-guided and multi-modal hybrid learning approaches, closed-loop generative methods, and large language models (LLMs) predicted frameworks. This review compares models' benchmark performances, highlighting AI-predicted novel hybrid approaches for designing AMPs, validated by in vitro and in vivo methods against clinical and resistant pathogens to increase overall experimental hit rates. Based on observations, multimodal paradigm strategies are proposed, focusing on identification, prediction, and characterization, followed by design frameworks, linking active-learning lab cycles, mechanistic interpretability, curated data resources, and uncertainty estimation. Therefore, for reproducible benchmarks and interoperable data, collaborative computational and wet lab experimental validations must be required to accelerate AI-driven novel AMP discovery to combat multidrug-resistant Gram-negative pathogens.},
}
@article {pmid41463758,
year = {2025},
author = {Papamentzelopoulou, M and Vrioni, G and Pitiriga, V},
title = {Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121257},
pmid = {41463758},
issn = {2079-6382},
abstract = {Bloodstream infections (BSIs) pose a significant global health challenge, particularly due to the increasing prevalence of antimicrobial resistance (AMR). Timely and accurate identification of pathogens and resistance determinants is critical for guiding appropriate therapy and improving patient outcomes. Traditional culture-based diagnostics are limited by prolonged turnaround times and reduced sensitivity, especially in culture-negative or polymicrobial infections. This review systematically examined current and emerging sequencing technologies for AMR detection in BSIs, including whole-genome sequencing (WGS), targeted next-generation sequencing (tNGS), metagenomic next-generation sequencing (mNGS), and long-read sequencing platforms (Oxford Nanopore, PacBio). We compared their clinical performance using key metrics such as diagnostic sensitivity, turnaround time, and cost, highlighting contexts in which each technology is most effective. For example, tNGS can achieve the rapid detection of known resistance genes within 8-24 h, while WGS provides comprehensive genome-wide resistance profiling over 24-48 h. mNGS offers broader detection, including rare or unexpected pathogens, although at higher cost and longer processing times. Our analysis identifies specific strengths and limitations of each approach, supporting the use of context-specific strategies, such as combining rapid targeted sequencing for common pathogens with broader metagenomic approaches for complex cases, to improve diagnostic yield and guide antimicrobial therapy. Quantitative comparisons indicate that sequencing technologies can complement conventional methods, particularly in cases where culture-based approaches fail. In conclusion, sequencing-based diagnostics offer measurable improvements in sensitivity and speed over traditional methods for AMR detection in BSIs. Future work should focus on optimizing workflows, integrating sequencing data into clinical decision-making, and validating approaches in prospective studies.},
}
@article {pmid41463733,
year = {2025},
author = {Xin, R and Lin, H and Li, Z and Yang, F},
title = {Plasmid-Mediated Spread of Antibiotic Resistance by Arsenic and Microplastics During Vermicomposting.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121230},
pmid = {41463733},
issn = {2079-6382},
support = {23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; 42277033//National Natural Science Foundation of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; },
abstract = {Background: The efficiency of vermicomposting in reducing antibiotic resistance genes (ARGs) in dairy manure may be compromised by co-pollutants like arsenic (As) and microplastics. Specifically, plasmids serving as carriers and vectors of ARGs were largely distributed in this process. However, the impact of As and microplastics on plasmids carrying ARGs during vermicomposting is largely unknown. Methods: This study utilized a controlled experimental design and applied plasmid metagenomics to investigate the individual and combined effects of As and polyethylene terephthalate (PET) microplastics on plasmid-mediated ARG dynamics during vermicomposting. Results: We found that vermicomposting alone mainly enriched non-mobilizable plasmids, while PET microplastics selectively promoted conjugative and mobilizable plasmids, whereas As significantly increased all plasmid types. Moreover, both PET or As alone and combined exposure (PET and As) increased total ARG abundance, with their combination inducing synergistic ARG enrichment despite unchanged total plasmid abundance. Furthermore, co-occurrence network analysis combined with ARGs/plasmid ratio assessments demonstrated that As influences ARGs through co-selective pressure by enriching ARGs co-localized with As resistance genes (e.g., the ars operon) on plasmids while simultaneously promoting horizontal gene transfer (HGT) via activation of oxidative stress and SOS response pathways. In contrast, PET primarily facilitates ARG dissemination through a "metabolism-resistance" coupling strategy by enriching colonizing bacteria with PET-degrading capacity. Their co-exposure formed As-enrichment hotspots on PET microplastic surfaces, functioning as a "super-mixer" that selectively screened for superbugs carrying potent resistance mechanisms (e.g., blaOXA-50 and mdtB/mdtE). Conclusions: This study provides the first plasmidome-level evidence of synergistic ARG propagation by As and PET microplastics during vermicomposting, highlighting mobile genetic elements' critical role in co-pollutant risk assessments.},
}
@article {pmid41463365,
year = {2025},
author = {Trachtmann, NV and Toshchakov, SV and Izotova, AO and Korzhenkov, AA and Evteeva, MA and Kachmazov, GS and Agboigba, EE and Validov, SZ},
title = {Cloning and Characterization of the Novel Endoglucanase Identified in Deep Subsurface Thermal Well of Biragzang (North Ossetia) by Metagenomic Analysis.},
journal = {Biomolecules},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/biom15121710},
pmid = {41463365},
issn = {2218-273X},
support = {075-15-2025-471//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Cellulase/genetics/metabolism/chemistry/isolation &amp; purification ; Cloning, Molecular ; *Metagenomics ; Phylogeny ; Enzyme Stability ; Hydrogen-Ion Concentration ; Escherichia coli/genetics ; Metagenome ; Recombinant Proteins/genetics/metabolism ; Temperature ; *Bacterial Proteins/genetics/metabolism/chemistry ; },
abstract = {The phylum Armatimonadota represents one of the least characterized bacterial lineages, with only three formally described species despite its widespread distribution in various environments. Deep subsurface thermal environments harbor significant microbial diversity and represent promising sources for novel enzyme discovery through metagenomic approaches. This study reports the identification, cloning, and biochemical characterization of Cel7465, a novel endoglucanase from an uncultured GBS-DC family within the order Fimbriimonadales. The enzyme was identified through metagenomic analysis of microbial mats from the Biragzang deep thermal well (North Ossetia, Russia, 48 °C) and successfully expressed in cells of Escherichia coli strain ArcticExpress (DE3). Phylogenetic analysis assigned Cel7465 to glycoside hydrolase family 5 subfamily 36. The purified recombinant enzyme exhibited optimal activity at 55 °C and pH 8.0, with high specific activity of 4347 U/mg. The enzyme demonstrated broad pH tolerance (50% activity retained from pH 4.0 to 10.0) and notable thermal stability, retaining 60% activity after one hour at 80 °C and 20% after four hours. Remarkably, the presence of Mn[2+] ions enhanced enzyme activity more than 7-fold, while Mg[2+] and Ca[2+] ions provided moderate activation. Cel7465 represents the first biochemically characterized glycoside hydrolase from the order Fimbriimonadales, expanding our understanding of enzymatic capabilities within the understudied phylum Armatimonadota and demonstrating the continued potential of extreme environments as sources of novel industrial biocatalysts.},
}
@article {pmid41462784,
year = {2025},
author = {Li, T and Fang, L and Chen, X and He, Y and Pang, X and Lin, L and Chen, H and Su, Y and Huang, Y and Guo, Y and Xiao, T and Liu, A and Wang, Y and Yang, H and Nie, C and Zhou, W and Yang, G and Cai, C and Zhou, X and Zeng, S and Yu, Y and Li, L and Zhang, H and Yu, L and Cheng, G and Zhou, W and Chen, C and Yu, Z and Wang, M and Xie, Y},
title = {The Premature Infants' Gut Microbiota Assembly and Neurodevelopment (PIGMAN) Cohort Study: Protocol for a Prospective, Longitudinal Cohort Study.},
journal = {Children (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/children12121644},
pmid = {41462784},
issn = {2227-9067},
abstract = {BACKGROUND: Early-life gut microbiota colonization plays a significant role in the neurodevelopment of infants and young children. However, the causal relationship between early-life gut microbiota colonization and neurodevelopment in preterm infants has not yet been conclusively established. Our research will initiate the PIGMAN (Premature Infants Gut Microbiota Assembly and Neurodevelopment) cohort study to systematically examine the dynamic interplay between gut microbiota developmental trajectories and neurodevelopmental processes in preterm infants.<br><br>METHODS: This study will employ a longitudinal cohort design and utilize data from the PIGMAN cohort, examining the interplay between gut microbiota metabolism and neurodevelopmental outcomes. The study design incorporates longitudinal stool sample collection, which will be analyzed through 16S rRNA gene sequencing and metagenomic shotgun sequencing, enabling comprehensive characterization of microbial community dynamics and functional metabolic pathways.<br><br>ANTICIPATED RESULTS: Advanced analytical approaches incorporating causal inference methodologies will be implemented to identify significant microbial and metabolic biomarkers associated with neurodevelopmental outcomes in preterm neonates, and to establish causal pathways between these biomarkers and neurodevelopment. These analytical advancements will facilitate the construction of predictive models that utilize temporal microbial signatures and metabolite trajectories as prognostic indicators for neurodevelopmental outcomes. Causal inference method evaluations will further reveal that specific gut-derived metabolites, particularly those involved in cholesterol metabolism and neural signaling pathways-such as bile acids and GABA (gamma-aminobutyric acid)-exhibit superior predictive capacity for cognitive development trajectories. Anticipated Conclusions: The findings will collectively suggest that longitudinal metabolic profiling of the gut ecosystem, when combined with causal network analysis, provides a novel paradigm for developing clinically actionable predictive models of neurodevelopment in vulnerable preterm populations.},
}
@article {pmid41462411,
year = {2025},
author = {Vila-Nistal, M and Martinez-Hernandez, F and Lluesma-Gomez, M and Fornas, O and Roux, S and Martinez-Garcia, M},
title = {Limited consensus of marine viral diversity observed across techniques.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {157},
pmid = {41462411},
issn = {2524-6372},
support = {ACIF2020//Conselleria de Cultura, Educaci&#xf3;n y Ciencia, Generalitat Valenciana/ ; CSP award no. 506015//Joint Genome Institute-Department of Energy of EEUU/ ; PID2021-125175OB-I00 and RTI2018-094248-B-I00//Spanish Ministry of Science and Innovation/ ; },
abstract = {BACKGROUND: Viruses are fundamental to many aspects of life influencing ecosystem functions. The `number of lenses´ we use for exploring the viral diversity has expanded, yet each has limitations that constrain our view of the uncultured virosphere. It is fundamental to evaluate the different viromic approaches and sequencing methods on their ability to recover the extant viral diversity and microdiversity present in a sample. The differences in genome recovery between technologies have downstream impacts on subsequent estimates of viral diversity and function within a sample that can limit our comprehension of natural viral assemblages and their interactions with their microbial hosts.<br><br>RESULTS: Here, using the same surface seawater sample, we compare short- and long-read viromics (i.e., Illumina, PacBio-HiFi and MinION sequencing) along with high-throughput single-virus genomics (sequencing of 700 uncultured single-viruses) to explore the consensus between approaches to uncover the extant viral diversity (sequencing effort &#x2248;1.6 Tbp). Overall, &#x2248;42,000 viral contigs (>&#x2009;10&#xa0;kb) were obtained, resulting in &#x2248;12,500 and &#x2248;23,400 viral OTUs at the genus and species levels, respectively, infecting mostly Flavobacteriaceae and Pelagibacteracea. At the viral family level, single-virus genomics (SVG) recovered viruses with a more distinct taxonomic profile compared to other methods. At lower taxonomic resolution, only&#x2009;<&#x2009;1% of all species and genera, including some of the most abundant viruses, were captured by all methods; reaching a value of &#x2248;2% when only viromics excluding SVG were considered. The highest pairwise diversity consensus was observed between PacBio-HiFi and Illumina, with approximately &#x2248;11% of PacBio-HiFi species-level vOTUs also detected by Illumina. To understand how different methods resolve the co-occurring genomic microdiversity within species, we used one of the most abundant and microdiverse viruses -the uncultured pelagiphage vSAG 37-F6, proposed to be classified as Pelagimarinivirus ubique- originally discovered by single-virus genomics, as a reference. None of the methods alone were able to assemble the complete genome, which was only achieved by combining all datasets. Similarly, none of the viral clusters at the strain level were recovered by all methods.<br><br>CONCLUSIONS: Our study suggests that the inherent bias of each method still represents a challenge for the recovery of marine viral diversity and potentially for other environmental viral samples. Nevertheless, regarding standard viromic techniques, PacBio HiFi in combination with Illumina seem to perform the best in absolute recovery of viral species and genera.},
}
@article {pmid41461922,
year = {2025},
author = {Jin, S and Cenier, A and Wetzel, D and Arefaine, B and Moreno-Gonzalez, M and Stamouli, M and Mohamad, M and Lupatsii, M and Ríos, E and Lee, S and Zamalloa, A and Chokshi, S and Mardinoglu, A and Shoaie, S and Beraza, N and Patel, VC and Schirmer, M},
title = {Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41461922},
issn = {2058-5276},
support = {426120468//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BBS/E/F/000PR13632//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/CCG1860/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 268211/1134579//Foundation for Liver Research/ ; },
abstract = {Microbiome perturbations are associated with advanced chronic liver disease (ACLD), but how microorganisms contribute to disease mechanisms is unclear. Here we analysed metagenomes of paired saliva and faecal samples from an ACLD cohort of 86 individuals, plus 2 control groups of 52 healthy individuals and 14 patients with sepsis. We identified highly similar oral and gut bacterial strains, including Veillonella and Streptococcus spp., which increased in absolute abundance in the gut of patients with ACLD compared with controls. These microbial translocators uniquely share a prtC gene encoding a collagenase-like proteinase, and its faecal abundance was a robust ACLD biomarker (area under precision-recall curve = 0.91). A mouse model of hepatic fibrosis inoculated with Veillonella and Streptococcus prtC-encoding patient isolates showed exacerbation of gut barrier impairment and hepatic fibrosis. Furthermore, faecal collagenase activity was increased in patients with ACLD and experimentally confirmed for the prtC gene of translocating Veillonella parvula. These findings establish mechanistic links between oral-gut translocation and ACLD pathobiology.},
}
@article {pmid41461645,
year = {2025},
author = {Moradi, J and Berggreen, E and Gerdts, E and Kringeland, E and Bolstad, AI and Bunæs, DF and Bertelsen, RJ},
title = {Taxonomic and functional signatures of smoking and periodontitis severity in the subgingival microbiome of older adults.},
journal = {npj aging},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41514-025-00319-9},
pmid = {41461645},
issn = {2731-6068},
support = {318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; },
abstract = {Periodontitis and smoking are major contributors to oral and systemic health deterioration in aging adults. This study investigated the combined effects of smoking status and periodontitis severity on the subgingival microbiome in 1107 individuals aged 69-72 using shotgun metagenomic sequencing. Smoking was linked to reduced microbial diversity, enrichment of periodontal pathogens, and depletion of health-associated commensals, while increasing periodontitis severity was associated with broader dysbiotic shifts, including enrichment of canonical pathogens. The presence of overlapping taxa suggests shared dysbiotic pathways that may accelerate disease progression in older adults. Notably, the combination of smoking and severe periodontitis was characterized by enrichment of key pathogens, such as Tannerella forsythia, Fusobacterium nucleatum, Actinomyces israelii, and Mogibacterium timidum. Although former smokers showed fewer opportunistic pathogens than current smokers, their microbiomes remained altered compared to never smokers, suggesting persistent differences potentially related to past smoking. Functional profiling revealed largely additive effects of smoking and periodontitis, with enrichment of lipopolysaccharide biosynthesis, proteolysis, and sulfur metabolism, alongside depletion of commensal biosynthetic functions. Overall, the findings highlight the persistent and additive impacts of smoking and periodontitis on the subgingival microbiome, underscoring the importance of addressing both exposures jointly in long-term oral health strategies for older adults.},
}
@article {pmid41461507,
year = {2026},
author = {Su, Q and Du, Y and Du, D and Zhang, TC},
title = {New insights into the anaerobic digestion of high carbon wastewater with ciprofloxacin: Methane production and ARGs inhibition.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {612-621},
doi = {10.1016/j.jes.2025.05.037},
pmid = {41461507},
issn = {1001-0742},
mesh = {*Methane/metabolism ; *Wastewater/chemistry/microbiology ; *Ciprofloxacin ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; Carbon ; },
abstract = {Ciprofloxacin (CIP), as a quinolone antibiotic, has broad-spectrum antibacterial properties and can affect methanogenic performance in anaerobic digestion (AD). While previous studies focused on synthetic wastewater, the fate of CIP in real distillery wastewater (RDW) and its impact on microbial adaptation mechanisms remain unclear (such as biotransformation pathways, population dynamics, and the enzymes involved) in RDW is largely unclear. In this study, we investigated AD performance, metabolic pathways, and antibiotic resistance gene (ARG) dynamics using real wastewater spiked with CIP (0.3-2 mg/L). Results indicate that 0.5 mg/L CIP (631.83 mL CH4/g·VS) enhanced the methane yield by 6.67 % (592.34 mL CH4/g·VS in control), correlating with upregulated enzyme in glycosis, TCA cycle, and methanogenesis (F420 increased). With full use of short-chain acids, transient volatile fatty acid (VFA) inhibition (≤ 50 mg/L on Day 3) was overcome by Day 10. Metagenomics revealed CIP promoted the production of stress proteins (e.g., cysteine synthase activity doubled). Furthermore, CIP (0.3-1 mg/L) suppressed mobile genetic elements (MGEs) encoding horizontal gene transfer, including isfinder (15.15 %) and integrases (6.25 %), while ARG and virulence factor abundances remained unchanged versus control. This study firstly shows that low-dose CIP in RDW increases methanogenesis via metabolic adaptation without exacerbating ARG risks. MGE suppression implies that CIP may lessen the possibility of ARG diffusion in AD systems. These results offer vital information for improving AD performance in the treatment of wastewater contaminated by antibiotics and developing methods to strike a balance between antibiotic removal and ARG control.},
}
@article {pmid41461486,
year = {2026},
author = {Kang, S and Lee, JY and Cho, KS},
title = {Bacterial and fungal metagenomes associated with atmospheric particulates in Republic of Korea: Comparison of PM2.5 and TSP larger than PM2.5.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {400-410},
doi = {10.1016/j.jes.2025.08.021},
pmid = {41461486},
issn = {1001-0742},
mesh = {*Particulate Matter/analysis ; Republic of Korea ; Bacteria/genetics ; *Air Pollutants/analysis ; *Environmental Monitoring ; Particle Size ; *Fungi/genetics ; *Metagenome ; *Air Microbiology ; Microbiota ; Air Pollution/statistics &amp; numerical data ; },
abstract = {Particulate matter (PM) significantly contributes to air pollution, potentially causing health issues, with PM-associated microorganisms implicated in some cases. While studies have explored microbial concentration and structure in PM based on particle size, comprehensive analysis of microbial functional traits and environmental influences is limited. This study evaluated microbial concentrations and diversity in PM with a diameter of 2.5 µm or lower (PM2.5) and total suspended particles (TSP) greater than PM2.5 (PM>2.5) samples relative to air temperature and other factors. DNA extracted from PM2.5 and PM>2.5 filters was sequenced to characterize bacterial and fungal community structures and functional genes. Results showed that microbial concentrations and diversity were greater in PM>2.5, with similar dominant species across PM sizes. Higher air temperatures correlated with increased microbial concentrations and diversity in PM>2.5, attributed to enhanced microbial growth. An Asian dust event from the Mongolian desert disrupted the PM microbiome. Despite consistent species dominance, gene function analysis revealed abundant drug resistance pathways in bacterial communities of both particle types, while pathotroph prevalence was higher in PM2.5 fungal communities. These findings indicate that PM2.5 microbial community analysis suffices for understanding PM ecosystems, offering valuable insights for air quality management and microbial pollution control, especially concerning potential pathogens.},
}
@article {pmid41461481,
year = {2026},
author = {Qian, J and Bai, S and Wu, L and Geng, M and Chen, G and Jiang, F},
title = {Energy recovery from corn straw-based biochar@MIL-88A(Fe)-mediated anaerobic digestion of waste activated sludge under norfloxacin: Metabolism and antibiotic resistance gene fates.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {350-359},
doi = {10.1016/j.jes.2025.07.034},
pmid = {41461481},
issn = {1001-0742},
mesh = {*Norfloxacin ; Sewage/microbiology/chemistry ; Zea mays/chemistry ; Anaerobiosis ; Charcoal/chemistry ; *Waste Disposal, Fluid/methods ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; },
abstract = {Norfloxacin (NOR), a commonly detected antibiotic in waste activated sludge (WAS), remains understudied in anaerobic digestion (AD). This study investigated the effect of NOR on WAS AD, with corn straw-based biochar modified with MIL-88A(Fe) (BM) added to enhance energy recovery during digestion. Accumulated methane production was inhibited by 41.86 % in the BM-mediated digestion system under 1 mg/L NOR. Moreover, NOR induced the build-up of volatile fatty acids (VFAs), hindering methanogenic pathways subsequently. Microbial community structure was altered, with an enrichment of bacteria responsible for NOR degradation and a 13.20 % reduction in the abundance of hydrogenotrophic methanogens under antibiotic stress. Methanogenesis was inhibited with the expression of related genes and enzymes suppressed. The high enzymatic activities of cytochrome P-450 (CYP450) and acetate kinase contributed to the high NOR biodegradation efficiency (88.79 %). Twelve typical antibiotic resistant genes (ARGs) types, including multidrug, aminoglycoside, macrolides (MLs), etc., were examined in the AD system. The total abundance of ARGs type and subtype increased under NOR addition, implying ARGs removal was inhibited by NOR stress. Resistance to NOR exposure was primarily associated with antibiotic efflux and alterations in antibiotic target. Horizontal gene transfer (HGT) and vertical gene transfer (VGT) were the mechanistic routes for ARG evolution, with HGT inhibited and VGT promoted following NOR addition. The dominant genus Acinetobacter was the potential host for nearly all ARGs. This study advanced understanding of the impact of NOR on WAS digestion with BM mediation, providing new insights for optimizing WAS digestion.},
}
@article {pmid41461466,
year = {2026},
author = {Cui, M and Chen, S and Zhang, Z and Yu, Y and Xu, Y and Liu, L and Gao, H and Chen, X and Liu, Z and Zhang, X and Yuan, W and Chen, S and Li, D and Chen, L and Xing, X and Xiao, Y and Chen, W and Liu, Y and Wang, Q},
title = {Nanoplastics and triclosan co-exposure aggravates DSS-induced colitis in mice by interfering with Akkermansia muciniphila and tryptophan metabolism.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {189-200},
doi = {10.1016/j.jes.2025.06.029},
pmid = {41461466},
issn = {1001-0742},
mesh = {Animals ; Mice ; *Colitis/chemically induced ; *Tryptophan/metabolism ; *Triclosan/toxicity ; Dextran Sulfate/toxicity ; *Microplastics/toxicity ; Akkermansia ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; },
abstract = {The global incidence of inflammatory bowel disease (IBD) has been escalating. Recent studies have identified co-exposure to polystyrene nanoplastics (PSNP) and triclosan (TCS), two prevalent environmental pollutants, as emerging risk factors for IBD. However, the molecular mechanisms contributing to its deteriorative effect remain elusive. To explore the mechanisms, we conducted an integrative analysis of metagenomic and metabolomic data in a mouse model of colitis induced by dextran sulfate sodium (DSS) following co-exposure to PSNP and TCS. Results demonstrated that co-exposure to PSNP and TCS significantly exacerbated DSS-induced colitis, as evidenced by elevated disease activity indices and pro-inflammatory cytokine levels. Mechanistically, this aggravation correlated with a marked reduction in Akkermansia muciniphila abundance, which was further associated with the disruption of tryptophan metabolism. Specifically, the disruption of this metabolic pathway led to decreased production of two key tryptophan-derived metabolites: indole acetic acid (IAA) and indole acetamide (IAM). In-vitro experiments confirmed that co-exposure to PSNP and TCS inhibited the growth of A. muciniphila rather than affecting the integrity of intestinal epithelial cells. Additionally, IAA and IAM reduced inflammatory cytokine secretion in THP-1 cells. These findings suggest that the reduction in A. muciniphila abundance might decrease the production of IAA and IAM by disrupting tryptophan metabolism. This disruption ultimately contributes to the inflammatory response induced by co-exposure to PSNP and TCS. Our study offers a novel insight into microbiota-host interactions and potential therapeutic targets for intestinal disease.},
}
@article {pmid41460777,
year = {2025},
author = {Geraerts, M and Gombeer, S and Nebesse, C and Akaibe, D and Akaibe, D and Baelo, P and Chaber, AL and Gaubert, P and Gembu, GC and Joffrin, L and Laudisoit, A and Laurent, N and Leirs, H and Mande, C and Mariën, J and Ngoy, S and Těšíková, J and Vanderheyden, A and van Vredendaal, R and Verheyen, E and Gryseels, S},
title = {A wide diversity of viruses detected in African mammals involved in the wild meat supply chain.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013643},
pmid = {41460777},
issn = {1553-7374},
mesh = {Animals ; *Meat/virology ; *Mammals/virology ; *Animals, Wild/virology ; Democratic Republic of the Congo ; *Viruses/genetics/isolation &amp; purification/classification ; Zoonoses/virology ; Humans ; Phylogeny ; Belgium ; Genetic Variation ; },
abstract = {The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome of many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. Here, we present the findings of a metagenomic viral screening of 101 mammalian specimens belonging to 28 wild African species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected in various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of sixteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during close interactions with wildlife in the wild meat supply chain.},
}
@article {pmid41460729,
year = {2025},
author = {Chen, X and Sheng, Y and Wang, G and Liao, F and Zhou, P},
title = {Deciphering Sulfur-Based Denitrification in Confined Alluvial-Lacustrine Aquifers through Multi-isotope ([15]N, [34]S, [13]C, and [18]O) and Metagenomic Analyses.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09851},
pmid = {41460729},
issn = {1520-5851},
abstract = {Sulfur-based denitrification offers unique advantages in nitrogen removal in low-carbon environments. Despite its importance, the prevalence, controlling factors, and microbial mediators of sulfur-based denitrification in aquifers remain largely unknown. By integrating multiple stable isotopes and genome-resolved metagenomics, we investigated the coupling of nitrogen and sulfur cycling along the groundwater flowpath from unconfined to confined alluvial-lacustrine aquifers in the Poyang Lake Plain, China. Isotope (i.e., δ[15]N-NO3[-], δ[18]O-NO3[-], δ[34]S-SO4[2-], δ[18]O-SO4[2-], δ[18]O-H2O, δ[13]C-DIC, and δ[13]C-DOC) fractionation and hydrogeochemical trends indicated a transition from nitrification-dominated processes in the unconfined aquifer to denitrification, sulfide oxidation, and sulfate reduction in the confined aquifer. A significant negative correlation between δ[34]S-SO4[2-] and δ[15]N-NO3[-], along with a significant positive correlation between genes involved in sulfide oxidation and nitrate reduction, suggested cryptic coupling between sulfide oxidation and nitrate reduction. Sulfur-autotrophic denitrifying metagenome assembly genomes encoding Calvin-Benson-Bassham carbon fixation and rTCA pathways, such as Burkholderiales, Rhodocyclaceae, and Sulfurimonas, were enriched in the confined aquifer and co-occurred with sulfate reducers (Pseudomonadota and Desulfobacterota). These results highlighted sulfur cycling consortia when sulfate was reduced to facilitate removal of nitrate via sulfur-based denitrification. These findings reveal the role of cryptic sulfur cycling in sustaining denitrification in aquifers, offering new insights into nitrogen-sulfur interactions in subsurface ecosystems.},
}
@article {pmid41460655,
year = {2025},
author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE},
title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251407700},
doi = {10.1177/13872877251407700},
pmid = {41460655},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.},
}
@article {pmid41460182,
year = {2025},
author = {Petersen, NP and Le, M and Renevey, A and Emua, E and Ryter, S and Annibaldis, G and Camara, J and Boumbaly, S and Erameh, C and Laske, T and Baumbach, J and Lemey, P and Günther, S and Duraffour, S and Kafetzopoulou, LE},
title = {ViMOP: A user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf687},
pmid = {41460182},
issn = {1367-4811},
abstract = {MOTIVATION: Untargeted, also known as metagenomic, nanopore sequencing is a powerful tool for virus genomic surveillance, particularly in resource-limited settings and when paired with the portability of the MinION device (Oxford Nanopore Technologies, ONT). However, a major bottleneck for global access is the absence of a user-friendly software capable of efficiently analyzing untargeted nanopore sequencing data to generate high-quality consensus genomes.<br><br>RESULTS: We share ViMOP, a pipeline built on our long-term experience in nanopore field sequencing. The pipeline emphasizes field user-friendliness, flexibility and versatility to analyze reads generated directly from human clinical samples. The software assembles de novo contigs, matches contigs to known viral references and uses them to assemble consensus genomes. Executed with a single Nextflow command or via the EPI2ME Desktop interface (ONT), results are summarized in an HTML report. ViMOP, through its user-centered design, lowers the barrier to high-quality virus genome reconstruction and advances capacity for genomic surveillance.<br><br>AVAILABILITY: ViMOP is freely available for non-commercial use (https://github.com/opr-group-bnitm/vimop and https://zenodo.org/records/17913089), along with the associated database (https://zenodo.org/records/17652512), the scripts used to generate it (https://zenodo.org/records/17632662) and benchmarking code (https://zenodo.org/records/17633185).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid41459959,
year = {2025},
author = {Asai, N and Igarashi, Y and Miyazaki, N and Osugi, A and Matsumoto, Y and Nakamura, S and Mitarai, S and Mikamo, H},
title = {Complete genome sequence of a new Mycobacterium sp. nov. from a compromised Japanese individual.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042125},
doi = {10.1128/mra.00421-25},
pmid = {41459959},
issn = {2576-098X},
abstract = {Here, we report the complete genome sequencing of a new Mycobacterium sp. nov. from a compromised Japanese individual with hematological malignancy. This will represent the essential data for future phylogenetic and comparative genome studies and will be useful for better understanding the evolution of the pathogen.},
}
@article {pmid41459746,
year = {2025},
author = {Duncan, A and Koon, W and Sidorczuk, K and Quince, C and Frioux, C and Hildebrand, F},
title = {Detecting signatures underlying the composition of biological data.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
pmid = {41459746},
issn = {1362-4962},
support = {BB/Z516168/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //UK Research and Innovation/ ; //Earlham Institute Strategic Programme/ ; BBX011070/1//Grant Cellular Genomics/ ; BBS/E/ER/230001C//workpackage/ ; BBS/E/ER/230002A//workpackage/ ; BBS/E/F/000PR13631//workpackage/ ; ISP BBX011089/1//Decoding Biodiversity/ ; ISP BB/X011054/1//Quadram Institute Bioscience/ ; erc-stg-948219/ERC_/European Research Council/International ; ANR-22-PEAE-001//French National Research Agency/ ; //Earlham Institute and Quadram Institute Bioscience/ ; },
mesh = {Humans ; *Software ; Metagenome ; Rhizosphere ; Microbiota/genetics ; *Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology ; Lung Neoplasms/genetics/pathology ; },
abstract = {Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decomposition of large compositional data and to capture gradients in co-occurring features, called signatures, we developed a new software package 'cvaNMF'. Our benchmarks on synthetic data show the effectiveness of cross-validation and our novel signature-similarity method to identify a suitable decomposition using non-negative matrix factorization (NMF). This software provides a complete set of tools to identify and visualize biologically informative signatures which we demonstrate in a wide range of microbial and cellular datasets: 'Enterosignatures' detected in gut metagenomes differentiated human hosts with diverse diseases; five 'terrasignatures' from rhizosphere metagenomes differentiated root- or soil-associated microbiomes, while being refined enough to infer geographic distances between plants. Large-scale data from >13 000 metagenomes representing 25 biomes were decomposed into environmental and host-associated microbiomes based on five newly discovered signatures. Finally, analysis of the cell composition of non-small cell lung cancer samples allowed separation of cancerous and inflamed tissues based on four cell-type signatures.},
}
@article {pmid41459742,
year = {2025},
author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, SM and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM},
title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf284},
pmid = {41459742},
issn = {1751-7370},
abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line, Saeilmi, particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation or promoting microbial symbiosis. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. This study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.},
}
@article {pmid41459349,
year = {2025},
author = {Nandi, S and Stephens, TG and Walsh, K and García-Camps, R and Villalpando, MF and Sellares-Blasco, RI and Zubillaga, AL and Croquer, A and Bhattacharya, D},
title = {Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD).},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf226},
pmid = {41459349},
issn = {2730-6151},
abstract = {Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigated microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes and correlated their abundance with disease phenotypes, which revealed significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses in our dataset that increase in abundance in SCTLD-affected corals and are present in existing coral data from other Caribbean regions. In addition, we identified the first putative instance of asymptomatic/resistant SCTLD-affected corals. These are apparently healthy colonies that share the viral profile of diseased individuals. However, these colonies contain a different prokaryotic microbiome than do diseased corals, suggesting microbe-induced resilience (i.e. beneficial microbiome) to SCTLD. Finally, utilizing differential abundance analysis and gene inventories, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.},
}
@article {pmid41459229,
year = {2025},
author = {Mulec, J and Pašić, L and Oarga-Mulec, A},
title = {Metabolic traits of sediment bacteria in karst caves in the light of environmental changes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1724116},
pmid = {41459229},
issn = {1664-302X},
abstract = {INTRODUCTION: Karst subterranean systems are vulnerable ecosystems that have not yet been studied adequately at the microbial functional level. Cave sediments deposited over different time periods host diverse microbial communities that play a critical role in nutrient cycling and pollutant degradation.<br><br>METHODS: In this study, we investigated microbial diversity and metabolic capacity in recently deposited alluvial sediments and an ancient palaeo-river deposit in a karst cave system. Using 16S rRNA gene amplicon metagenomic analysis, community-level physiological profiling (CLPP), and chemical characteristics of the environment, the influence of key environmental factors on microbial community composition and substrate degradation, concentrating particularly upon sediment age, oxygen availability, and temperature, was assessed.<br><br>RESULTS: The results showed different microbiome compositions and metabolic characteristics between sites. The old alluvial sediment exhibited low taxonomic and functional diversity, accompanied by elevated heavy-metal concentrations, suggesting that sediment age might act as a geochemical filter, limiting microbial function. In contrast, a periodically flooded site showed high metabolic versatility and taxonomic diversity, emphasizing the ecological role of hydrological pulses in maintaining functional microbial diversity. CLPP metrics linked community structure to functional potential, revealing adaptive traits in key taxa such as Polaromonas, Methylibium, and Beggiatoa.<br><br>DISCUSSION: These results demonstrated the value of integrating functional and taxonomic approaches in subsurface environments and provide insights into microbial resilience, biogeochemical processes, and the potential for applied environmental use.},
}
@article {pmid41459228,
year = {2025},
author = {Ruiz-Blas, F and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A},
title = {Cryptic sulfur cycling in the deep biosphere of ferruginous Lake Towuti, Indonesia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725877},
pmid = {41459228},
issn = {1664-302X},
abstract = {Lake Towuti, Sulawesi, Indonesia is an ancient tectonic lake, exhibiting iron-rich, sulfate-poor anoxic deep waters. Temporal variations in water column stratification led to sediment accumulation under variable redox conditions. Such ferruginous settings make Lake Towuti an ideal study site to evaluate how a cryptic sulfur cycle could possibly operate under a scarcity of sulfate and abundance of iron minerals, similar to Earth's primitive oceans. Here, we integrate downcore profiles for pore water geochemistry, reactive iron mineralogy, and bulk sediment elemental composition with microbial cell counts, sulfate reduction rates, 16S rRNA genes and metagenomes to resolve microbial sulfur transformations down to 15 m below lake floor (mblf). Sulfate concentrations and reduction rates dropped within the upper mblf, while pore water ferrous iron increased to its highest concentration down to 3 mblf. Any microbially-produced sulfide precipitated as reduced inorganic sulfur in the sediment, apparently forming authigenic millerite (NiS) during burial. The decrease in cell densities tracked the decline in electron acceptors in pore waters with depth. From 3 to 10 mblf, low but sustained sulfate reduction rates were observed with intermittent presence of nitrate in pore water and increased goethite in the sediment, both acting as potential oxidants of sulfur intermediates. A subsequent re-increase in pore water sulfate occurred in parallel with syntrophic fermentation of volatile fatty acids. Consistent with geochemical evolution, the taxonomic diversity of microbial populations shifted from a bacterial assemblage near the surface to selective but prevailing Bathyarchaeia down to 15 mblf. The corresponding metagenome-assembled genomes predicted metabolic potential for complete sulfate reduction (aprAB, dsrAB) in Thermodesulfovibrionia, whereas Desulfobacterota (incl. Geobacterales, Desulfuromonadales, Syntrophales) and Aminicenantia exhibited versatility in reducing iron, nitrate (narG, napA), nitrite (nirS, nrfA) and sulfate (dsrAB, asrA). By contrast, Bathyarchaeia were predicted to disproportionate sulfur to polysulfides and reduce ferredoxin via electron bifurcation (hyd I-II, sudA, dsrC, dsrE) to fuel a Wood-Ljungdahl pathway, defining homoacetogenesis as terminal electron sink. Together, these mineralogical, geochemical, and metagenomic features provide evidence for a spatially confined but active cryptic sulfur cycle with tight coupling between reduction of mineral ferric iron and intermittent pore water nitrate to syntrophic and lithotrophic (homo)acetogenesis.},
}
@article {pmid41459220,
year = {2025},
author = {Zhao, X and Qiao, J and Wang, Y and Xiong, H and Wang, R and Su, F and Guo, Z},
title = {Shotgun metagenomics reveals antibiotic resistome dynamics and metabolic specialization in fungal-dominated microbiomes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626799},
pmid = {41459220},
issn = {1664-302X},
abstract = {BACKGROUND: Metagenomics offers a culture-independent framework for comprehensively characterizing microbial communities by directly extracting and sequencing DNA from environmental samples. In this study, we employed high-throughput metagenomic sequencing to explore microbial communities inhabiting fungal-rich environments, emphasizing taxonomic composition, functional potential, and antibiotic resistance gene (ARG) dynamics.<br><br>METHODS: Six samples from two distinct groups (HFJ and QFJ) were subjected to Illumina-based shotgun sequencing, followed by rigorous quality control, taxonomic classification, KEGG-based functional annotation, and ARG identification via the CARD database. Comparative analysis revealed stark contrasts between the two groups.<br><br>RESULTS: HFJ samples were dominated by eukaryotic taxa, particularly Saccharomyces cerevisiae, and exhibited elevated carbohydrate metabolism, aligning with the ecological role of fermentative fungi. Conversely, QFJ samples displayed higher bacterial diversity, particularly Firmicutes and Proteobacteria, and were enriched in lipid and amino acid metabolism pathways. Striking differences were also observed in ARG profiles. QFJ samples harbored greater ARG abundance, particularly genes conferring resistance to beta-lactams, aminoglycosides, and tetracyclines, indicating higher resistance potential and possible horizontal gene transfer activity.<br><br>CONCLUSION: Our results reveal distinct microbial, functional and resistome profiles in fungal-rich versus bacterial-rich fermentation environments. Fungal dominance correlated with lower bacterial diversity and a reduced abundance of certain ARGs, whereas bacterial-rich samples exhibited higher diversity and ARG prevalence. These correlations generate the hypothesis that fungal dominance may suppress bacterial growth or ARG dissemination; however, causal relationships cannot be inferred from our cross-sectional data. The study highlights the potential of metagenomic surveillance to elucidate ecological niches that influence bacterial diversity and resistance dynamics.},
}
@article {pmid41459217,
year = {2025},
author = {Li, P and Wang, M and Zhang, H and Gao, X and Chen, L and Chen, H and Xu, Q and Chen, W and Liu, W and Dai, M},
title = {Integrative metagenomic and metabolomic profiling identifies gut microbial and metabolite signatures associated with lymph node metastasis in pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706084},
pmid = {41459217},
issn = {1664-302X},
abstract = {BACKGROUND: Lymph node metastasis (LNM) is a prognostic factor in pancreatic cancer. The association between the gut microbiota and LNM remains unexplored. This study aimed to characterize the gut microbiota and metabolomic profiles associated with LNM and to investigate their potential as predictive biomarkers.<br><br>METHODS: Fecal samples from pancreatic cancer patients undergoing surgery were analyzed using metagenomic sequencing and untargeted metabolomics. The patients were categorized into LNM and non-LNM (NLNM) groups. Differential microbiome taxa were analyzed using the DESeq2 package. Random forest predictive models were developed based on metagenomic and metabolomic data, with performance assessed using leave-one-out cross-validation (LOOCV).<br><br>RESULTS: A total of 26 patients with LNM and 29 patients without LNM were included. Principal coordinates analysis (PCoA) revealed significant differences in microbiota composition between the two groups (Anosim, p&#x202f;=&#x202f;0.047). The absolute counts of Ruminococcus gnavus and Blautia wexlera were significantly decreased in LNM. Tryptophan-derived metabolites, indole-3-lactic acid (3-ILA) and indole-3-acrylic acid (3-IA), were downregulated in LNM. Functional pathway analysis showed downregulation of tryptophan metabolism in LNM, while cancer-related pathways were upregulated. Correlation analysis revealed a significant positive association between Ruminococcus gnavus and 3-ILA/3-IA levels. Moreover, Ruminococcus gnavus was positively correlated with CD8[+] T cells. Predictive models based on the gut microbiota and metabolites distinguished LNM from NLNM, with AUC values of 0.854 and 0.940, respectively.<br><br>CONCLUSION: The gut microbiota and metabolites exhibit significant alterations during lymph node metastasis in pancreatic cancer, especially Ruminococcus gnavus, Blautia wexlera, and tryptophan metabolites (3-ILA and 3-IA). Gut microbial and metabolite signatures may serve as potential non-invasive biomarkers for predicting LNM in pancreatic cancer. Further functional validation is required to determine whether and how the gut microbiota and metabolites may mediate lymph node metastasis.},
}
@article {pmid41459208,
year = {2025},
author = {Brenes-Guillén, L and Vidaurre-Barahona, D and Agüero, K and Ulloa, A and Zuñiga, Y and Alvarado, GE and Uribe-Lorío, L},
title = {Novel diversity of Anaerolineae and Tepidiformia recovered from metagenomes of thermal microbial mats in Costa Rica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1693256},
pmid = {41459208},
issn = {1664-302X},
abstract = {Tropical thermal and mineral springs are ideal for studying microbial life in extreme environments, their microbial diversity, and functional profiles. In this study, we investigated the abundance and genomic diversity of the phylum Chloroflexota in microbial mats from 33 thermal and acidic springs across Costa Rica using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Our results demonstrated that pH and temperature are the main environmental drivers shaping the abundance and diversity of Chloroflexota. Acidic conditions favored the presence of Ktedonobacteria and the candidate division AD3, while thermal environments were dominated by unclassified Anaerolineae. From a subset of thermal springs, we reconstructed 72 metagenome-assembled genomes (MAGs), many of which represent previously uncharacterized lineages. Comparative genomic analyses revealed two novel families and seven new genera within Anaerolineae and a distinct lineage within Tepidiformia. We proposed the following names: Ca. Sittenfelaceae, Ca. Mariellaceae, and Ca. Tepidiforma platanarica. Functional annotation of Anaerolineae and Tepidiformia MAGs suggested a degree of functional redundancy. Genes associated with methanogenesis, dissimilatory nitrate reduction, sulfur metabolism, and methylotrophy were detected, while genes involved in photosynthesis, nitrogen fixation, and nitrification were absent. Unique gene clusters were identified in each family, and interestingly, 23% of these unique genes were of unknown function, highlighting the unexplored genetic potential of these organisms. Canonical correspondence analysis (CCA) revealed that temperature significantly influences the microdiversity of Anaerolineae. Despite their taxonomic novelty, these lineages exhibit strong functional redundancy across major metabolic pathways, where overlapping metabolic capabilities may confer stability under fluctuating conditions and support the persistence of diverse Chloroflexota populations. This study provides the first genomic dataset of Chloroflexota from Central American geothermal environments and highlights tropical geothermal springs as reservoirs of novel microbial diversity and functional potential.},
}
@article {pmid41459205,
year = {2025},
author = {Ng, C and Abrazaldo, J and de Vera, P and Goh, SG and Tan, B},
title = {Antibiotic Resistance in the Philippines: Environmental Reservoirs, Spillovers, and One-Health Research Gaps.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711400},
pmid = {41459205},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) remains a major health threat in the Philippines, where high antimicrobial use, intensive aquaculture, and recurrent typhoon-driven flooding and monsoon seasons shape distinctive transmission pathways. This narrative review synthesizes published Philippine data across clinical, agriculture, and environmental sectors to map evidence and gaps relevant to policy. Clinically, vancomycin resistant Enterococcus faecium is 23%, Klebsiella pneumonia shows ∼15% carbapenem resistance, and Escherichia coli resistance to third generation cephalosporins (3GC) and fluoroquinolone are ∼43 and ∼46%, respectively. In food animals, ceftriaxone resistance in non-typhoidal Salmonella (NTS) increased from ∼8% (2010) to ∼43% (2020s), with ciprofloxacin resistance between 14 and 23%. Environmental studies report extended spectrum beta-lactamase (ESBL)-producing E. coli in Manila estuaries and multiple antibiotic resistance (MAR) indices of up to 0.15 in tributaries. Hospital sewage and nearby rivers have yielded carbapenemase-producing Enterobacterales (CPE) bearing bla NDM/bla KPC in clinically relevant lineages (e.g., E. coli CC10, K. pneumoniae ST147). Cross sector comparisons remain constrained by method heterogeneity and data gaps. To operationalize One-Health monitoring, we propose (i) a two window surveillance design: late dry baseline and 24-72 h post-storm flood pulses; and (ii) a two tier analytics model: Tier 1 HT-qPCR ARG/MGE panels at regional hubs for rapid screening, and Tier 2 metagenomics/isolate whole genome sequencing (WGS) at national hubs for source attribution and plasmid tracking. We translate these findings into a modular AMR risk assessment toolkit to prioritize surveillance and targeted interventions.},
}
@article {pmid41459152,
year = {2025},
author = {Zhao, Z and Zhang, Y and Fu, J and Yu, L},
title = {Metagenomic next-generation sequencing for cryptococcal meningitis diagnosis: a single-center experience.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1626290},
pmid = {41459152},
issn = {2235-2988},
mesh = {Humans ; *Meningitis, Cryptococcal/diagnosis/microbiology/cerebrospinal fluid ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; *Cryptococcus/genetics/isolation &amp; purification ; Sensitivity and Specificity ; Aged ; Antigens, Fungal/cerebrospinal fluid ; Tertiary Care Centers ; *Molecular Diagnostic Techniques/methods ; },
abstract = {PURPOSE: Cryptococcal meningitis (CM) is a devastating central nervous system infection with substantial mortality, particularly when diagnosis is delayed. This study aims to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for CM detection in comparison with conventional tests.<br><br>METHODS: We enrolled 23 consecutive patients with suspected CM at a tertiary center. All patients met a composite reference standard (CRS) based on CSF cryptococcal antigen (CrAg), CSF/sterile-site culture for Cryptococcus, or CNS histopathology; mNGS was excluded from the CRS. Primary outcomes were CRS-based sensitivity (computed only among CRS-positive patients who underwent each assay) and turnaround times (TATs); pairwise agreement metrics (PPA/NPA) between mNGS and conventional assays were estimated in co-tested subsets.<br><br>RESULTS: mNGS identified Cryptococcus in 18/23 (78.3%) cases and detected viral co-pathogens (EBV/CMV/HIV-1) in 5 patients. CRS-based sensitivities were: CrAg LFA (CSF) 83.3% (5/6), Alcian blue 72.7% (16/22), India ink 50.0% (3/6), and CSF culture 66.7% (8/12). Pairwise agreement favored mNGS against culture and CrAg (e.g., PPA 100% vs culture 8/8] and vs CSF CrAg [5/5]), with limited NPA where denominators were small. Median (IQR) TATs were 0.5 (0.5-0.5) days for CrAg LFA, 1 (0.5-1) day for India ink, 5 (3-8) days for first positive culture, and 2 (1-4) days for mNGS.<br><br>CONCLUSION: CSF mNGS complements CrAg, microscopy, and culture by increasing Cryptococcus detection and revealing mixed infections, with particular utility in atypical, pretreated, or complex hosts. Larger studies are warranted to validate clinical utility and define optimal integration with existing workflows.},
}
@article {pmid41459151,
year = {2025},
author = {Dai, L and Mao, L and Shi, W and Ndjekadom, A and Wang, X and Liu, Y and Yang, S and Ji, L and Wang, J and Ma, J and Zhang, W and Shen, Q},
title = {A circovirus-like genomic sequence with unique architecture and phylogenetic relatedness to human-linked viral lineages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1698076},
pmid = {41459151},
issn = {2235-2988},
mesh = {*Phylogeny ; *Circovirus/genetics/classification/isolation &amp; purification ; Animals ; Swine ; *Genome, Viral ; *Circoviridae Infections/virology/veterinary ; Humans ; China ; *Swine Diseases/virology ; Open Reading Frames ; Feces/virology ; Whole Genome Sequencing ; DNA, Viral/genetics ; Macaca mulatta ; Genomics ; Sequence Analysis, DNA ; },
abstract = {Circoviruses are small viruses in the Circoviridae family that associate with a wide spectrum of disease from asymptomatic to lethal in different animal. In the current study, a novel swine-origin circovirus with unique genomic architecture was determined from both oropharyngeal swabs and fecal samples collected from febrile pigs in Jiangsu Province, China. The complete genome sequence of this novel porcine circovirus strain (named as PCV-CH-ZJ01) was determined to be 2544 nt in length, containing four major open reading frames: Rep1, 498-833 nt, 112 aa; Rep2, 1055-1546 nt, 164 aa; Cap1, 1756-2055 nt, 100 aa; Cap2, 2089-2529 nt, 147 aa. Comparative sequence analysis revealed differential conservation patterns across viral components and shared low amino acid similarity with other strains on the whole. Phylogenetic trees based the whole genome and amino acid of two Reps revealed that PCV-CH-ZJ01 belonged to circovirus and clustered with human and rhesus macaque circovirus strains, which raised the concerns of potential cross-species transmission between swine and human.},
}
@article {pmid41459106,
year = {2025},
author = {Wróbel, M and Gawryś, R and Tereba, A and Frąk, M and Sikora, K and Sokołowski, K and Boczoń, A},
title = {Dependence of Bacterial OTUs on Selected Features of Beaver Ponds.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72790},
pmid = {41459106},
issn = {2045-7758},
abstract = {Ponds created by beavers represent unique aquatic ecosystems that influence hydrological, chemical and biological conditions, including the microbiology of the water. The activity of these animals promotes biodiversity and water purification processes, but can also lead to the accumulation of pollutants. Water retention in beaver ponds promotes the development of bacteria and other microorganisms that play an important role in biogeochemical cycles. Long-term water stagnation can lead to anaerobic conditions and the formation of toxic compounds, which in turn can limit the diversity of benthic organisms. Beavers play a key role in shaping these habitats, and microbiological studies of their reservoirs provide a better understanding of their impact on aquatic ecosystems, self-purification processes and potential biological threats. Metagenomic analysis revealed the presence of 365 bacterial species in water and sediment samples, belonging to 174 genera and 83 families. 83 operational taxonomic units (OTUs) were identified, 62 of which were present in both water and sediments. Although the overall OTU composition was similar in both environments, greater variability was observed in the sediments. The statistical differences in OTU distribution between water and sediments were confirmed using the Wilcoxon test.},
}
@article {pmid41459044,
year = {2025},
author = {Wu, X and Shao, T and Huang, Y and Cui, X and Luo, Y and Ji, Q and Hu, Z and Teng, S and Bao, G and Liu, Y},
title = {Effects of dietary nisin supplementation on the growth performance, serum biochemistry, digestive enzyme activities, intestinal morphology, and intestinal microbiota in rabbits.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1726365},
pmid = {41459044},
issn = {2297-1769},
abstract = {INTRODUCTION: This study evaluated the impact of dietary supplementation with varying doses of nisin (NI) on the growth performance, serum biochemical parameters, intestinal digestive enzyme activity, short-chain fatty acid (SCFA) profiles, mucosal morphology, and the cecal microbiota composition in rabbits.<br><br>METHODS: Healthy female New Zealand white rabbits (5 weeks old; n = 90) of comparable body weight were randomly allocated to five groups: a positive control (PC) group receiving a basal diet supplemented with kitasamycin (300 mg/kg), three NI groups supplemented with nisin at 600 (NI600), 800 (NI800), or 1,000 (NI1000) mg/kg, and a negative control (NC) group receiving the basal diet without additives. Each treatment was comprised of three replicates (n = 6 per replicate), and the trial lasted 42 days.<br><br>RESULTS: The results showed that the rabbits administered NI displayed significantly enhanced final body weights as compared to the NC group (P < 0.05), with a dose-dependent effect. Notably, the NI800 and NI1000 groups exhibited a superior average daily gain (ADG) and average daily feed intake (ADFI). Serum analyses showed improved lipid profiles and elevated antioxidant enzyme activities concomitant with reduced lipid peroxidation in the NI-supplemented groups. Enzymatic assays indicated elevated duodenal a-amylase activity in the NI800 group as compared to the PC (P < 0.05) and enhanced ileal trypsin activity in the NI800 as compared to NI1000 and PC (P < 0.05). Histological evaluation confirmed that the NI800 group displayed optimal intestinal villi morphology, characterized by increased density, height, and structural integrity relative to the PC and NC controls. Metagenomic analysis of the cecal microbiota further revealed dose-dependent shifts in the diversity and composition of the microbiota, with the NI800 group exhibiting pronounced restructuring. Enriched functional pathways in the NI groups, including cofactor/vitamin metabolism, amino acid biosynthesis, energy homeostasis, and environmental adaptation.<br><br>DISCUSSION: Collectively, these findings highlight that NI supplementation enhances digestive efficiency, augments systemic antioxidant defenses, fortifies intestinal barrier function, and modulates microbial ecology and SCFA production, there by promoting growth and metabolic health in rabbits. Nisin, especially at 800 mg/kg, demonstrates significant potential as an antibiotic alternative.},
}
@article {pmid41458691,
year = {2025},
author = {Gopep, NS and Odukale-Okuneye, AO and Osanakpo, IM and Ugwu, HC and Amure, OO and Khan, KA and Obaisi, OG and Akueme, NT and Akinboboye, AC and Nwankwor, I and Nwodo, CN},
title = {Association Between Gut Microbiota Diversity and Body Mass Index (BMI) in Healthy Young Adults in the United States: Insights Into the Gut-Brain-Metabolic Axis Using the Curated Metagenomic Data.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97746},
pmid = {41458691},
issn = {2168-8184},
abstract = {BACKGROUND: Emerging evidence suggests that gut microbiota diversity plays a critical role in metabolic regulation and may influence body mass index (BMI). However, findings in healthy populations remain inconsistent.<br><br>OBJECTIVE: This study aims to determine whether gut microbiota alpha-diversity is associated with BMI among healthy young adults aged 18-39 years in the United States&#xa0;and to explore potential implications for the gut-brain-metabolic axis.<br><br>METHODS: This cross-sectional study utilized publicly available metagenomic data from the CuratedMetagenomicData repository. After preprocessing in R version 4.5.0 (R Foundation for Statistical Computing, Vienna, Austria), data were analyzed using Stata version 18 (Released 2023; StataCorp LLC, College Station, TX). Alpha-diversity indices (Shannon, Simpson, and Richness) were computed and examined across BMI categories (normal, overweight, and obese) using one-way analysis of variance (ANOVA) and chi-square tests. Linear regression models were employed to assess associations between BMI and diversity measures, adjusting for age and gender.<br><br>RESULTS: Among 147 participants, BMI differed significantly across weight categories (p < 0.001), but no significant association was observed between Shannon diversity and BMI (p = 0.527). Age emerged as the only significant predictor of BMI in adjusted models (p < 0.001).<br><br>CONCLUSION: Gut microbial alpha-diversity was not significantly associated with BMI among healthy young adults. Functional microbial characteristics, rather than diversity alone, may better explain variations in metabolic status.},
}
@article {pmid41458320,
year = {2025},
author = {Ghiotto, G and Francescato, L and Biancalani, MA and Treu, L and Campanaro, S},
title = {Hydrogen excess drives metabolic reprogramming and viral dynamics in syngas-converting microbiomes.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100637},
pmid = {41458320},
issn = {2666-4984},
abstract = {Microbial communities drive essential bioprocesses, including the conversion of synthesis gas into biomethane, a sustainable energy source that supports circular carbon economies. In anaerobic environments, specialized consortia of bacteria and archaea facilitate syngas methanation through syntrophic interactions, where hydrogenotrophic methanogens play a central role in reducing carbon dioxide and monoxide with hydrogen. However, imbalances in gas ratios, particularly excess hydrogen, can disrupt these interactions and impair overall efficiency. Yet, the molecular mechanisms underlying microbial responses to such imbalances remain poorly understood. Here we show that hydrogen excess triggers profound metabolic and viral remodeling in a thermophilic anaerobic microbiome, leading to reduced methane yields and ecological instability. This reprogramming involves transcriptional downregulation of methanogenesis genes in the dominant archaeon Methanothermobacter thermautotrophicus, coupled with upregulation of CRISPR-Cas and restriction-modification systems that correlate with diminished activity of an associated phage, indicating activated host defenses against viral threats. Concurrently, bacterial species such as those from Tepidanaerobacteraceae enhance carbon fixation via the Wood-Ljungdahl pathway, serving as electron sinks to mitigate redox imbalance. These adaptive responses highlight the microbiome's resilience mechanisms under stress, revealing viruses as both stressors and selective forces in syntrophic systems. Such insights advance our understanding of microbiome dynamics in bioconversion processes and guide the engineering of more stable microbial consortia for optimized syngas-to-methane conversion amid variable feedstocks.},
}
@article {pmid41457546,
year = {2025},
author = {Han, X and Shao, X and Chen, H and Dai, Y and Cheng, J and Jiang, H},
title = {[P450Diff2: a diffusion model-based method for generating P450 enzyme sequences].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {12},
pages = {4734-4744},
doi = {10.13345/j.cjb.250282},
pmid = {41457546},
issn = {1872-2075},
mesh = {*Cytochrome P-450 Enzyme System/genetics/chemistry ; Amino Acid Sequence ; Diffusion ; Algorithms ; },
abstract = {Cytochrome P450 enzymes constitute the largest superfamily of oxidoreductases in nature, playing pivotal roles in drug metabolism, plant secondary metabolism, and biotransformation of environmental pollutants. To generate artificial P450 enzyme sequences with high fidelity and diversity, we propose P450Diff2, a novel diffusion model-based approach for generating P450 enzyme sequences. Built upon the EvoDiff-Seq framework comprising 640 million parameters, P450Diff2 was trained on a comprehensive dataset of 1 041 254 non-redundant P450 protein sequences collected from NCBI, GMind annotations, RNA-Seq assemblies, and metagenomic databases. Evaluation of the generated sequences revealed that P450Diff2 outperformed the previously proposed P450Diffusion model across multiple metrics, including amino acid composition distribution, sequence feature space coverage, sequence similarity profiles, and structural plausibility. Notably, the generated sequences achieved an average pLDDT score of 72.29. Experimental results further demonstrate that 60% of the generated sequences can correctly fold into biologically active P450 enzymes, indicating that the proposed method not only effectively preserves the structural features of natural sequences but also exhibits strong potential for functional sequence generation. By integrating large-scale sequence generation and screening workflows, this approach holds promise for the rapid design of efficient novel enzymes while significantly reducing the time and cost of experimental validation, offering a valuable and scalable paradigm for de novo enzyme engineering.},
}
@article {pmid41457488,
year = {2025},
author = {Li, J and Quan, Q and Chen, J and Jian, X and Zhan, W and Wang, J and Jiang, R},
title = {The Application Value of Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Moderate-to-Severe Bronchiectasis.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70156},
doi = {10.1002/jcla.70156},
pmid = {41457488},
issn = {1098-2825},
abstract = {BACKGROUND: Bronchiectasis, a leading chronic airway disease, often worsens due to infections, making rapid pathogen detection crucial. This study aims to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in identifying pathogens in moderate-to-severe bronchiectasis and compare its advantages to conventional methods.<br><br>METHODS: Fifty-two hospitalized patients initially diagnosed with moderate-to-severe bronchiectasis at Foshan Hospital of Traditional Chinese Medicine from May 2022 to March 2024 were enrolled. Clinical data and BALF samples were collected and subjected to both mNGS and conventional pathogen detection methods. The differences and concordance in pathogen distribution between mNGS and conventional methods, as well as their diagnostic performance, were compared.<br><br>RESULTS: The positive detection rate of pathogens by mNGS was significantly higher than that by conventional methods (p&#x2009;<&#x2009;0.01). Both methods predominantly identified bacterial pathogens, with Pseudomonas aeruginosa being the most common bacterium and Aspergillus fumigatus the most frequent fungus. However, mNGS detected a broader range of pathogens and demonstrated superior sensitivity in identifying mixed infections (p&#x2009;<&#x2009;0.01). The sensitivity of mNGS was 66% higher than that of conventional methods (p&#x2009;<&#x2009;0.01), and the complete concordance rate between the two methods in double-positive cases was 41.18%. Additionally, mNGS-guided anti-infection treatment significantly improves patient symptoms, reduces hospital stays, and lowers costs (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Compared with conventional methods, BALF mNGS demonstrates higher sensitivity, a greater positive detection rate, superior capability in identifying mixed infections, improved diagnostic performance, and a better guiding effect on anti-infection treatment in moderate-to-severe bronchiectasis.},
}
@article {pmid41457319,
year = {2025},
author = {Smith, DDN and Subasinghe, RM and Kehoe, C and Grégoire, DS},
title = {Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198425},
doi = {10.1128/aem.01984-25},
pmid = {41457319},
issn = {1098-5336},
abstract = {UNLABELLED: Microbial consortia show promise for bioremediation of environmental pollution, but performance optimization and risk assessment remain challenging due to unculturable species and limitations of traditional biochemical and sequencing tools. This study demonstrates how a multi-omics approach can provide deeper insight into the performance and risks of using a model aerobic ammonia-oxidizing consortium under conditions representative of wastewater treatment. Long-read DNA sequencing recovered several high-quality genomes, revealing dominance by an unclassified Nitrosospira species with expected ammonia oxidation capabilities. Lower-abundance taxa with nitrogen cycling potential were also detected, though species-level identification was limited by poor taxonomic database representation. Multi-omics and nitrogen analyses showed shifts in community composition and nitrogen cycling activity when the consortium was grown along a redox gradient typical of wastewater. All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter. The dominant Nitrosospira population declined in abundance and activity in aerobic cultures while shifting toward nitrogen reduction under anoxic conditions. This metabolic shift would not have been detected using amplicon sequencing alone. Multi-omics also supported risk assessment through detection of waterborne pathogens from the Legionella genus and other lineages harboring virulence genes resembling those from known pathogens. This study highlights the value of multi-omics for optimizing microbial consortia and assessing biosafety risks but also underscores challenges related to effective data analyses and the feasibility of risk assessment under realistic conditions. Addressing these challenges will be essential to support the broader adoption of multi-omics strategies by stakeholders working with microbial consortia across diverse environmental applications.<br><br>IMPORTANCE: Microbial consortia are increasingly used to advance a sustainable bioeconomy. Optimizing consortia for environmental applications and ensuring regulatory compliance remains challenging, largely due to reliance on culturing microbes with unknown physiology. In this study, we apply cutting-edge sequencing to a consortium designed for ammonia removal from wastewater. Long-read DNA sequencing enabled complete genome recovery and revealed that populations integral to nitrogen cycling are poorly represented in taxonomic databases. By integrating multi-omics with biochemical assays, we uncovered how environmental conditions drive off-target nitrogen reactions and the potential risks of exposure to pathogens carrying virulence genes. Our findings underscore how whole-community approaches provide insights that are not obtainable with traditional amplicon sequencing and biochemical analysis methods. However, our study also provides recommendations on how hurdles related to data integration and environmental representation must be addressed to support stakeholders adopting such approaches in the context of commercializing microbial consortia.},
}
@article {pmid41457274,
year = {2025},
author = {Catry, A and Abrouk, D and Fierling, N and Mendoza, AIS and Rey, M and Vesga, P and Heiman, CM and Garrido-Sanz, D and Bouffaud, ML and Buscot, F and Giongo, A and Smalla, K and Comte, G and Keel, C and Muller, D and Moënne-Loccoz, Y},
title = {Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03911-0},
pmid = {41457274},
issn = {1474-760X},
support = {BiodivERsA3 ERA-Net SuppressSOIL//Biodiversa+/ ; grant SuppressSOIL no. ANR19-EBI3-0007//Agence Nationale de la Recherche/ ; grant SuppressSOIL no. 31BD30_186540//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
abstract = {BACKGROUND: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant-microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.<br><br>RESULTS: Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.<br><br>CONCLUSIONS: Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.},
}
@article {pmid41457271,
year = {2025},
author = {Sakr, EAE and Mansour, NM and Sabaa, HM and El-Khatib, KM and Khater, DZ},
title = {Biodegradation potential of used motor oil by mixed bacterial community: optimization, emulsification activity, bioelectrochemical and metagenomics analyses using single chamber microbial fuel cell.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-025-02889-5},
pmid = {41457271},
issn = {1475-2859},
abstract = {BACKGROUND: Used motor oil (UMO) is a dangerous environmental pollutant that needs to be treated effectively. This work introduces a novel approach for producing bioelectricity and UMO biodegradation simultaneously in a single-chamber microbial fuel cell (SCMFC) using native mixed bacterial cultures.<br><br>RESULTS: Under certain conditions (2% oil, 1% peptone, 4% inoculum, 21 days), the optimized bacterial culture degraded UMO by about 80%. Through bioelectrochemical studies, a maximum voltage of 257 mV and a power density of 36.6 mW/m&#xb2; were demonstrated, showing a strong correlation between UMO removal and electricity generation. Moreover, metagenomic data showed that Firmicutes, particularly Bacillus, dominated the biofilm at roughly 65%. Fourier Transform Infrared (FTIR) and Gas Chromatography-Mass Spectroscopy (GC-MS) verified the breakdown of complex hydrocarbon molecules, highlighting their crucial role in UMO biodegradation and bioenergy production. The effective elimination of UMOs and simultaneous power generation, supported by metagenomic and biochemical tests, showed the microbial activity and hydrocarbon breakdown.<br><br>CONCLUSIONS: The results suggest SCMFC technology as a sustainable solution for managing petroleum waste while producing renewable energy.},
}
@article {pmid41457176,
year = {2025},
author = {Paul, D and Talukdar, D and Kapuganti, RS and Gupta, V and Narendrakumar, L and Jana, P and Kumar, P and Singh, J and Kumari, S and Basak, C and Kamboj, K and Bakshi, S and Lal, S and Tanwar, S and Kumar, R and Babele, P and Bajpai, M and Kumar, Y and Mutreja, A and Mandal, S and Wadhwa, N and Banerjee, SK and Das, B},
title = {Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68034-3},
pmid = {41457176},
issn = {2041-1723},
support = {RAD/22017/19/2022-KGD-DBT//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; GCI-13012/2/2025-GCl//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.},
}
@article {pmid41457077,
year = {2025},
author = {Peng, L and Chen, JW and Chen, YZ and Di, XP and Lin, LD and Li, BY and Zhang, C and Wang, W and Gao, XS and Ma, YC and Shen, SH and Li, HR and Xu, XF and Zeng, X and Shen, H and Sun, Q and Jin, T and Luo, DY},
title = {Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68060-1},
pmid = {41457077},
issn = {2041-1723},
support = {82422015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82270720//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400904//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82500827//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M752250//China Postdoctoral Science Foundation/ ; 2025T180613//China Postdoctoral Science Foundation/ ; },
abstract = {Hunner-type interstitial cystitis/bladder pain syndrome (HIC) is a debilitating condition defined by bladder pain and urinary urgency, yet its upstream drivers remain poorly understood. To identify upstream mechanisms that exacerbate urothelial injury, here we apply an integrative multi-omics framework combining metagenomic sequencing, targeted metabolomics of urine and serum, and single-cell RNA sequencing. This approach reveals a microbial signature enriched in Enterococcus avium and a marked alteration in bile acid metabolism, including increased taurochenodeoxycholic acid (TCDCA). Single-cell analysis indicates that these changes converge on Toll-like receptor 3 (TLR3) activation in urothelial cells. Further validations show that a microbiota-bile acid-TLR3 axis disrupts epithelial barrier integrity and triggers inflammatory responses in experimental models. Transplantation and metabolite administration confirm the causal role of E. avium and TCDCA, while TLR3 inhibition ameliorates injury. These findings uncover an upstream pathway linking gut-derived metabolites to bladder pathology and suggest opportunities for biomarker development and targeted therapies for HIC.},
}
@article {pmid41456824,
year = {2025},
author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W},
title = {Elucidating the Therapeutic Mechanism of Orthosiphon aristatus in Hyperuricemic Nephropathy: An Integrated Microbiome-Metabolomics Approach.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121115},
doi = {10.1016/j.jep.2025.121115},
pmid = {41456824},
issn = {1872-7573},
abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.<br><br>AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.<br><br>METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750 mg/kg) and uric acid (300 mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25 g/kg/day), using allopurinol (5 mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&amp;E and Masson's trichrome staining), immunohistochemistry (&#x3b1;-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.<br><br>RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p < 0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p < 0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p < 0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p < 0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.<br><br>CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.},
}
@article {pmid41456766,
year = {2025},
author = {Wang, L and Qian, J and Zheng, Q and Yang, L and Jiang, J and Wang, J and Ying, H and Qin, J},
title = {Metagenomic Next-Generation Sequencing in Suspected Septic Arthritis: A Critical Appraisal of Clinical Utility in 82 Cases.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108352},
doi = {10.1016/j.ijid.2025.108352},
pmid = {41456766},
issn = {1878-3511},
abstract = {OBJECTIVES: To evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) compared to conventional culture in patients with suspected septic arthritis, stratified by synovial fluid white blood cell (WBC) count.<br><br>METHODS: A retrospective observational study was conducted on 82 consecutive patients with clinically suspected septic arthritis. Patients were categorized based on actual clinical testing pathways: complete triple testing (routine analysis, culture, and mNGS; n=54), culture and mNGS only (n=27), or mNGS only (n=1). Detection rates, turnaround times, and clinical impact were analyzed across WBC strata.<br><br>RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (65.9% vs. 33.3%, p < 0.001). This diagnostic advantage was most pronounced in the diagnostically challenging subgroup of patients with synovial fluid white blood cell count <25,000/&#x3bc;L, where mNGS had a significantly higher pathogen detection rate than culture (50.0% [19/38] vs. 23.7% [9/38]; p < 0.05). Among the 27 patients positive by both methods, mNGS revealed discrepant or additional findings in 9 cases (33.3%), including viruses, fungi, and fastidious bacteria, which required clinical adjudication. The median reporting time was shorter for mNGS than culture (67 vs. 86 hours, p < 0.001). Clinical management was guided solely by mNGS in 23 patients (28.0%), including 21 culture-negative cases and 2 where mNGS results preceded culture.<br><br>CONCLUSION: mNGS provides significant diagnostic value in suspected septic arthritis, particularly in culture-negative cases and those with low synovial fluid WBC counts. It should be used selectively as an adjunct to culture, which remains essential for antimicrobial susceptibility testing.},
}
@article {pmid41456694,
year = {2025},
author = {Ning, Z and Zhang, J and Cao, R and Kou, Y and Zhong, W and Huang, Y and Qin, X and Zhu, C},
title = {Substrate-structure-oriented product prediction framework unlocking short-chain fatty acids profiles during anaerobic fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133889},
doi = {10.1016/j.biortech.2025.133889},
pmid = {41456694},
issn = {1873-2976},
abstract = {Anaerobic fermentation experiments using 16 pure substrates, integrated with metagenomic analyses, were conducted to investigate the association between substrate molecular structure and short-chain fatty acids (SCFAs) production profile. Substrate chemical properties were found to govern microbial community selection, metabolic pathway activation, and SCFAs profile, thereby enabling the development of a substrate-structure-oriented product prediction framework (SSOPPF). The six-carbon backbone and abundant hydroxyl groups of monosaccharides favored near-equal acetate and butyrate production. The three-carbon skeleton of glycerinum specifically drove propionate synthesis (49%). The carbon skeletons of amino acids determined product specificity; for example, branched-chain isoleucine yielded 83 % isovalerate, whereas aspartate, characterized by a succinate-like backbone, produced 69 % propionate. Amino acids simultaneously acted as acid precursors and endogenous pH buffers. This study advances beyond coarse predictions based on broad substrate classifications by preliminarily establishing a causal link from molecular structural features to product spectra, pending validation in complex fermentation systems.},
}
@article {pmid41456586,
year = {2025},
author = {Du, Z and Wang, J and Kong, Y and Peng, M and Zhang, Y and Lu, H and Qu, D and Zhang, F and Peng, Y},
title = {Mainstream anammox achieved in a two-stage acidophilic partial-nitrification/anammox system: Ultra-high enrichment of anammox bacteria and identification of a potential novel acidophilic ammonia-oxidizing bacterium.},
journal = {Water research},
volume = {291},
number = {},
pages = {125218},
doi = {10.1016/j.watres.2025.125218},
pmid = {41456586},
issn = {1879-2448},
abstract = {Acidophilic partial nitrification (PN) is a promising approach to ensure a stable nitrite supply for anaerobic ammonium oxidation (anammox). Integrated acidophilic PN-anammox (PN/A) facilitates sustainable nitrogen removal. However, managing the acidic environment created by acidophilic PN process and controlling its detrimental effects on anammox remain critical technical challenges. To elucidate the key mechanism of acidophilic PN/A, a two-stage system was operated for 332 days to treat actual municipal wastewater. The acidophilic PN system, synergistically driven by a potential novel acidophilic ammonia-oxidizing bacterium (MAG187, 0.72%) and Nitrosomonas (0.94%), achieved 97.72% nitrite accumulation, accompanied by a decrease in effluent pH to 5.86. Although the acidic environment severely impaired anammox within 17 days, mixing the acidic effluent with municipal wastewater restored and enhanced anammox activity. Remarkably, ultra-high enrichment of Candidatus Brocadia (23.22%) was achieved, which has rarely been observed in actual municipal wastewater treatment. The metagenome-assembled genome analysis revealed Brocadia sapporoensis as the dominant anammox bacteria in the anammox system (TPM abundance=281,225). The findings provide crucial insights into the application of anammox in mainstream treatment and demonstrate an effective approach that transforms the inherent challenges of acidophilic PN into opportunities.},
}
@article {pmid41456557,
year = {2025},
author = {Li, Y and Chen, Y and Du, Z and Guo, Y and Zhang, W and Xu, X and Liu, Z and Duan, H and Duan, X and Zhang, A and Zhou, A and Li, X and Makinia, J},
title = {Oriented butyrate production through a novel bacteria-yeast microbiome: batch verification, key electron donor identification, and long-term validation.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133892},
doi = {10.1016/j.biortech.2025.133892},
pmid = {41456557},
issn = {1873-2976},
abstract = {Recovering butyrate from organic waste enables its high-value conversion, aligning with the principles of a circular economy. Traditional butyrate fermentation emphasizes carbohydrates and protein degradation, with limited focus on chain elongation (CE). This study, for the first time, systematically evaluated the effects of different Saccharomyces cerevisiae (SC) concentrations (1, 2, 4, 6, and 8 g/L) on ethanol production (a key electron donor) and subsequent CE for butyrate synthesis, identifying 2 g/L as the optimal SC dosage. At this concentration, butyrate production reached 15.41 ± 2.84 g COD/L, which was 2.72 times higher than that of the blank. Metabolic pathway analysis revealed that yeast not only enhanced substrate degradation (＞90 %) but also facilitated the in situ generation and utilization of ethanol. 16S rRNA indicated 54.10 % relative abundance of butyrate-producing bacteria (Clostridium). Long-term tests found that adding SC reversed the halt in production from prolonged distiller yeast inoculum, stabilising output at 15 g COD/L. Metagenomic analysis revealed that SC inoculation primarily enriched Clostridium luticellarii and Clostridium tyrobutyricum. In addition to raising reverse β-oxidation gene abundance, this treatment also enhanced lactate utilization genes, thereby strengthening acetyl-CoA to butyrate conversion. Through further experiments involving different electron donor ratios and long-term operation, this study highlights the critical role of yeast-bacteria synergy in enhancing butyrate synthesis, providing a theoretical foundation and technical strategy for food waste valorization in line with circular economy principles.},
}
@article {pmid41455737,
year = {2025},
author = {Li, C and Yin, W and Pan, Y and Hu, H},
title = {Interactions with bacteria shape diatom adaptation to carbon concentration changes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68050-3},
pmid = {41455737},
issn = {2041-1723},
abstract = {Diatoms are key contributors to global primary production, and have developed intricate partnerships with bacteria through long-term co-evolution. Here, we uncover a syntrophic relationship between the model obligate photoautotroph diatom Phaeodactylum tricornutum and the rod-shaped bacterium Loktanella vestfoldensis, which enables the diatom to indirectly utilize glucose. To be specific, growth of the diatom depends on the support of L. vestfoldensis for the supply of necessary carbon source when glucose serves as the sole carbon source, while L. vestfoldensis shows dependence on P. tricornutum when CO2 is the sole carbon source. Reanalysis of Tara Oceans metagenomic data shows frequent co-occurrence of Loktanella with diatoms including Chaetoceros and Thalassiosira, indicating the ecological relevance of this partnership. Co-culture with L. vestfoldensis supports robust growth of Chaetoceros muelleri and Thalassiosira pseudonana in the presence of glucose as the sole carbon source. Transcriptomic and metabolomic analyses reveal that P. tricornutum maintains a photoautotrophic metabolism in co-culture, as indicated by the up-regulation of genes involved in inorganic carbon concentration and photosynthesis, while the co-cultured bacterium likely supplies CO2 and growth-stimulating metabolites such as indole-3-acetic acid. Our findings demonstrate that bacterial-algal interactions may shape diatom adaptation to carbon changes and contribute to marine carbon cycling.},
}
@article {pmid41455576,
year = {2025},
author = {Kitagawa, H and Kajihara, T and Yahara, K and Kitamura, N and Shigemoto, N and Doi, H and Shimbara, K and Yoshimura, K and Nakashima, I and Uegami, S and Watadani, Y and Kawada-Matsuo, M and Komatsuzawa, H and Ohge, H and Sugai, M},
title = {Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.12.014},
pmid = {41455576},
issn = {2213-7173},
abstract = {BACKGROUND: The use of antibiotics may facilitate the colonisation of antimicrobial-resistant organisms and genes within the host microbiome. However, studies on the effects of antibiotics on microbiomes and resistomes in clinical settings are limited.<br><br>AIM: The aim of this study was to determine the effects of antibiotic prophylaxis during colorectal cancer surgery on the oral and gut microbiomes and resistomes of patients.<br><br>METHODS: We conducted a single-centre prospective observational cohort study on patients who underwent colorectal cancer surgery with antibiotic prophylaxis. DNA was extracted from oral and stool samples 1 day prior to the procedure and on postoperative days 1, 7, and 28. Subsequently, metagenomic sequencing was performed.<br><br>FINDINGS: Among the eight patients with colorectal cancer, &#x3b1;-diversity in the oral and stool samples significantly decreased from baseline to each of the three post-administration time points. The abundance of anaerobic genera significantly decreased from baseline to Day 7. In the stool samples, Enterococcus, Limosilactobacillus, and Lacticaseibacillus abundances were markedly increased. Total antibiotic resistance gene (ARG) abundance significantly increased from the baseline to Day 7 in both oral and stool samples. The impact of the increase observed on Day 7 decreased but still persisted until Day 28 for diversity and total abundance of ARGs.<br><br>CONCLUSIONS: Oral and gut microbiomes and resistomes exhibited marked alterations that gradually reversed over time. Changes in the microbiome were associated with the spectrum of antibiotics used.},
}
@article {pmid41455545,
year = {2025},
author = {Zhang, JS and Zhang, Y and Huang, S and Chu, CH and Jakubovics, NS and Yu, OY},
title = {High-Resolution Microbial Changes in Root Caries Revealed by Type IIB Restriction-site Associated DNA for Microbiome.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106319},
doi = {10.1016/j.jdent.2025.106319},
pmid = {41455545},
issn = {1879-176X},
abstract = {OBJECTIVES: This study aimed to characterize the species-level microbial and functional alterations in the dental biofilms associated with root caries leveraging the high-resolution sequencing.<br><br>METHODS: Twenty-five older adults with active root caries (Patients) and 31 older adults without untreated caries (Healthy controls) were enrolled. Site-specific supragingival plaque was collected from spatially-matched carious (CC) and caries-free (CH) root surfaces from patients, and from caries-free root surfaces of healthy controls (HH). Plaque samples were analysed using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M). Microbial diversity, species-level relative abundance, and predicted functional pathways were compared across groups using nonparametric tests.<br><br>RESULTS: No significant differences in overall microbial diversity were observed between groups. The microbial divergence between paired carious (CC) and caries-free (CH) root microbiota from patients was significantly greater than that between paired caries-free (HH) root microbiota in healthy controls. Several species showed increased abundance in CC microbiota compared to CH microbiota, with Propionibacterium acidifaciens, Prevotella multisaccharivorax, Mitsuokella sp000469545, and Parascardovia denticolens exhibiting the highest level of abundance difference. Predicted metagenomic analysis indicated that nine KEGG pathways, primarily involved in alternative carbohydrate metabolism, were positively associated with root caries status.<br><br>CONCLUSION: Within-subject comparison revealed a significant difference in microbiota between carious and caries-free root surfaces. These differences were characterized by shifts in specific species and their associated metabolic potentials, rather than by broad changes in community diversity.<br><br>CLINICAL SIGNIFICANCE: This study underscores the importance of tooth-level resolution in investigating the microbial etiology of root caries and revealed the species-level changes in carious root microbiota.},
}
@article {pmid41455317,
year = {2025},
author = {Caly-Simbou, E and Ramin-Mangata, S and Poussier, S and Pecrix, Y},
title = {Bacteriocins in plant pathology: current knowledge, application, challenges and perspectives.},
journal = {Biochemical and biophysical research communications},
volume = {797},
number = {},
pages = {153203},
doi = {10.1016/j.bbrc.2025.153203},
pmid = {41455317},
issn = {1090-2104},
abstract = {To address the growing emergence of multi-resistant phytopathogenic bacteria, innovative solutions are being explored in the field of plant health. Among them, bacteriocins, antimicrobial peptides or proteins secreted by bacteria, characterized by a highly specific spectrum of activity and involved in intra-specific competition, are gaining increasing interest. Bacteriocins can confer a positive selective advantage in both natural and agricultural environments, thereby contributing to microbiome modulation. Bacteriocin-producing rhizobacteria and lactic acid bacteria are already used as biocontrol agents against phytopathogenic bacteria, as well as plant growth stimulators. Bacteriocins can be produced in situ by using avirulent strains, or ex situ through industrial synthesis and applied as biopesticides. Nowadays, genetic engineering enables production of chimeric bacteriocins and their direct production in transgenic plants, avoiding the need for repeated treatments and limiting emergence of resistances. The selection of promising bacteriocins can be guided by omics-based approaches, notably metagenomics, which involve the direct extraction and sequencing of DNA from environmental samples and provides access to the genetic diversity in complex soil or plant-associated microbiomes. Combined with open-access databases and recently developed integrated tools, this approach not only facilitates the identification of known structures of bacteriocins, but also enables the prediction of potentially active peptides even those never experimentally characterized. Bacteriocin-based strategies, at the crossroads of molecular biology, microbial ecology and agronomy, hold significant potential for promoting sustainable agriculture through highly specific pathogen targeting. However, their large-scale implementation still faces several challenges, including standardization of strain screening protocols, compliance with regulatory frameworks and farmer acceptance.},
}
@article {pmid41455311,
year = {2025},
author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS},
title = {Harnessing methane proxies to understand and mitigate enteric emissions from ruminant production systems.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181258},
doi = {10.1016/j.scitotenv.2025.181258},
pmid = {41455311},
issn = {1879-1026},
abstract = {Methane emissions from livestock, particularly ruminants, significantly contribute to global warming, necessitating the development of accurate methane monitoring systems. Direct methane measurement is technically complex, time-consuming, labour-intensive, and costly. Recent advances in methane inhibitors, such as 3-nitrooxy propanol and halogenated analogues, plant secondary compounds, including polyphenols and essential oils, to reduce methane emissions have necessitated the discovery of processes underlying rumen methane synthesis and inhibition. The identification of methane proxies, such as behavioural and input proxies (dry matter intake, neutral detergent fibre), microbial community proxies (rumen metagenome profiles), metabolic pathway proxies (fatty acids), molecular and genetic proxies (microbial genes), and downstream and non-invasive proxies (milk fatty acids and faecal lipidomes), is leading to more viable solutions. New developments in 'omic' techniques, including lipidomics, metagenomics and metatranscriptomics, have enabled the detection of proxies at the molecular level utilising rumen liquor, milk, blood, urine, and faeces. In addition to traditional methane proxies, rumen microbiota profiles, and specific genes involved in rumen methanogenesis (such as mcr and mrt, which encode methyl coenzyme reductase 1 and 2), these markers can be used to identify methane-producing pathways. Protozoa-associated methanogens (PAMs), propionate-producing bacteria, and methane-oxidising methanotrophs (Methylocystis sp.) are emerging as new proxies. Methane proxies provide scalable, affordable, and mechanistically insightful alternatives to conventional direct measuring techniques, which improve the understanding of rumen function and the biological causes of methane releases, enabling large-scale methane monitoring and will enable designing effective methane mitigation strategies in livestock production systems.},
}
@article {pmid41455196,
year = {2025},
author = {Xia, R and Zhang, L and Li, G and Luo, W and Xu, Z},
title = {A small technology for big health: Blocking the potential spread of antibiotic resistomes from home composting of food waste by mature compost.},
journal = {Waste management (New York, N.Y.)},
volume = {211},
number = {},
pages = {115312},
doi = {10.1016/j.wasman.2025.115312},
pmid = {41455196},
issn = {1879-2456},
abstract = {Home composting is a popular lifestyle for onsite treatment and recycling of food and garden wastes, but potentially spreads antimicrobial resistance to affect human health. Thus, the dynamics of antibiotic resistomes during home composting and their control by mature compost were investigated. Results show that the relative abundance of antibiotic resistance genes (ARGs) decreased significantly at thermophilic stage and then increased at cooling stage. Integrative and conjugative elements (ICEs) located on chromosomes and mobilizable plasmids reduced at thermophilic stage to restrain horizontal gene transfer (HGT) events and relative abundance of ARG. Nevertheless, HGT events were driven by mobile genetic elements (MGEs) on chromosomes to rebound in relative abundance of ARG at cooling and mature stages. Mature compost could improve the control of antibiotic resistomes by reducing ARG and MGE hosts and blocking their HGT events. Specifically, mature compost significantly accelerated microbial metabolisms and increased composting temperature to sterilize ARG hosts and thus vertical gene transfer events during thermophilic stage. Thus, the rebound in relative abundance of ARG was effectively inhibited to increase their overall removal by 8.3% - 14.9%, particularly for high-risk ones. These results propose a simple but pragmatic strategy to mitigate significant antimicrobial resistance risks from home composting to safeguard environmental and public health.},
}
@article {pmid41455002,
year = {2025},
author = {Karim, F and Lin, Q and Xie, H and Nargis, S and Xiao, H and Yang, S and Xiong, Y and Xie, M and Ni, Q and Yao, Y and Xu, H},
title = {Seasonal dynamics of gut microbiota in rhesus macaques (Macaca mulatta) from western Sichuan Plateau and their adaptability to high altitude climate change.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {99},
pmid = {41455002},
issn = {1432-0991},
support = {31870355//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; Seasons ; Altitude ; Feces/microbiology ; *Climate Change ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; },
abstract = {Seasonal fluctuations in diet and climate shape animal gut microbiota, especially those living in extreme climatic conditions. Yet their role in facilitating primate adaptation to high-altitude remains unclear. This study investigates the seasonal dynamics in gut microbiome of wild rhesus macaques (Macaca mulatta) from high altitude (over 3,000 m) in Yajiang couke. We collected 117 fecal samples across four seasons and analyzed using 16S rRNA high-throughput sequencing combined with predictive functional metagenomics. We observed clear seasonal shifts in gut microbial diversity and composition. High α-diversity in autumn and winter reflected increased dietary diversity during these periods. Firmicutes predominated in summer, while Bacteroidota increased during winter. LEfSe analysis revealed seasonal specific taxa: UCG-005, Christensenellaceae R-7, and Prevotella_9 were dominated in winter but declined in summer and spring, whereas Blautia peaked during summer and decreased toward winter. Redundancy analysis showed that temperature, humidity, and precipitation were positively associated with Blautia and Sarcina, but negatively with Monoglobus and Helicobacter, underscoring the strong influence of climatic variables on gut community structure. Functional predictions revealed seasonal differences in gut microbiota related to energy metabolism (spring), glycan biosynthesis (summer), membrane transport (autumn), and environmental adaptation (winter) indicating microbial contributions to host adaptation under fluctuating climatic conditions. These findings demonstrate that gut microbiome of high-altitude macaques is highly responsive to changes in seasonal diet and climate. By integrating microbiome dynamics with climatic drivers, our study provides new insights into host-microbe-environment interactions and advances our understanding of primate adaptation under extreme climatic conditions.},
}
@article {pmid41454990,
year = {2025},
author = {Tang, CJ and Su, Y and Ma, Y and Guan, H and Wang, W and Yang, ZH and Zhai, K and Feng, F and Tang, X},
title = {Moisture regulation induced nitrite-mediated Fe(II) oxidation for cadmium immobilization in paddy soils.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {2},
pages = {71},
pmid = {41454990},
issn = {1573-2983},
support = {U21A20294//National Natural Science Foundation of China/ ; 2024QK3001//Major Technology Innovation Projects of Hunan Province/ ; 52121004//Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {*Cadmium/chemistry/metabolism ; Oxidation-Reduction ; *Soil Pollutants/chemistry/metabolism ; *Nitrites/chemistry/metabolism ; Soil Microbiology ; *Soil/chemistry ; *Ferrous Compounds/chemistry/metabolism ; Bacteria/metabolism/genetics ; Oryza ; Water/chemistry ; *Iron/chemistry ; },
abstract = {Cadmium (Cd) contamination in paddy soils poses significant risks to human health and food security, while traditional remediation methods may cause secondary pollution through external amendments. Nitrite oxidized Fe(II) to lepidocrocite and goethite, which immobilized Cd through adsorption and structural incorporation, effectively decreasing Cd mobility. Building on this mechanistic insight, a moisture regulation strategy was applied to enhance nitrite accumulation in paddy soil, and its role in Fe(II) oxidation for Cd immobilization was investigated. Metagenomic analysis identified nitrogen transformation pathways, showing that nitrite accumulation was limited by a higher abundance of ammonia-oxidizing bacteria (AOB, 19.2%) compared to nitrite-oxidizing bacteria (NOB, 11.7%), and predominance of nitrite consumption pathways. Maintaining 50% soil moisture selectively enhanced AOB activity while suppressing NOB, resulting in nitrite accumulation up to 9.56 mg/kg after 90 days incubation, reducing bioavailable Cd from 35 to 16% and increasing residual Cd from 7 to 48%. This study is original in integrating moisture regulation with microbial nitrogen cycling to enhance nitrite accumulation, thereby promoting Fe(II) oxidation and Cd immobilization. It provides a sustainable and chemical-free strategy for Cd management in paddy soils.},
}
@article {pmid41454580,
year = {2026},
author = {Xu, H and Zhou, H and Zhou, N and Jiang, X and Pei, Q and Huang, S and Xiong, T and Liu, Z},
title = {Exploration of the Core Microorganisms and Mechanisms of Biogenic Amine Production During PDM Fermentations.},
journal = {Journal of food science},
volume = {91},
number = {1},
pages = {e70784},
doi = {10.1111/1750-3841.70784},
pmid = {41454580},
issn = {1750-3841},
support = {32260576//National Natural Science Foundation of China/ ; 20232BBF60024//Jiangxi Provincial KeyR&amp;D Program/ ; 202401AS070025//Yunnan Fundamental Research Projects/ ; },
mesh = {*Fermentation ; *Biogenic Amines/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Putrescine/metabolism ; Cadaverine/metabolism ; Food Microbiology ; Metabolic Networks and Pathways ; Metabolomics ; },
abstract = {Pickled and dried mustard (PDM) is a traditional Chinese ingredient. Research is currently focused on detecting its flavor substances and exploring production methods. However, the microbial metabolic pathways of biogenic amines (BAs), a significant hazardous substance, remain to be elucidated. We elucidated the dynamics of BAs and their metabolic pathways during PDM fermentation by means of metabolomics and macro genomics analysis. The main BAs identified were putrescine and cadaverine. Metagenomic analysis revealed key active microorganisms in BA metabolism within PDM, including Pseudomonas, Pseudoalteromonas, Psychrobacter, Oceanisphaera, Halomonas, Glutamicibacter, Levilactobacillus, Vibrio, Idiomarina, and Enterobacteriaceae. In conclusion, the results obtained have enhanced the comprehension of the mechanism of BA formation during the fermentation of PDM. Moreover, they have facilitated the development of fermenters capable of degrading BAs in industrial PDM production.},
}
@article {pmid41454247,
year = {2025},
author = {Liu, S and Mao, N and Du, E and Deng, Z and Zhang, S and Zhang, H and Fan, M and Chen, J and Yin, H and Zheng, Y and Sun, H and Yang, F and Xie, Y},
title = {Effects of different additives and chopping lengths on the biosafety of Sophora Davidii silage.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04580-6},
pmid = {41454247},
issn = {1471-2180},
support = {CCPTZX2023B07//2023 National Grassland Technology Innovation Center (Under Construction) Major Innovation Platform Construction Special Fund/ ; Qian Ke He Platform Talent - BQW[2024]003//the Guizhou Provincial Science and Technology Plan Project/ ; QN[2025]076//Guizhou Provincial Basic Research Program (Natural Science)/ ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) represent growing threats to global public health. Sophora davidii silage is a common feed in livestock production, may potentially serve as a reservoir and vector for the dissemination of these genetic determinants. The biosafety risks associated with Sophora davidii silage remain poorly evaluated. Consequently, mitigating these risks through improved processing techniques has become an urgent priority. This study systematically elucidates the effects of additives and chopping lengths on the microbial community structure, ARGs, MGEs, and VFs during the ensiling of Sophora davidii.<br><br>RESULTS: Metagenomic analyses demonstrated that both additives and chopping length significantly influenced the biosafety profile of Sophora davidii silage. Additives markedly reduced the abundance of ARGs, MGEs, and VFs (P&#x2009;<&#x2009;0.05). Formic acid (FA) demonstrated the most pronounced suppression, whereas cellulase (CE) was least effective. Notably, although inoculation with Lactiplantibacillus plantarum (LP) reduced the overall abundance of these risk factors, the strain may be associated with the vanY gene in the vanB cluster, mobile genetic elements (MGEs) such as ISLpl1 and ISLp1, as well as specific virulence factors (VFs). Furthermore, at a 5&#xa0;cm chopping length, the Control group exhibited significantly higher levels of ARGs and VFs compared to the 1&#xa0;cm and 3&#xa0;cm treatments (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: The findings highlight the efficacy of reducing chopping length (to 1&#xa0;cm) in controlling the proliferation and dissemination of ARGs, MGEs, and VFs. Moreover, the use of direct acidifying agents, particularly formic acid, offers considerable advantages in enhancing the microbial safety of silage.},
}
@article {pmid41454237,
year = {2025},
author = {Wu, X and Zhang, H and Wu, M and Zhou, K and Liao, Y and Liu, F and Zheng, Q},
title = {Severe paediatric scrub typhus with complications: a case report and literature review.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-025-06435-5},
pmid = {41454237},
issn = {1471-2431},
abstract = {This case report documents a rare case of scrub typhus with multiple serious complications in a 8-year-old patient. Scrub typhus is usually more prevalent in adults, but serious complications in children are uncommon. This report examines a severe pediatric case involving septic shock, acute respiratory distress syndrome (ARDS), and hemophagocytic lymphohistiocytosis (HLH). The patient initially presented with erythema of the umbilicus, which then progressed to characteristic crusting with high fever, hepatosplenomegaly, and enlarged lymph nodes. Metagenomic next-generation sequencing (mNGS) confirmed the presence of Scrub typhus in the patient's blood sample. Notably, this is the first case of scrub typhus found in lung using mNGS, providing strong evidence for early detection. Treatment included a combination of antibiotics, particularly doxycycline and rifampicin, as well as supportive measures such as invasive mechanical ventilation, plasma exchange, continuous renal replacement therapy (CRRT) and chemotherapy. With this comprehensive treatment approach, the patient's condition gradually improved and he was eventually discharged with complete recovery. This case emphasizes the importance of timely and accurate diagnosis and multidisciplinary supportive care in the treatment of severe scrub typhus in children.},
}
@article {pmid41454225,
year = {2025},
author = {Domić, J and Grootswagers, P and Pinckaers, PJ and Groenendijk, I and Rubert, J and van Loon, LJ and de Groot, LC},
title = {The effect of a vegan diet with or without resistance exercise on thigh muscle volume in older adults. Research protocol of the Vold-study: a 12-week randomized controlled trial.},
journal = {BMC geriatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12877-025-06708-9},
pmid = {41454225},
issn = {1471-2318},
support = {162135//Regio Deal Foodvalley/ ; 162135//Regio Deal Foodvalley/ ; 162135//Regio Deal Foodvalley/ ; 162135//Regio Deal Foodvalley/ ; },
abstract = {BACKGROUND: Plant-based diets are increasingly adopted. Plant-based foods exhibit a lower protein quantity and quality compared to animal-based foods. As such, a fully plant-based, i.e. vegan, diet may be suboptimal for the maintenance of skeletal muscle mass later in life. The primary objectives of this study protocol are therefore: (1) To assess the effect of a 12-week self-composed vegan diet in comparison to an omnivorous diet on thigh muscle volume in community-dwelling older adults; and (2) To assess the effect of a 12-week self-composed vegan diet combined with twice-weekly resistance exercise (RE) on thigh muscle volume in comparison to a vegan diet without RE in community-dwelling older adults.<br><br>METHODS: Seventy-two community-dwelling individuals aged&#x2009;&#x2265;&#x2009;65 years with a BMI between 23 and 32&#xa0;kg/m[2] will be included in this randomized controlled trial. Eligible participants will be randomly allocated to either follow their habitual omnivorous diet, a self-composed vegan diet, or a self-composed vegan diet combined with two sessions of RE per week for 12 weeks. Participants will be guided through monthly nutrition information meetings. Dietary intake and physical activity levels will be assessed using food records and accelerometery. The primary study outcome will be thigh muscle volume, assessed at baseline and after 12 weeks using magnetic resonance imaging (MRI). Secondary outcomes will be: body composition, muscle fat infiltration, muscle strength, bone mineral density, bone turnover markers, metabolic profile, insulin levels, cobalamin, iron and vitamin D status, hs-CRP, gut metabolomics and metagenomics, gastro-intestinal symptoms and dietary intake. Measurements will take place at baseline, after 6 weeks, and after 12 weeks. Additionally, mixed muscle protein synthesis rates will be assessed during the first ten days of the intervention using a deuterium oxide protocol. Data will be analysed using independent t-tests and linear mixed models.<br><br>DISCUSSION: The results will provide valuable insights regarding the implications of consuming a vegan diet later in life for skeletal muscle and other health outcomes, and may contribute to the substantiation of the envisaged more plant-based dietary guidelines.<br><br>TRIAL REGISTRATION: The trial is registered at clinicaltrials.gov (NCT05809466; registered on 22 February 2023).},
}
@article {pmid41454222,
year = {2025},
author = {Li, J and Sun, Z and Chai, S and Li, H and Wang, Y and Tian, J},
title = {AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-025-06357-0},
pmid = {41454222},
issn = {1471-2105},
support = {No.GZY-ZJ-SY-2303//Zhejiang Province Traditional Chinese Medicine Key Laboratory Project/ ; },
abstract = {Advances in metagenomic sequencing have increasingly implicated gut microbiome dysbiosis in numerous complex diseases, yet its application for precise differential diagnosis remains a major challenge. Existing computational approaches often show limited predictive performance and insufficient robustness when applied to large-scale, imbalanced microbiome datasets, and they typically lack mechanisms to effectively capture microbial community-level or functional guild interactions. To address these limitations, we developed AR-CDT Net, a novel deep learning framework that integrates a Multi-Scale Deformable Convolution (MS-DConv) module with a Channel-wise Dynamic Tanh (CD-Tanh) activation function to achieve more accurate and robust classification of host disease states. Evaluated on a large-scale cohort comprising over 8000 samples spanning eight disease phenotypes, AR-CDT Net demonstrated highly competitive within-cohort performance, outperforming nine representative models across the majority of classification tasks. Importantly, in a stringent cross-dataset generalization test, the model was trained on the highly imbalanced primary multi-disease cohort and validated on relatively balanced independent external cohorts. It achieved a statistically significant AUC of 0.7921 on the highly heterogeneous external T2D cohort, confirming that AR-CDT captures transferable biological signals rather than dataset-specific artifacts. Furthermore, by combining dimensionality reduction with SHAP-based interpretation of our One-vs-Rest (OvR) classifiers, AR-CDT disentangles disease-specific pathogenic signatures from the shared dysbiotic background among clinically distinct yet microbially similar diseases.},
}
@article {pmid41454163,
year = {2025},
author = {Bovio-Winkler, P and Orellana, E and Campanaro, S and de Jesús Montoya-Rosales, J and Fuess, LT and Carrillo-Reyes, J and Castelló, E and Muñoz-Páez, KM and Moreno-Andrade, I and Buitrón, G and Razo-Flores, E and Etchebehere, C},
title = {Unraveling the biological mechanisms of biohydrogen production through dark fermentation using assembled genomes from metagenomic data.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41454163},
issn = {1615-7605},
support = {project A1-S-37174//Fondo Sectorial SEP-CONACYT/ ; },
abstract = {Dark fermentation represents a sustainable and promising approach for biohydrogen generation. However, achieving high yields depends on understanding the complex microbial interactions driving the process. This study used genome-centric metagenomics to analyze microbial communities from 11 hydrogen-producing reactors. In total, 44 metagenome-assembled genomes (MAGs) were analyzed in detail. High-yield reactors demonstrated a strong synergy between hydrogen-producing bacteria (HPB) and lactic acid bacteria (LAB), particularly Clostridium butyricum and Clostridium beijerinckii. These species encode the electron-transferring flavoprotein-lactate dehydrogenase complex (EtfAB-ldh complex), enabling hydrogen production from lactic acid. In contrast, reactors with lower hydrogen yields exhibited a higher prevalence of hydrogenotrophic microorganisms, including homoacetogens and methanogens, which redirected electron flow toward competing pathways, thereby decreasing hydrogen output. These results emphasize the importance of promoting HPB while suppressing hydrogen consumers to maintain an optimal microbial community. By linking community composition with metabolic potential, this study provides a framework for improving reactor performance, increasing hydrogen yields, and advancing sustainable hydrogen production from organic waste streams.},
}
@article {pmid41453903,
year = {2025},
author = {Lin, Z and Li, S and Liu, M and Li, J and Liu, F and Cao, J and Chen, S and Huang, K and Wang, Y and Li, H and Wang, Y and Yang, B and Xing, D and Wang, Q and Ji, X and Bai, X and Hu, D and Zhang, M and Guo, D and Huang, J and Geng, B and Gu, D and Lu, X},
title = {Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67513-x},
pmid = {41453903},
issn = {2041-1723},
support = {91857118//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 12126602//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt, and high-salt interventions. SSBP was assessed and used as the primary outcome, and fecal shotgun metagenome and plasma targeted metabolome were measured. We found that high salt significantly altered 85 gut-microbial species (p < 9.42 × 10[-5]) and 70 metabolites (p < 2.26 × 10[-4]). Among them, the changes in 22 species and 8 metabolites were associated with SSBP (p < 0.05), and a gut microbiota-acylcarnitine network implicated in SSBP was identified, with a gut microbiota-derived metabolite, isovalerylcarnitine, as the core metabolite. Isovalerylcarnitine was also inversely associated with SSBP in the GenSalt study (p = 0.0102). Importantly, increased isovalerylcarnitine attenuated SS hypertension and improved endothelial function in rats, and was associated with reduced risk (ranging from 13% to 19%) of BP progression and incident hypertension in a prospective cohort (n = 3907, median follow-up = 5.5 years). This study demonstrated that the gut-acylcarnitine axis may play roles in the development of SS hypertension. Trial number: ChiCTR1900025171.},
}
@article {pmid41453848,
year = {2025},
author = {Li, XL and Li, ZQ},
title = {Gut microbiota of economically important termites: functional convergence, harmfulness and precision control.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70490},
pmid = {41453848},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
abstract = {As typical social insects and key decomposers in ecosystems, termites, like other insects, harbor a complex array of microbial communities with diverse functions in their gut. These microorganisms are not only closely related to key survival aspects of termites, including nutritional acquisition, metabolic adaptation and colony resilience, but also play crucial roles in their ecological adaptability. This demonstrates that termite survival strategies are highly dependent on the synergistic interactions within their gut microbiota. Notably, some termites, such as Coptotermes formosanus, exhibit both decomposition ability and damaging capacity. Whether their gut microbiota is closely related to their destructive potential has become one of the core issues of concern to researchers. Moreover, with the rapid development of metagenomics and bioinformatics technologies in recent years, an increasing number of termite gut microbiota functions have been predicted and validated, making it possible to analyze their destructive capacity from a microbial perspective. Therefore, based on a systematic synthesis of the functional commonalities and mechanistic roles of gut microbiota in economically significant termite species, this review further highlights evidence linking microbial functions with termite damaging capacity and discusses microbiota-based strategies for precision control of pest termites. It aims to provide comprehensive references and a solid theoretical foundation for in-depth research and rational utilization of termite gut microbiota, as well as scientifically grounded and targeted management of destructive termite pests. © 2025 Society of Chemical Industry.},
}
@article {pmid41453533,
year = {2025},
author = {Guo, K and Li, D and Li, S and Zeng, H and Zhang, J},
title = {Enhanced synergistic interaction between AOA and anammox bacteria: a novel mechanism for stability under nitrite shock loading in PN-A systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133879},
doi = {10.1016/j.biortech.2025.133879},
pmid = {41453533},
issn = {1873-2976},
abstract = {Fluctuating ammonia concentrations in wastewater often exceed the adaptive capacity of ammonia-oxidizing archaea (AOA), thereby limiting the efficacy of partial nitritation/anammox (PN/A) systems that rely on AOA-driven nitritation. Although nitrite addition may enhance process stability, the underlying microbial mechanisms remain unclear. This study investigated the response of an AOA/anammox bacteria enriched counter-current biological aerated filter under low intermittent aeration to nitrite shock loading. At an NO2[-]-N concentration of 21.95 ± 1.36 mg/L and NH4[+]/NO2[-] ratio of 0.44 ± 0.027, the system achieved high nitrogen removal efficiencies: 99.10 ± 0.72 % for NH4[+]-N and 83.89 ± 0.35 % for total nitrogen. AOA were identified as the dominant nitrifiers via dual-inhibition, phylogenetic, and functional gene analyses. Metagenomics revealed upregulation of key functional genes, including AOA-associated nirK, anammox-related hzs/hzo/hdh, and denitrification genes nir/nap/nor/nos, enhancing AOA-anammox synergy. Copiotrophic AOA (93.49 % of AOA community, primarily Nitrososphaera and Nitrosocosmicus) and Candidatus Brocadia (35.95 % of bacteria) dominated the system. Genomic binning further revealed horizontal transfer of nap/nor genes between AOA and denitrifiers, reinforcing metabolic adaptability under selective conditions. Metabolic profiling indicated that AOA competitiveness under nutrient stress was reinforced by genes involved in nitrogen assimilation, urea utilization, polysaccharide synthesis and energy metabolism, thereby strengthening their partnership with anammox bacteria. These findings demonstrate that nitrite supplementation can reinforce AOA-based PN/A systems under variable ammonia loads, supporting energy-efficient mainstream wastewater treatment.},
}
@article {pmid41453532,
year = {2025},
author = {Liao, Q and Sun, L and Qin, X and Chen, M and Zhu, X and Yang, C and Li, RH},
title = {Ethanol utilization strategies in chain Elongation: insights from bio-iron systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133881},
doi = {10.1016/j.biortech.2025.133881},
pmid = {41453532},
issn = {1873-2976},
abstract = {Carbon chain elongation plays a pivotal role in biomass valorization by enabling the efficient conversion of organic substrates into higher-value biochemicals. Ethanol is a key substrate in chain elongation, yet how its oxidation reshapes carbon flux under complex electron transfer networks remains unclear. Based on an open-culture system, this study elucidates how iron species regulate ethanol oxidation. Metagenomic analysis revealed that iron acting as an electron acceptor (e.g., hematite, magnetite) enhanced electron transfer and iron respiration, while serving as an electron donor (e.g., iron powder) activated ethanol metabolism and promoted ATP generation to couple it with chain elongation pathways. These processes improved ethanol oxidation efficiency, redirected carbon flux toward acetate accumulation, and facilitated even-chain elongation of acetate. This study demonstrates an iron-regulated ethanol self-upgrading pathway with significant potential. However, in the presence of fermentation substrates, this phenomenon may reduce substrate conversion efficiency and alter product selectivity. To quantitatively characterize these processes, an integrated evaluation method for ethanol oxidation and self-upgrading was established, providing a robust analytical framework for related phenomena. Overall, this work uncovers the mechanism of bio-iron-mediated carbon flux reorganization and offers both theoretical and practical guidance for the development of advanced ethanol valorization systems and resource-efficient solid waste utilization strategies.},
}
@article {pmid41453043,
year = {2025},
author = {Yang, I and Hendler, K and Scannapieco, FA and Boykins, G and Wharton, W},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e103436},
doi = {10.1002/alz70856_103436},
pmid = {41453043},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/cerebrospinal fluid ; Female ; Male ; *Alzheimer Disease/cerebrospinal fluid ; Middle Aged ; *Microbiota ; *Periodontal Diseases/microbiology ; *Social Determinants of Health ; Aged ; Inflammation ; },
abstract = {BACKGROUND: Evidence suggest an association between periodontal disease (PerioD) and Alzheimer's disease (AD), with PerioD-associated microbial ecosystems driving oral and systemic inflammation that may activate or accelerate neuroinflammation, a hallmark of AD. Social determinants of health (SDoH) are critical factors influencing both oral health and AD risk yet are often overlooked, and rarely investigated together. This study aims to characterize and compare the oral microbiome of age- and education-matched individuals at high risk for AD by virtue of family history, with and without PerioD, and to investigate the relationships between PerioD-associated microbiome features, SDoH, systemic inflammation and brain inflammation, and AD biomarkers (in cerebrospinal fluid [CSF]).<br><br>METHOD: This two-year NINDS-funded study collects oral microbiome samples, blood, and CSF annually in a cognitively normal, racially diverse cohort (n&#xa0;=&#xa0;165). Metagenomic sequencing will be used to investigate cross-kingdom microbial communities and their association with inflammatory and systemic markers. Surveys and interviews investigate behaviors and SDoH influencing PerioD and AD risk.<br><br>RESULT: To date, 55 participants have been recruited. Participants are 62 years of age on average, predominantly white (70%), female (63.3%), with Stage 1-2 periodontitis (85.7%). Preliminary analyses found no significant relationships between bleeding on probing, behavioral factors, SDoH variables, and Montreal Cognitive Assessment (MoCA) scores, which was expected given the small sample size. As recruitment continues, we anticipate identifying associations between oral microbiome features, inflammatory markers, AD biomarkers and cognitive outcomes. SDoH, such as access to dental care and oral hygiene behaviors, may mediate these relationships, offering insights into the interplay between periodontal disease, systemic inflammation, and AD risk.<br><br>CONCLUSION: By leveraging longitudinal data and exploring upstream sociocultural factors, this research addresses critical gaps in understanding PerioD's contribution to AD risk. Findings will provide novel insights into the interplay between the oral microbiome, systemic inflammation, brain inflammation, and AD risk.},
}
@article {pmid41452584,
year = {2025},
author = {Li, M and Zhou, M and Gong, L and Zhu, J and Tan, H and Zhou, J and Yang, P and Wang, W},
title = {Effect of hydrothermal pretreatment on the biogas production performance of co-digestion of Chlorella and sludge.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10934529.2025.2607916},
pmid = {41452584},
issn = {1532-4117},
abstract = {To address growing energy demand and promote environmental sustainability, the development of diverse biomass-based renewable energy is crucial. Co-digestion of Chlorella and sludge has been recognized as an effective strategy to improve methane production efficiency from biomass. This study aimed to explore the optimal ratio of Chlorella and sludge. On this basis, hydrothermal pretreatment was applied to the Chlorella-sludge mixture to investigate the temperature effects on co-digestion performance. This step aimed to optimize methane yield and identify the most suitable pretreatment temperature. The anaerobic digestion kinetics were evaluated by fitting experimental data to both the Fitzhugh first-order kinetic model and the Modified Gompertz model. Additionally, metagenome sequencing was performed on samples before and after hydrothermal pretreatment to elucidate the impact of pretreatment on microbial community dynamics during the acidogenesis phase of anaerobic digestion. The experimental results demonstrated that a 20-day co-digestion period with a VS Chlorella to VS sludge ratio of 2:1 yielded the highest biogas production, reaching 250.98 mL/g VS. After 30 min of hydrothermal pretreatment at 180 °C, the co-digestion efficiency of Chlorella and sludge reached the optimal level, with a cumulative methane production of 261.02 mL/g VS, which had a significant impact on microbial diversity.},
}
@article {pmid41452254,
year = {2026},
author = {Pan, LH and Hu, WF and Fu, ZY and Yu, XC and Li, ZQ and Guo, MF and Wu, JW and Zhu, H},
title = {Yacon (Smallanthus sonchifolius) Root Increases Bowel Movement Frequency in Healthy Adults via Modulating Gut Microbiota and Intestinal Metabolites: A Pilot Study.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {1},
pages = {e70358},
doi = {10.1002/mnfr.70358},
pmid = {41452254},
issn = {1613-4133},
support = {TZKY2024RC01//Scientific Research Starting Foundation for High-level Talents of Taizhou School of Clinical Medicine, Nanjing Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Adult ; *Plant Roots/chemistry ; Male ; Female ; Middle Aged ; Young Adult ; *Intestines/microbiology/drug effects ; *Plant Extracts/pharmacology ; *Defecation/drug effects ; },
abstract = {Yacon root (YR) is a functional food that can increase bowel movement frequency, but with an unclear mechanism. In this study, a UPLC-Orbitrap-MS/MS system was employed to characterize the chemical composition of YR. Subsequently, a 10-day pilot intervention trial involving 11 healthy adults was conducted to evaluate the effects of YR on bowel movement frequency. Concurrently, the involved mechanisms were explored through metagenomic and metabolomic approaches. A total of 82 chemical components were identified in YR. Clinical trials indicated that continuous intake of YR significantly increased bowel movement frequency without noticeable adverse effects. Metagenomic analysis revealed that YR substantially increased the abundance of beneficial bacteria such as Bifidobacterium and inhibited the generation of potential pathogens, including Escherichia-Shigella, thereby promoting a more balanced and healthier gut microbiota structure. Metabolomic analysis indicated that YR significantly upregulated metabolites, including cholic acid, taurine, and amino acids, which mainly focus on the biosynthesis of primary bile acid and the metabolism of taurine and hypotaurine. In summary, YR can safely and effectively increase bowel movement frequency in healthy individuals. The mechanism may involve synergistic regulation of gut microbiota and metabolites, which offered new insights to support YR as a natural functional food for laxative effects.},
}
@article {pmid41452179,
year = {2025},
author = {Park, A and Koslicki, D},
title = {Elucidating Transitions of k-mer-Based Objects Across k-mer Sizes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15578666251401600},
pmid = {41452179},
issn = {1557-8666},
abstract = {The widespread adoption of k-mers in computational biology has enabled efficient methods for utilizing genomic sequences in a variety of biological tasks. However, understanding the influence of k-mer sizes within these methods remains a persistent challenge. Slicing sequences into a fixed size lacks grounding in biological insight, and complex bioinformatics pipelines obscure the effect of the parameter k due to various noisy factors. The choice of k-mer size is typically arbitrary, with justification omitted in both the literature and method tutorials. Furthermore, the lack of theoretical understanding has caused recent multi-k-mer approaches to face significant computational challenges. Nevertheless, most methods are built on well-defined objects related to k-mers, such as de Bruijn graphs, Jaccard similarity, Bray-Curtis dissimilarity, and k-mer spectra. The role of k-mer sizes within these objects is more intuitive and can be described by numerous quantities and metrics. Therefore, exploring these objects across k-mer sizes opens opportunities for robust analyses and new applications. However, the evolution of k-mer objects with respect to k-mer sizes is surprisingly elusive. We introduce a novel substring index, the Prokrustean graph, that elucidates the transformation of k-mer sets across k-mer sizes. Our framework built upon this index rapidly computes k-mer-based quantities for all k-mer sizes, with computational complexity independent of the size range and dependent only on maximal repeats. For example, counting unitigs (maximal simple paths) in de Bruijn graphs for k = 1, …, 100 is achieved in seconds using our index on a gigabase-scale dataset. We present a variety of algorithms for applications relevant to pangenomics and metagenomics. The Prokrustean graph is directly derived from the affix tree and can be constructed space-efficiently from the Burrows-Wheeler transform. This derivation grounded in modern substring indexes that are all theoretically based on longest common prefixes reveals that such extension-based substring representations inherently struggle to explore k-mer objects across different sizes, which motivated our data structure. Our implementation is available at: https://github.com/KoslickiLab/prokrustean.},
}
@article {pmid41452102,
year = {2025},
author = {Ragupathy, V and Kelley, K and Zhao, J and Mazo, I and Hewlett, I},
title = {Unbiased metagenomic exploration of transfusion-transmitted infections with nanopore sequencing.},
journal = {Transfusion},
volume = {},
number = {},
pages = {},
doi = {10.1111/trf.70051},
pmid = {41452102},
issn = {1537-2995},
support = {10.13039/100000038//Intramural Research Funding from the US Food and Drug Administration (FDA)/ ; },
abstract = {BACKGROUND: Despite advances in blood safety, emerging infectious agents continue to pose risks to the blood supply. Traditional nucleic acid testing assays primarily target known pathogens, limiting the detection of novel microbes. Nanopore metagenomic sequencing enables agnostic identification of diverse pathogens, potentially enhancing transfusion safety surveillance.<br><br>STUDY DESIGN AND METHODS: We assessed the analytical performance and limit of detection (LoD) of a nanopore MinION metagenomic sequencing workflow for pathogen detection in clinical plasma samples. DNA/RNA was extracted from 14 archived samples from individuals with confirmed infections (HIV, HBV, HCV, WNV), followed by cDNA synthesis, barcoded library preparation, and nanopore sequencing. Quantitative reference panels were tested, and data were analyzed using a comprehensive bioinformatics pipeline.<br><br>RESULTS: Metagenomic sequencing generated over 2 million reads, with 2.3% of reads mapping to microbial sequences. Key transfusion-transmissible viruses, including West Nile virus (WNV), HIV, and hepatitis C virus (HCV), were reliably detected, while protocol modifications enabled HBV identification. Strain-level characterization identified HIV-1 subtype B, HCV genotypes 1a, 2b, 4a, HBV genotype C, and WNV lineage 1A. High viral loads produced extensive genome coverage, while lower loads yielded limited recovery. Co-infections, including human pegivirus (HPgV-2) and torque teno virus (TTV), were identified. The workflow detected viral targets at 10[3] genome copy equivalents (GCEs)/mL, with >&#x2009;50% genome coverage achieved at 10[4] GCE/mL.<br><br>DISCUSSION: Nanopore metagenomic sequencing enables comprehensive detection of blood-borne pathogens in plasma samples. This approach offers a promising complementary strategy for enhancing transfusion safety surveillance, and the demonstrated strain-level characterization supports its potential utility for blood safety applications.},
}
@article {pmid41451983,
year = {2025},
author = {Fan, Y and Ju, T and Bhardwaj, T and Korver, DR and Willing, BP},
title = {Chicken cecal microbial functional gene content and resistome differ by age and barn disinfection practice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0373725},
doi = {10.1128/spectrum.03737-25},
pmid = {41451983},
issn = {2165-0497},
abstract = {Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Studies showed that disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functional gene content. The current study compared the effects of disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after two production cycles at seven barns. Shotgun metagenomic sequencing performed on cecal contents collected at days 7 and 30 also allowed the evaluation of age-associated characteristics of the microbiome. The age of the chickens had the largest effects on the resistome, with younger birds having higher relative abundance of total ARGs (P < 0.05) and differences in resistance mechanism; however, functional gene content and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically disinfected barns had decreased gene content related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically disinfected conditions (FDR-P < 0.05), suggesting the selection for stress resistance. Lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecal Helicobacter pullorum was observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P < 0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial gene function and resistome.IMPORTANCEThis is the first study to evaluate the effect of sanitation practices on microbial functional gene content and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.},
}
@article {pmid41451552,
year = {2025},
author = {Xu, F and Yang, K and Abass, OK and Su, JQ and Cui, L},
title = {Integrative Phenotypic and Genotypic Surveillance and Risk Assessment of Foodborne Antimicrobial Resistance in Meat-Environment Continuum.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12275},
pmid = {41451552},
issn = {1520-5851},
abstract = {Foodborne antimicrobial resistance (AMR) poses a significant One Health challenge. However, the risk and transmission of AMR within the meat-environment continuum remain poorly understood. Here, we conducted an integrative AMR surveillance of meats and associated environments from three markets using culture-independent single-cell Raman spectroscopy for phenotypic profiling and metagenomics for genotypic analysis. We found that environments consistently harbored a higher abundance of metabolically active antibiotic-resistant bacteria than meats. By incorporation of phenotypic AMR (abundance and activity of antibiotic-resistant bacteria), genotypic AMR (percentage of high-risk antibiotic resistance genes), and transmission potential, a new risk assessment framework was established. The integrated assessment revealed that environments were critical AMR reservoirs with risk levels higher than or comparable to those in meats, underscoring the necessity of integrating multiple factors for accurate risk assessment. Moreover, source tracking analysis suggested reciprocal cross-contamination between the samples, which was further confirmed by 25 shared metagenome-assembled genomes (MAGs) hosting high-risk ARGs among samples. By bridging phenomic and genomic insights, this work advances precision AMR surveillance and provides a more accurate risk assessment framework, offering critical guidance for mitigating AMR in the environment and the food chain.},
}
@article {pmid41451037,
year = {2025},
author = {Li, W and Yang, S and Yuan, K and Lu, H and Lin, T and Luo, Y and Xian, L and Shan, H and Zhang, J},
title = {Recurrent Talaromyces Marneffei Infection Revealing X-Linked Hyper IgM Syndrome in an HIV-Negative Infant: A Diagnostic and Therapeutic Challenge.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6757-6762},
pmid = {41451037},
issn = {1178-6973},
abstract = {Talaromyces marneffei (TM), a temperature-dependent dimorphic fungus and opportunistic pathogen, poses a significant threat to immunocompromised individuals, particularly in Southeast Asian regions such as China and India. This case report details an 8-month-old HIV negative Chinese infant with recurrent cough and fever, who was diagnosed with TM infection through blood culture and metagenomic next-generation sequencing (mNGS). Additionally, whole exome sequencing identified a point mutation (c.346+1G>T) in the child's CD40LG gene, primary immunodeficiency calized to chromosome position chrX:135736590, leading to X-linked Hyper IgM Syndrome (XHIGM). The patient was managed with intravenous immunoglobulin (IVIG) and a 12-day course of amphotericin B and itraconazole, which led to significant clinical improvement and discharge on a quarterly IVIG regimen. However, he required readmission for recurrent TM pneumonia at 9 and 40 months post-discharge. This case highlights the diagnostic challenge and management complexity of TM infection in the context of primary immunodeficiency.},
}
@article {pmid41450573,
year = {2025},
author = {Zhang, G and Zeng, L and Chen, B and Dai, H and Tang, K and Huang, R and Xiang, X and Yang, J and Yang, J and Song, X and Ma, Y and Lin, R and Huang, Y},
title = {Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1674341},
pmid = {41450573},
issn = {2235-2988},
mesh = {Humans ; *Bile/microbiology ; *Biliary Tract/microbiology ; Drainage/adverse effects ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Despite years of research, knowledge about the microbial populations of human physiological bile has remained limited. Bile sampling techniques, such as Endoscopic Retrograde Cholangiopancreatography (ERCP), percutaneous biliary drainage, and intra-operative sampling, are invasive procedures typically performed only in the presence or suspicion of biliary tract disease. Furthermore, the increased incidence of bacterial infections following biliary drainage poses a significant clinical concern; however, the relationship between biliary drainage and biliary flora remains poorly understood. In this study, we present a distinct taxonomic composition of bacterial communities identified in bile samples from disease-free individuals, as well as from obstructive and post-drainage biliary tracts.<br><br>METHODS: A metagenomic sequence analysis of bile samples from patients with MBO who underwent percutaneous biliary drainage (PTBD) at our center from 1st May 2021 to 1st March 2022, which were divided into 2 groups, as the MBO group (n = 29) and BD group (n = 27). Eight liver donors were included as a control group.<br><br>RESULTS: Abundant bacterial populations were detected in the bile of liver donors, revealing a highly similar microbial composition in both disease-free and malignant obstructive biliary trees. Notably, biliary drainage was found to alter the composition of bile microbiota, resulting in decreased microbial diversity and an association with an increase in antibiotic resistance genes.<br><br>DISCUSSION: These findings provide fundamental knowledge on the composition of the human bile microbiota and present new evidence to support that biliary drainage induces a shift in bile microbiota, rendering it more aggressive and resistant to antibiotics.},
}
@article {pmid41450342,
year = {2025},
author = {Liao, R and Zhang, L and Wang, D and Tan, N},
title = {Microscopic polyangiitis complicated with pulmonary hepatitis B virus infection: A case report and literature review.},
journal = {Infectious medicine},
volume = {4},
number = {4},
pages = {100218},
pmid = {41450342},
issn = {2772-431X},
abstract = {Microscopic polyangiitis (MPA) is a subtype of anti-neutrophil cytoplasmic antibody-associated vasculitis characterized by inflammatory changes in small vessel walls. Its clinical manifestations are nonspecific, and pulmonary involvement often presents as cough and production of sputum, which can be misdiagnosed as pneumonia. However, to the best of our knowledge, no cases of MPA coexisting with pulmonary hepatitis B virus (HBV) infection have been reported. This report describes the first such case. A 66-year-old man presented with a productive cough, swelling of the finger joints, and bilateral hearing loss. Initial imaging suggested pulmonary infection or malignancy. MPA was diagnosed based on positive myeloperoxidase-ANCA serology and vasculitic changes on histopathological examination of a lung biopsy specimen. Metagenomic next-generation sequencing of biopsy tissue revealed HBV, confirming a concurrent pulmonary HBV infection. Treatment with methylprednisolone, rituximab, and entecavir resulted in a favorable outcome.},
}
@article {pmid41448605,
year = {2025},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Johnson, S and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary Nitrate Intake and 16S rRNA-Inferred Nitrite-Generating Capacity of the Subgingival Microbiome May Influence Glucose Metabolism: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70084},
pmid = {41448605},
issn = {1600-051X},
support = {R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; DK-63608//Vagelos College of Physicians and Surgeons, Columbia University/ ; UL1TR001873/TR/NCATS NIH HHS/United States ; },
abstract = {AIMS: To investigate whether the association between the nitrite-generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake.<br><br>MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31&#x2009;&#xb1;&#x2009;9&#x2009;years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome-Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA-IR), blood pressure) on nitrate intake and MINES together with a MINES &#xd7; nitrate intake interaction term.<br><br>RESULTS: Mean nitrate intake was 190&#x2009;&#xb1;&#x2009;171&#x2009;mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p&#x2009;<&#x2009;0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA-IR (1.2 [1.1-1.4] vs. 1.5 [1.3-1.6]; p&#x2009;=&#x2009;0.002), but levels were similar in those with high MINES (p&#x2009;=&#x2009;0.84).<br><br>CONCLUSIONS: A biomarker of higher microbial NO-generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate-rich diets should incorporate measures of the entire oral microbiome.},
}
@article {pmid41448339,
year = {2025},
author = {Ghosh, S and Ganguly, A and Dong, TS and Lagishetty, V and Jacobs, JP and Devaskar, SU},
title = {Intestinal Microbiome in Response to Air Pollutant Exposure in Pregestational and Gestational Murine Females and their Male and Female Offspring.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {},
number = {},
pages = {109150},
doi = {10.1016/j.reprotox.2025.109150},
pmid = {41448339},
issn = {1873-1708},
abstract = {We investigated the impact of chronic air pollutant (AP) exposure upon intestinal microbial diversity, composition, and metagenomic inferred functional pathways in murine pregestational and late gestational adult females, and male and female postnatal offspring (P21), compared to age- and sex- matched controls (CON). Intestinal microbiome analysis was undertaken with certain phenotypic characteristics in adult non-pregnant and pregnant females and the male and female offspring. In response to AP, pooled male and female offspring displayed no difference in E19 fetal and P1 postnatal body weights. At P21, females exposed in-utero to AP were heavier with increased fat and muscle mass at one month versus CON. Males were no different at P21 and 1 month revealing decreased fat mass and hyperglycemia. In pregestational/gestational females, AP did not change microbial α- or β-diversity from the respective CON. Gestational females showed AP induced changes in taxonomic composition such as reduced Bacteroides and increased Firmicutes, Verrucomicrobia, and Akkermansia, among others. In response to intra-uterine AP exposure, the offspring intestinal microbiome revealed more compelling differences in α- and β- diversity than adult females. While certain microbial changes were common in both sexes, sex-specific differences also emerged with reduced α-diversity, decreased Bacteroides and increased Akkermansia in males only. The metagenomic inferred pathways revealed perturbations in multiple pathways. We conclude that the offspring exposed in-utero to AP revealed sex-specific changes in microbial diversity, composition and function, displaying certain similarities with distinct differences from mothers. These early life changes were associated with the subsequent emergence of pre-diabetes and adiposity.},
}
@article {pmid41448087,
year = {2025},
author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M},
title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140887},
doi = {10.1016/j.jhazmat.2025.140887},
pmid = {41448087},
issn = {1873-3336},
abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.},
}
@article {pmid41448010,
year = {2025},
author = {Chang, C and Ma, Y and Ye, S and Tang, X and Ren, M and Hu, E and Li, M},
title = {Network-scale spatiotemporal dynamics and drivers of nitrogen-cycling genes and their microbial hosts in a multi-tributary mountain river.},
journal = {Water research},
volume = {291},
number = {},
pages = {125211},
doi = {10.1016/j.watres.2025.125211},
pmid = {41448010},
issn = {1879-2448},
abstract = {Rivers are critical regulators of the global nitrogen (N) cycle, yet their microbial nitrogen-cycling dynamics and feedbacks to environmental change remain poorly understood at the river-network scale. Here, we combined systematic field sampling at 187 water-column sites spanning two mainstems and 22 tributaries of the upper Hanjiang River with shotgun metagenomics, metatranscriptomics and 30 environmental variables representing geography, climate, hydromorphology, land use, and water quality. Our results showed that nitrogen-cycling genes (NCGs) mediating six major pathways showed clear longitudinal differentiation along the cumulative dendritic distance upstream. Compared to small-river-network (SN), Large-river-network (LN) consistently exhibited higher abundances, diversity and expression of denitrification, DNRA, ANRA, ODAS, and N fixation genes, identifying LN as convergence zones for N transport and hotspots of N removal. By contrast, nitrification genes (amoA, nxrB, hao) and their hosts were scarce, with only a transient autumn increase in LN. We recovered 1508 medium- to high-quality NCG-hosting MAGs spanning a broad phylogenetic range but strongly skewed toward a few bacterial phyla. Pseudomonadota, Actinomycetota and Bacteroidota together accounted for ∼87% of total NCG-host abundance. Assembly- and MAG-based community analyses revealed a shift from low-diversity, Pseudomonadota-dominated assemblages in SN to diverse, high-evenness communities in LN. Along the SN-LN gradient, MAG co-occurrence networks became richer, denser and more modular, and keystone MAGs were disproportionately enriched in denitrification and DNRA genes, with nitrification genes rare among hubs. Water quality emerged as the dominant driver of NCGs and their hosts, explaining up to 47.3% of the variance, while geography and land use exerted pathway-specific influences through indirect effects mediated by hydromorphology and water quality. Metatranscriptomic norB/nosZ further revealed a nitrate tipping point at ∼0.8 mg L[-1], above which microbial N2O emission potential increased by an order of magnitude and formed spatially confined, seasonally shifting hotspots. Collectively, our results demonstrate that riverine nitrogen-cycling functions are structured by hierarchical multi-scale controls and that N2O emission potential responds nonlinearly to nitrate loading, with LN acting as critical integrators of SN inputs. These findings highlight the need for river-network-scale N management to enhance riverine self-purification while mitigating microbial N2O feedbacks arising from human activities.},
}
@article {pmid41447958,
year = {2025},
author = {Lee, Y and Liu, Q and Sun, Y and Maszczyk, P and Wang, M and Yang, Z and Lee, JS},
title = {Hypoxia and the microbiome: Significance and application for ecotoxicological studies.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119171},
doi = {10.1016/j.marpolbul.2025.119171},
pmid = {41447958},
issn = {1879-3363},
abstract = {Hypoxia, or low oxygen availability, is a growing environmental concern that significantly impacts microbial communities. Recent studies highlight the effects of hypoxia on microbial composition and function, favoring anaerobic taxa involved in nitrogen, sulfur, and carbon cycling. These shifts influence ecotoxicological processes by modulating pollutant degradation, metal bioavailability, and greenhouse gas emissions. For instance, oxygen depletion enhances the activity of anaerobic dechlorinators but may reduce heavy metal detoxification. Advances in metagenomics and multi-omics have offered new perspectives on microbial adaptation under hypoxic stress, revealing key metabolic pathways linked to pollutant transformation. However, knowledge gaps remain in our understanding of the long-term ecological consequences of hypoxia-induced microbiome shifts. This review synthesizes recent findings on hypoxia-microbiome interactions, focusing on both environmental (e.g., sediment and water column) and host-associated (e.g., gut) microbiomes, and emphasizes their application in ecotoxicology. In addition, we discuss how hypoxia-induced microbial shifts in hypoxic environments and highlight potential applications of microbiome-based approaches for environmental risk assessment. Future research integrating experimental and modeling approaches is crucial to better predict the ecological impacts of hypoxia-driven microbial changes in contaminated environments.},
}
@article {pmid41444534,
year = {2025},
author = {Wang, R and Shen, S and Zheng, T and Zhang, Y and Xu, W and Wu, J},
title = {Effective sequential therapy of linezolid and contezolid against HA-MRSA-induced necrotizing pneumonia in a 95-year-old patient with multimorbidity.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1738},
pmid = {41444534},
issn = {1471-2334},
support = {22KJA320003//the Major Natural Science Research Projects in Colleges and Universities of Jiangsu Province/ ; },
abstract = {BACKGROUND: Despite progress in new antibiotic development, active surveillance, and infection prevention, health care-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) remains a major pathogen; it continues to pose a high-risk threat, especially in extremely elderly patients with necrotizing pneumonia and multiorgan dysfunction on polypharmacy. Multimorbidity, immunosenescence, and frailty in the elderly increase the risk of adverse outcomes, severely restricting therapeutic options.<br><br>CASE PRESENTATION: We present the case of a long-term hospitalized 95-year-old woman with multimorbidity and multiorgan dysfunction who developed hospital-acquired necrotizing pneumonia due to MRSA. The diagnosis was established through metagenomic next-generation sequencing, bacterial culture of bronchoalveolar lavage fluid (BALF), and imaging. Linezolid was initially incorporated into the antimicrobial treatment regimen. After three weeks, owing to the bone marrow suppression caused by linezolid, contezolid (400&#xa0;mg PO every 12&#xa0;h) was adopted as an alternative therapy; this led to a significant reduction in the size of the lung cavity. Considering the cost-effectiveness and persistent risk of Pseudomonas aeruginosa and Elisabethia pacificus infection, as evidenced by the BALF culture results obtained at that time, the treatment was subsequently adjusted to oral linezolid combined with intravenous levofloxacin to achieve better infection control.<br><br>CONCLUSIONS: This case demonstrates the effectiveness of a sequential approach with a linezolid&#x2012;contezolid strategy for treating HA-MRSA-induced necrotizing pneumonia, leading to the regression of cavitary lesions and significant clinical improvement in elderly patients with multimorbidity, highlighting the importance of individualized treatment strategies in managing complex infections in vulnerable patient populations and offering valuable insights for future clinical practice.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12161-1.},
}
@article {pmid41447442,
year = {2025},
author = {Mishra, SP and Jain, S and Yadav, D and Buddendorff, L and Hoover, JP and Shukla, R and Kumar, V and Holland, P and Masternak, MM and Labyak, C and Williams, C and Golden, A and Agronin, M and , and Yadav, H},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e104153},
doi = {10.1002/alz70856_104153},
pmid = {41447442},
issn = {1552-5279},
mesh = {Humans ; Biomarkers/blood ; Male ; Female ; *Interleukin-6/blood ; Aged ; *Cognitive Dysfunction/blood/microbiology ; *Gastrointestinal Microbiome ; Inflammation/blood ; Cohort Studies ; Feces/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: The increasing prevalence of cognitive decline and dementia poses a significant public health challenge for older adults, and effective preventive and therapeutic strategies remain elusive. This is largely due to an incomplete understanding of the precise etiology and contributing factors underlying these conditions. Increased systemic inflammation is suspected to elevate the risk of dementia and cognitive decline, yet the causes of chronic inflammation remain poorly understood. Emerging evidence suggests that gut microbiome abnormalities are linked to increased inflammation and a higher risk of dementia. However, it remains unclear whether the rate of cognitive impairment differs with higher systemic inflammation and whether unique microbiome signatures are associated with inflamed cognitive decline and dementia.<br><br>METHOD: Using 165 samples from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort, systemic inflammatory marker interleukin-6 (IL-6) was measured in human plasma via ELISA. Cognitive function was assessed using the Montreal Cognitive Assessment (MoCA) questionnaire, and fecal microbiomes were analyzed through shotgun metagenomic sequencing. Subjects were grouped based on IL-6 levels (high and low) and cognitive status (normal cognition and cognitive impairment), and their corresponding microbiome signatures were analyzed.<br><br>RESULT: Interestingly, individuals with high IL-6 levels (IL-6[High]) exhibited over twice the prevalence of mild cognitive impairment (MCI) compared to those with low IL-6 levels (IL-6[Low]) (n&#xa0;=&#xa0;41 IL-6[High] vs. 18 IL-6[Low]). Older adults with low IL-6 and MCI displayed higher abundances of Bacteroides, Prevotella, Alistipes, Fusicatenibacter, and Parabacteroides, but lower levels of Lachnospira, Akkermansia, and Subdoligranulum compared to sex- and age-matched cognitively healthy controls with low IL-6. Conversely, those with high IL-6 and MCI exhibited higher abundances of Blautia, Prevotella, and Fusicatenibacter and lower abundances of Lachnospira, Akkermansia, and Subdoligranulum compared to IL-6[High] controls with normal cognition.<br><br>CONCLUSION: These findings reveal that butyrate-producing genera such as Lachnospira, Akkermansia, and Subdoligranulum are significantly reduced, while potentially pathogenic Fusicatenibacter and commensal Prevotella are elevated in individuals with MCI and high IL-6 levels. These distinct microbial profiles may serve as biomarkers for the early detection of cognitive decline in older adults, highlighting potential targets for therapeutic strategies to preserve brain health during aging.},
}
@article {pmid41447357,
year = {2025},
author = {Worachotsueptrakun, K},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e100663},
doi = {10.1002/alz70856_100663},
pmid = {41447357},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/blood ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Alzheimer Disease/blood ; Aged ; tau Proteins/blood ; Amyloid beta-Peptides/blood ; },
abstract = {BACKGROUND: The imbalance of microbial composition in the gut of elderly individuals can contribute to the development of Alzheimer's disease due to the bidirectional communication between the brain and the gut. Certain groups of gut bacteria can produce metabolites that are toxic to neurons, leading to inflammation and neuronal death in the central nervous system through various pathways. Diet plays a crucial role in influencing the composition of gut bacteria. Consuming prebiotic foods or dietary fibers from vegetables, fruits, and whole grains can stimulate the growth of bacteria that produce short-chain fatty acids or probiotic microorganisms.<br><br>METHOD: Patients who met the inclusion criteria were recruited for this study. Clinical conditions were assessed, and blood samples were collected to analyze the accumulation of abnormal beta-amyloid (as the ratio between 42/40), p-Tau 181, brain damage markers (neurofilament light chain [NFL] and glial fibrillary acidic protein [GFAP]), and APOE. Additionally, gut microbiome analysis was performed using amplicon-based metagenomic methods. The data analysis was conducted in correlation with clinical symptoms.<br><br>RESULT: To confirm the results from the discovery sample, participants were recruited for the study. Gut microbiome compositional analysis was performed on fresh stool samples collected from both the study group (n&#xa0;=&#xa0;40) and age- and sex-matched control participants (n&#xa0;=&#xa0;40). Microbiome features correlated with plasma phosphorylated tau 181 (p-tau181) and plasma neurofilament light chain (NFL), but not with APOE &#x3b5;3 or neurodegeneration biomarkers, suggesting that changes in the gut microbial community occur early in the disease process. Specific taxa and microbial pathways associated with preclinical Alzheimer's disease were identified.<br><br>CONCLUSION: These beneficial bacteria can produce anti-inflammatory metabolites and reduce the entry of neurotoxic metabolites into the system. Therefore, understanding the relationship between gut bacteria, prebiotics, and Alzheimer's disease could provide a preventative approach to reduce the risk of Alzheimer's disease caused by microbial imbalance in the elderly.},
}
@article {pmid41447103,
year = {2025},
author = {Shukla, R and Kumar, V and Yadav, D and Holland, P and Masternak, MM and Labyak, CA and Dangiolo, MB and Agronin, ME and , and Yadav, H and Jain, S},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e101631},
doi = {10.1002/alz70856_101631},
pmid = {41447103},
issn = {1552-5279},
mesh = {Humans ; Biomarkers ; Male ; Female ; Aged ; *Cognitive Dysfunction/microbiology ; Alzheimer Disease/microbiology ; *Microbiota ; *Dementia/microbiology ; Cohort Studies ; Metagenomics ; Aged, 80 and over ; Gastrointestinal Microbiome ; *Mouth/microbiology ; },
abstract = {BACKGROUND: Over recent decades, growing evidence has highlighted the pivotal role of the microbiome in Alzheimer's disease (AD) and dementia. Studies suggests the disruptions in the gut microbiome may contribute to cognitive impairment, but the association between the oral microbiome and cognitive impairment remains unclear. This study aims to characterize the oral microbiome and investigate its role in cognitive decline among elderly participants of MiaGB cohort.<br><br>METHOD: Whole-genome metagenomics sequencing was performed on 368 samples (Controls: 236, MCI: 107, and Dementia: 25) collected from the MiaGB (Microbiome in Aging Gut and Brain) consortium, a multi-site, clinical research study. The data was processed and analyzed using KneadData, MetaPhlAn, and HUMAnNnn tools.<br><br>RESULT: Taxonomic analysis revealed an increasing abundance of the genus Porphyromonas, and species Neisseria subflava, Neisseria sicca, and Streptococcus australis from controls to MCI to dementia participants. Random forest (RF) and LEfSe analysis identified significant increase in abundance of species N. subflava, Veillonella parvula, N. sicca, and Neisseria flavescens in MCI and dementia participants compared to controls. Additionally, Lautropia mirabilis, Eubacterium sulci, and Gemella sanguinis species were enriched in MCI compared to Controls and Dementia participants. Genera Porphyromonas are associated with cognitive impairment in other studies. Also, S. australis and V. parvula and Gemella sanguinis has been linked to neurodegenerative diseases and infective endocarditis. Distinct microbial profiles specific to each group could serve as biomarkers to identify the risk of cognitive impairment.<br><br>CONCLUSION: This study revealed a strong link between oral microbiome alterations and cognitive impairment. Further analysis will provide a more comprehensive understanding about the role of these microbes in cognitively impaired participants. These findings offer new insights into early biomarkers for cognitive impairment and the development of potential therapeutic approaches for the prevention and intervention of Alzheimer's disease (AD).},
}
@article {pmid41446276,
year = {2025},
author = {Chen, S and Jiang, Y and Lv, D and Zheng, Y and Zhang, R and Dai, H and Wang, Z and Li, S and Qi, R and Xu, H and Yu, Y and Xu, C and Lu, X and Xu, Y and Jin, S and Wu, X},
title = {Identification of subtypes and construction of a predictive model for novel subtypes in severe community-acquired pneumonia based on clinical metagenomics: a multicenter, retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1676502},
pmid = {41446276},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Community-Acquired Infections/microbiology/mortality/classification/diagnosis ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; China/epidemiology ; *Pneumonia/microbiology/classification/mortality ; Adult ; Microbiota/genetics ; Prognosis ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Intensive Care Units ; High-Throughput Nucleotide Sequencing ; Nomograms ; Community-Acquired Pneumonia ; },
abstract = {OBJECTIVE: It is well recognized that high heterogeneity represents a key driver of the elevated mortality in severe community-acquired pneumonia (sCAP). Precise subtype classification is therefore critical for both treatment strategy formulation and prognostic evaluation in this patient population. This study aimed to develop a predictive model for novel clinical subtypes of sCAP, leveraging microbiome profiles identified via metagenomic next-generation sequencing (mNGS).<br><br>METHODS: This retrospective multicenter cohort study enrolled adult patients with sCAP who underwent clinical mNGS testing of bronchoalveolar lavage fluid in intensive care units (ICUs) across 17 medical centers in China. Based on mNGS-identified microbiome characteristics, unsupervised machine learning (UML) was employed for clustering analysis of sCAP patients. LASSO regression and random forest (RF) algorithms were applied to screen and identify predictors of novel sCAP subtypes. A predictive model for the new clinical subtypes was constructed according to the screening results, with a nomogram generated. The discriminative ability, calibration, and clinical utility of the model were evaluated using ROC curves, calibration curves, and decision curve analysis, respectively.<br><br>RESULTS: A total of 1,051 sCAP patients were included in the final analysis. The 28-day all-cause mortality rate was 45% (473/1,051). UML clustering identified two distinct sCAP subtypes: the 28-day mortality rate was 42.19% (343/813) in subtype 1 and 54.62% (130/238) in subtype 2. Incorporating clinical and microbial features, a predictive model for the novel sCAP subtypes was developed using the following predictors: immunosuppression (OR = 37,411.46, P < 0.001), connective tissue disease (CTD) (OR = 12,144.60, P = 0.004), hematological malignancy (HM) (OR = 107,768.13, P < 0.001), chronic kidney disease (CKD) (OR = 49.71, P < 0.001), cytomegalovirus (CMV) (OR = 0.00, P < 0.001), Epstein-Barr virus (EBV) (OR = 131.97, P < 0.001), Pneumocystis (OR = 47,949.56, P < 0.001), and Klebsiella (OR = 0.02, P = 0.003). The model demonstrated excellent discriminative ability with an area under the ROC curve (AUC) of 0.992. Calibration curves showed good agreement between predicted and observed outcomes. Decision curve analysis confirmed high clinical utility for predicting novel sCAP subtypes.<br><br>CONCLUSION: This study identified novel clinical subtypes of sCAP based on mNGS-derived microbiome characteristics. This approach exhibits superior performance in identifying high-risk sCAP patients, facilitating precise subtyping.},
}
@article {pmid41445580,
year = {2025},
author = {Wang, H and Chen, Z and Qing, H and Huang, M and Xue, G and Lu, X and Che, Y and Dong, Y and Zhang, S and Yu, J and Song, P},
title = {Seasonal influence on the microbial diversity and flavor substances in the strong flavor Daqu fermentation.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100332},
pmid = {41445580},
issn = {2666-5662},
abstract = {Baijiu is highly dependent on open Daqu fermentation, which is easily affected by seasonal fluctuations. This study systematically analyzed winter (WID) and summer (SUD) strong flavor Daqu by integrating physicochemical analysis, microbial community detection, volatile component determination, and metabolomics technology. Results showed SUD had significantly higher starch consumption and acidity than WID, directly attributed to enhanced microbial activity and enzymatic efficiency. Metagenomic studies have identified key enzymes including α-amylase (EC:3.2.1.1) and carboxylic esterase (EC:3.1.1.1), as well as CAZy families such as GH65 and GH73. Based on this finding, the dominant microbes in SUD, such as Lactobacillus, Weissella, and Thermoactinomyces, can not only increase community diversity but also play a promoting role in starch saccharification and ester synthesis. Metabolomics detected 1034 differential metabolites, with SUD enriched in acetic/lactic acids and lipids that are critical flavor precursors. Redundancy analysis confirmed temperature as the core factor driving microbial succession and metabolic pathways. Thermoascus is enriched in high-temperature environments, and the affected metabolic pathways include cofactor biosynthesis and amino acid metabolism. This study clarified seasonal impacts on Daqu quality via microbe-enzyme-metabolite synergy, providing a theoretical and technical basis for stabilizing Baijiu production through microbial regulation and precise fermentation parameter control.},
}
@article {pmid41445292,
year = {2025},
author = {Govindarajan, M and Aware, C and Ivanich, K and Pathak, I and Zhu, Y and Balchandani, P and Davis, D and Ericsson, A and Ma, L and Lin, AL},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e105884},
doi = {10.1002/alz70855_105884},
pmid = {41445292},
issn = {1552-5279},
mesh = {Animals ; Mice ; *Alzheimer Disease/microbiology ; *Nitric Oxide Synthase Type II/genetics ; Humans ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Cognitive Dysfunction/microbiology ; Mice, Knockout ; *Dysbiosis ; Male ; Aged ; Fecal Microbiota Transplantation ; Female ; Cerebrovascular Circulation ; Mice, Transgenic ; Middle Aged ; Aged, 80 and over ; },
abstract = {BACKGROUND: Inducible Nitric Oxide Synthase (iNOS) is implicated in exacerbating Alzheimer's Disease (AD) mechanisms. The relationship between imbalanced gut microbiota composition (dysbiosis) and AD pathology is well characterized. Many gut bacteria, including E. Coli induce iNOS production, potentially contributing to AD development. To investigate the antagonistic role of iNOS, we created a novel iNOS knockout (iNOS-KO) mouse model using the 3xTg-AD mouse model background and performed fecal microbiome transplantation (FMT) to iNOS-KO/3xTg-AD mice from mild cognitive impairment (MCI) patients and age-matched healthy controls (HC). We aim to determine, whether iNOS-KO can protect cerebral blood flow (CBF), an early marker of AD progression, despite dysbiosis induced by FMT from MCI donors.<br><br>METHOD: Stool samples from MCI patients (n&#xa0;=&#xa0; 3) and HC (n&#xa0;=&#xa0; 3) (aged 55-80) were used for FMT in 4-month-old iNOS-KO/3xTg-AD mice (FMT-MCI, n&#xa0;=&#xa0;4 and FMT-HC, n&#xa0;=&#xa0;6) for three consecutive days after a 7-day antibiotic treatment. Mice without FMT (CTL, n&#xa0;=&#xa0;8) served as naive controls. Four weeks post-FMT, mouse fecal samples and corresponding donor samples were analyzed using 16S rRNA metagenomic sequencing. Global CBF was measured in a subset of mice (n&#xa0;=&#xa0;4/group) using 7T MRI with Continuous Arterial Spin Labelling (CASL) - Echo Planar Imaging (EPI) sequence.<br><br>RESULT: Beta diversity analysis revealed that the significant microbial diversity observed in MCI and HC donors was imprinted in their respective FMT-MCI and FMT-HC recipient mice, indicating a strong donor-derived microbial signature (Figure 1). FMT-MCI mice showed increased levels of pathobiont Gram-positive bacteria (Clostridium bolteae, Sellimonas intestinalis) when compared to FMT-HC mice indicating higher dysbiosis. Despite FMT induced dysbiosis, CBF levels (Figure 2) across the three groups were comparable to each other, attributable to the effect of the iNOS knockout.<br><br>CONCLUSION: We observe that MCI patients had higher gut dysbiosis than HC. However, despite increased dysbiosis, iNOS-KO may preserve CBF and mitigate AD-like symptoms, highlighting its potential neuroprotective role in the 3xTg-AD model. Future studies should investigate the impact of iNOS-KO on mitigating AD pathology, such as amyloid-&#x3b2; and tau accumulation, or preserving cognitive functions. Our preliminary data shows that iNOS could be a potential target to ameliorate AD risk.},
}
@article {pmid41445049,
year = {2025},
author = {Loew, EB},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e107794},
doi = {10.1002/alz70855_107794},
pmid = {41445049},
issn = {1552-5279},
mesh = {Humans ; *Alzheimer Disease/immunology/metabolism ; Aged ; Male ; Female ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; *Cognitive Dysfunction/immunology/metabolism ; Metabolomics ; Aged, 80 and over ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is the most common type of dementia which results in debilitating memory loss as the disease advances. However, among older adults with AD, some may experience rapid cognitive decline while others may maintain a stable cognitive status for years. In addition to the amyloid plaques, tau tangles, and neuronal inflammation characteristic of AD, there is strong evidence of dysregulation in the peripheral immune system, including decreased naïve T cells and increased memory T cells among older adults with AD. It is currently unknown what underlies dysfunction in the peripheral immune system or whether changes in peripheral immune cells are associated with cognitive decline.<br><br>METHOD: We have performed unbiased stool metabolomics combined with machine leaning to identify bacterial metabolites associated with AD versus propensity matched healthy controls. In our ongoing work, we are longitudinally characterizing resting peripheral immune cell populations by flow cytometry and gut microbiome composition by metagenomic sequencing.<br><br>RESULT: We have identified an increase in the metabolites methionine sulfone, homocysteine, and cysteine in the stool of older adults with AD compared to controls and found machine learning models supported bacterial methionine production as a key AD associated variable. Among the population of AD patients experiencing cognitive decline, determined by increasing ADAS-Cog score >6 points over one year (n&#xa0;=&#xa0;10 declining vs n&#xa0;=&#xa0;8 stable cognition), we have identified increases in the bacterial genes responsible for methionine production at the point of cognitive decline compared to previous timepoints and between patients with decline versus stable cognition. In accordance with the role of methionine in promoting immune cell proliferation and differentiation, we have compared the composition of peripheral immune cells among adults with declining versus stable cognition and identified increased CD4[+] effector memory T cells at the point of cognitive decline.<br><br>CONCLUSION: This longitudinal clinical study identifies changes in stool metabolites and resting peripheral T cell populations in AD patients and among AD patients with cognitive decline. We propose that gut bacterial produced methionine acts to promote peripheral immune differentiation and dysfunction, leading to cognitive decline in AD.},
}
@article {pmid41444596,
year = {2025},
author = {Tang, R and Shi, M and Ji, X and Zhang, Y and Fan, L and Huang, F and Li, X},
title = {Integrative oral and gut microbiome profiling highlights microbial correlates of complications in type 1 diabetes: a cross-sectional analysis.},
journal = {Cardiovascular diabetology},
volume = {24},
number = {1},
pages = {461},
pmid = {41444596},
issn = {1475-2840},
support = {2024XQLH049//Graduate Innovation Project of Central South University/ ; grant 2023ZD0508200 and 2023ZD0508205//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; grant 82470871//National Natural Science Foundation of China/ ; grant R2023001//Hunan Provincial Health High-Level Talent Scientific Research Project/ ; LYF2022039//Sinocare Diabetes Foundation/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications ; Male ; Female ; Adult ; Dysbiosis ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Mouth/microbiology ; Case-Control Studies ; Middle Aged ; *Diabetic Angiopathies/microbiology/diagnosis ; Young Adult ; Risk Factors ; Feces/microbiology ; Biomarkers/blood ; Host-Pathogen Interactions ; Risk Assessment ; Metagenomics ; Blood Glucose/metabolism ; },
abstract = {BACKGROUND/OBJECTIVE: Chronic vascular complications are the primary threat in long-standing type 1 diabetes (T1D) patients. We examined the associations between oral-gut microbiome dysbiosis and these complications, offering novel insights into therapeutic strategies and underlying mechanisms.<br><br>METHODS: This cross-sectional study enrolled 75 T1D participants (disease duration&#x2009;&#x2265;&#x2009;10&#xa0;years) and 43 healthy controls who underwent comprehensive clinical assessment, including blood glucose, lipid profile, and complication-related examinations. Fecal and oral rinse samples were collected for shotgun metagenomic sequencing. T1D participants were stratified by the presence of microvascular (retinopathy, nephropathy, or neuropathy) or macrovascular complications separately. Microbial differences across groups were assessed.<br><br>RESULTS: Significant differences in oral and gut microbiota compositions were observed between T1D participants with and without complications (both microvascular and macrovascular). A core set of 26 gut and 8 oral microbial species was specifically associated with vascular complications. Butyrate-producing gut bacteria (Blautia wexlerae, Anaerobutyricum hallii, Roseburia inulinivorans, A. soehngenii) and specific oral Neisseria species were enriched in T1D without complications individuals, suggesting protective effects against complications. Mediation analysis indicated associations consistent with partial mediation between certain microbial species and the relationships of glycemic control or insulin resistance (HbA1c, glucose risk index, estimated glucose disposal rate) with complication risk. Moreover, potential oral-gut microbiome interconnections were implicated in complication development. Finally, classification models integrating both oral and gut microbial features significantly outperformed models based on either site alone in distinguishing T1D patients with complications.<br><br>CONCLUSIONS: Distinct oral and gut microbiome features are associated with chronic vascular complications in T1D. These findings highlight the potential of microbiome-targeted strategies for understanding and preventing T1D-related complications.},
}
@article {pmid41443821,
year = {2025},
author = {Ketphan, W and Sato, M and Tsujimura, K and Mizutani, T and Takemae, H},
title = {Identification of a novel equine rhinitis B virus detected in horse from Japan.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0379},
pmid = {41443821},
issn = {1347-7439},
abstract = {Equine rhinitis B virus (ERBV), a member of the Picornaviridae family, is associated with mild to moderate respiratory illness in horses, yet its genomic diversity remains incompletely characterized. In this study, we performed metagenomic analysis on a rectal swab sample from a diarrheic foal confirmed to be positive for rotavirus A. Unexpectedly, we identified a highly divergent ERBV strain with a 9,448-nucleotide genome encoding a 2,721-amino-acid polyprotein. Sequence analysis revealed only 62.5-63.1% identity in the polyprotein and 47.1-49.8% in the VP1 region compared to known ERBV serotypes, suggesting a novel genotype. The genome exhibited typical picornavirus features, including a type II internal ribosome entry site (IRES), but also unique elements such as an 87-amino-acid insertion in the leader proteinase region and atypical cleavage motifs. A strain-specific RT-qPCR assay was developed alongside a broadly reactive assay targeting ERBV1-3. Screening of 37 rectal swab samples from horses revealed a 10.8% positivity rate using the new assay, with clustered cases from the same farm in 2022 and an additional case in 2024. No samples were positive using the broad-range primers, indicating potential gaps in surveillance. These findings highlight the importance of metagenomics in pathogen discovery and underscore the need for updated molecular tools to monitor genetically distinct ERBV strains and assess their clinical significance.},
}
@article {pmid41443599,
year = {2025},
author = {Wang, C and Narayanasamy, S and Shaabad, M and Dallol, A and Hala, S and Hong, PY},
title = {Monitoring Cross-Border Dissemination of Antimicrobial Resistance (AMR) via Air Travel to Saudi Arabia: Formulation of Monitoring Strategies to Mitigate AMR Concerns.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11553},
pmid = {41443599},
issn = {1520-5851},
abstract = {Antimicrobial resistance (AMR) is a global health challenge, and its dissemination can be accelerated by international air travel. Aircraft sewage, aggregating microbial material from global travelers, offers a unique surveillance opportunity for AMR at international entry points. However, specific AMR elements detected in aircraft sewage and how their relative abundance and transcriptional activity may be associated with flight characteristics such as flight duration or departure country remain unclear. This study analyzed 130 sewage samples from international flights arriving in Saudi Arabia across 27 countries. Metagenomic analyses revealed distinct AMR profiles in aircraft sewage compared to local municipal sewage, including elevated relative abundances of Enterococcus faecium and Staphylococcus aureus. Aircraft sewage harbored 51 antibiotic resistance genes (ARGs) that were not detected in local municipal sewage, predominantly carbapenem-resistant genes (e.g., blaNDM, blaVIM). Additionally, geographical origin of flights shaped AMR composition with lower ARG diversity observed from African-origin flights, whereas Asian and American flights exhibited enriched ARG profiles. Flight length affected AMR expression with long-haul flights (>3500 km) associated with elevated transcription levels. These findings demonstrated how international air travel facilitates the dissemination of AMR across regions and provided actionable insights to devise aircraft sewage surveillance strategies.},
}
@article {pmid41443232,
year = {2025},
author = {Dissanayaka, S and Jayasingh, T and Sohrabi, HR and Rainey-Smith, SR and Scott, K and Martins, RN and Fernando, WMADB and , },
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e105512},
doi = {10.1002/alz70855_105512},
pmid = {41443232},
issn = {1552-5279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Alzheimer Disease/metabolism/microbiology ; Aged ; *Cognitive Dysfunction/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Amyloid beta-Peptides/metabolism ; Brain/metabolism ; Positron-Emission Tomography ; Aged, 80 and over ; Middle Aged ; },
abstract = {BACKGROUND: Gut microbiota and their metabolites, particularly short-chain fatty acids (SCFAs), play a vital role in the gut-brain axis, and have been associated with neurodegenerative diseases like Alzheimer's disease (AD). However, the changes in gut microbiota composition and SCFA levels during the progression of AD are not yet well understood. This study seeks to investigate these variations to gain deeper insights into their potential role in disease development.<br><br>METHOD: This study examined changes in gut microbiota and SCFA across three groups; Cognitively unimpaired individuals with low amyloid-beta ((CU) A&#x3b2; Low (n&#xa0;=&#xa0; 71)), CU A&#x3b2; High (n&#xa0;=&#xa0; 19), and those diagnosed with mild cognitive impairment (MCI) or AD (Disease Group (DG), n = 10). Participants were selected from well characterised cohorts and underwent Pittsburg compound B-positron emission tomography to determine cerebral amyloid status. Faecal microbiota composition was assessed using shotgun metagenomics, while faecal SCFA concentrations were quantified via Gas Chromatography-Mass Spectrometry (GC-MS). Associations between taxa and SCFAs were assessed using Spearman correlation and MaAsLin2.<br><br>RESULT: Firmicutes, Proteobacteria, and Bacteroidetes exhibited significant correlations with SCFAs across all groups. In the CU A&#x3b2; Low and Disease Group (DG), Firmicutes showed Positive correlations with butyric acid. Group-specific patterns included negative correlations between Bacteroidetes and propionic acid in the DG group, a positive correlation between Firmicutes and total SCFAs in the CU A&#x3b2; Low group, and a positive correlations between Proteobacteria and Actinobacteria with butyric acid in the CU A&#x3b2; High group, alongside notable interactions with isovaleric acid. Furthermore, specific taxa such as Corynebacterium falsenii (Phylum: Actinobacteria), Ruthenibacterium lactatiformans (Phylum: Firmicutes), and Streptomyces capitiformicae (Phylum: Actinobacteria) showed significant associations with SCFAs, particularly propionic acid and butyric acid.<br><br>CONCLUSION: These findings suggest that changes in gut bacteria and their metabolites vary at different stages of AD. Key results show that certain bacteria, such as Firmicutes, Bacteroidetes, and Proteobacteria, are linked to SCFAs, especially butyric acid, which plays a role in gut and brain health. This suggests that modifying gut bacteria could help regulate SCFA levels and potentially slow the progression of AD. However, more research is needed to fully understand this connection.},
}
@article {pmid41443199,
year = {2025},
author = {Lucas, TN and Biehain, U and Gautam, A and Gemeinhardt, K and Lass, T and Konzalla, S and Ley, RE and Angenent, LT and Huson, DH},
title = {MMonitor for real-time monitoring of microbial communities using long reads.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101266},
doi = {10.1016/j.crmeth.2025.101266},
pmid = {41443199},
issn = {2667-2375},
abstract = {Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations.},
}
@article {pmid41443112,
year = {2025},
author = {Cao, Y and Xu, Y and Yan, C and Lu, Z and Zhou, Q and Wang, J and Wang, Y and Cheng, L and Zhang, L and He, Y and Guo, B and Li, B},
title = {Comparing the performance of targeted next-generation sequencing and metagenomic next-generation sequencing in diagnosing pneumonia: A systematic review and network meta-analysis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117234},
doi = {10.1016/j.diagmicrobio.2025.117234},
pmid = {41443112},
issn = {1879-0070},
abstract = {BACKGROUND: In terms of diagnosing pneumonia, there is currently limited evidence for a direct comparison of the performance of targeted next-generation sequencing (tNGS) and metagenomic next-generation sequencing (mNGS), and is no comprehensive conclusion yet. This systematic review and network meta-analysis (NMA) aimed to comprehensively compare the diagnostic performance of tNGS and mNGS in patients with pneumonia.<br><br>METHODS: A systematic literature search was conducted across PubMed, Embase, the Cochrane Library, and Web of Science. From the establishment of the database to September 10, 2025. Studies providing diagnostic data (true positive, false positive, false negative, true negative) for tNGS and/or mNGS in patients suspected of pneumonia were included. We conducted a frequency theory random effects network meta-analysis, and calculate pooled odds ratios (ORs) with 95 % confidence interval (CI) for sensitivity and specificity, and to rank diagnostic performance using surface under the cumulative ranking curve (SUCRA) values. Subgroup analyses based on sample type and patient status were conducted.<br><br>RESULTS: The NMA revealed no statistically significant differences in overall sensitivity (OR = 1.54, 95 % CI [0.47-5.06]) or specificity (OR = 1.29, 95 % CI [0.39-4.28]) between tNGS and mNGS. SUCRA rankings indicated that tNGS had the highest cumulative probability for sensitivity (91.9 %), followed by mNGS (74.6 %), and the cumulative specificity probability of tNGS (37.8 %) is higher than that of mNGS (17.1 %). In subgroup analysis, when multiple sample types were used, tNGS showed significantly higher specificity than mNGS (OR = 4.95, 95 % CI [1.13-21.75]).<br><br>CONCLUSION: These findings suggest tNGS may be a more specific and potentially cost-effective option for the etiological diagnosis of pneumonia, particularly when multi-sample testing is employed.},
}
@article {pmid41442943,
year = {2025},
author = {Huang, J and Zhang, J and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Liang, H and Lin, L and Li, X and Li, B},
title = {Combined exposure of enrofloxacin and disinfection byproducts under environmentally relevant concentrations enhances antibiotic resistance risks in livestock wastewater.},
journal = {Water research},
volume = {291},
number = {},
pages = {125189},
doi = {10.1016/j.watres.2025.125189},
pmid = {41442943},
issn = {1879-2448},
abstract = {Livestock wastewater is a crucial source of antibiotic resistance. However, the impact of disinfection byproducts (DBPs), stemming from disinfectants commonly used in livestock farming, on antibiotic resistance has scarcely been explored at the community level. Moreover, the combined effects of these DBPs with antibiotic pressure remain unknown. Herein, we added one antibiotic enrofloxacin, and two typical DBPs trichloromethane (TCM) and trichloroacetic acid (TCAA), individually or in combination to bioreactors simulating the biotreatment of livestock wastewater. Our time-series metagenomic analysis over 120 days showed that pollutant exposure significantly increased the abundance of antibiotic resistance genes (ARGs), elevating the peak ARG abundance by 23.4 % to 85.4 % compared to the control group. An increasing trend of ARG abundance was observed in the TCAA, enrofloxacin+TCAA, and enrofloxacin+TCM groups with increasing exposure time. Exposure to DBPs alone or in combination with enrofloxacin did not significantly increase the ARG copy number per cell compared to individual enrofloxacin exposure. However, under co-exposure to enrofloxacin and DBPs, the diversity of antibiotic-resistant bacteria (ARB) was significantly higher than those in both the control group and the single enrofloxacin group, indicating a stronger driving effect of combined exposure on the dissemination of ARGs. Genomic-centric analysis revealed a significant increase in the relative abundance of ARB when exposed to combined enrofloxacin and DBPs and individual TCM groups at environmentally relevant concentrations. We discovered that plasmids and integrative and conjugative elements (ICEs) play more essential roles in the spread of ARGs compared to that of integrons and phages. The relative abundance of ARB carrying shared ARGs on both chromosome and plasmids remained nearly stable in control groups but increased to varying extents in all treatment groups. The ARG-carrying ICEs were enriched when exposed to enrofloxacin, TCM, and TCAA alone. The long-term exposure of enrofloxacin or DBPs was in relation with the enrichment of putative pathogenic ARB. Overall, the increased antibiotic resistance levels and the co-occurrence of ARGs, virulence factors, and mobile genetic elements (MGEs) resulting from long-term exposure to enrofloxacin or DBPs underscore the considerable microbial risk associated with the release of ARGs from livestock wastewater.},
}
@article {pmid41442899,
year = {2025},
author = {Leonard, SR and Mammel, MK and Richter, TKS and Simko, I and Brandl, MT},
title = {Metagenomic characterization of the antibiotic, biocide, and metal resistome of soil and romaine lettuce from the field through processing and storage.},
journal = {International journal of food microbiology},
volume = {448},
number = {},
pages = {111595},
doi = {10.1016/j.ijfoodmicro.2025.111595},
pmid = {41442899},
issn = {1879-3460},
abstract = {The presence of antimicrobial resistance genes (AMRGs) on crops is of concern to public health since plant-derived foods may serve as vectors of AMRGs to human pathogens. This study mined the bacterial metagenomes of soil and lettuce from harvest through processing and storage to characterize their comprehensive resistomes (antibiotics, metals, and biocides). Cold-stored lettuce had the greatest number of AMRG reads per million of all sample types. AMRGs were overall dominated by metal resistance determinants, except those of processed lettuce (cut, washed in chlorinated water, and rinsed), which were heavily enriched in genes encoding biocide resistance. The greatest percentage of drug resistance genes, when averaged over all sample types, belonged to resistance to β-lactams (30 %) followed by aminoglycosides (6.7 %); and specific allele sequences from both classes were observed in common between lettuce and soil sampled next to lettuce heads. Genes for resistance to β-lactams were in highest relative abundance (RA) on cold-stored lettuce and lowest in soil. Several extended-spectrum β-lactamase genes and the colistin resistance gene mcr-9.1 were detected in the cold-stored lettuce resistome. Harvest season and field type had a significant effect on the comprehensive resistome of most sample types (PERMANOVA, P < 0.05). Notably, the RA of β-lactams resistance genes in the drug resistome of cold-stored lettuce represented 17.4 % and 2.0 % in spring vs. fall, and 11.3 % and 3.9 % in the commercial vs. experimental field, respectively. This study highlights the multifactorial role of the biotic and abiotic environment on the comprehensive resistome of lettuce during production and storage.},
}
@article {pmid41442808,
year = {2025},
author = {Wang, X and Chen, M and Zhang, X and Han, X and Hu, Y and Wang, X and Li, X and Zhang, D},
title = {Effect of sodium percarbonate in mitigating lactic acid inhibition and enhancing system performance during anaerobic digestion of acidified food waste.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128411},
doi = {10.1016/j.jenvman.2025.128411},
pmid = {41442808},
issn = {1095-8630},
abstract = {Food waste treatment poses a critical environmental challenge amid urbanization, and its resource recovery efficiency is hindered by acidification. In this study, sodium percarbonate (SPC) was used to treat acidified food waste. The results showed that SPC increased the short-chain fatty acids (SCFAs) production during anaerobic digestion from 363.89 ± 11.55 mg COD/L (control) to 15,431.60 ± 329.94 mg COD/L (0.4 g/g TSS). Quenching experiments revealed that CO3·[-] and ·O2[-] were the main reactive species from SPC responsible for promoting SCFAs generation and lactic acid degradation. High-throughput sequencing analysis indicated that SPC pretreatment enhanced the diversity and abundance of functional microbial communities involved in anaerobic digestion. Metagenomic analysis further demonstrated that pretreatment increased gene abundances related to organic matter metabolism, tricarboxylic acid cycle, acidogenesis, and methanogenic modules, thereby contributing to enhanced anaerobic digestion performance. This study elucidated the underlying impact mechanisms of SPC on the anaerobic digestion of acidified food waste, providing valuable insights for optimizing the efficient resource recovery of waste.},
}
@article {pmid41442804,
year = {2025},
author = {Zhang, K and Zheng, J and Liu, K and Gao, L and Bi, R and Ji, F},
title = {Optimizing intermittent rotary aeration to enhance efficiency and reduce greenhouse gas and ammonia emissions during fish manure composting.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128414},
doi = {10.1016/j.jenvman.2025.128414},
pmid = {41442804},
issn = {1095-8630},
abstract = {The treatment of fish manure from industrial recirculating aquaculture systems (IRAS) is challenging due to its low carbon-to-nitrogen (C/N) ratio and poor separability. This study investigated the optimization of composting efficiency and greenhouse gas mitigation for such manure using a rotating-bin system. A self-developed concentration technique was employed to obtain the feedstock, which was composted under varying rotational aeration frequencies. We comprehensively assessed the process by analyzing physicochemical parameters, product maturity, gas emissions (N2O, CH4, NH3, CO2), and microbial community metagenomics. Results identified an intermittent aeration regime of 5-min rotation followed by a 45-min rest (Treatment D) as optimal. Only Treatment D produced mature compost, achieving a seed germination index of 83.76 %. Critically, this regime reduced cumulative emissions of N2O, CH4, and NH3 by 47.6 %, 56.5 %, and 47.9 %, respectively, compared to continuous aeration, with a 44.2 % reduction in total CO2-equivalent emissions. Metagenomic analysis linked this improvement to a 23.5-31.2 % higher relative abundance of key nitrogen-cycle genes (amoA, hao), enhancing organic nitrogen assimilation and humification. This work demonstrates that optimized intermittent aeration in rotating bins significantly advances the sustainable, low-emission composting of fish manure from IRAS.},
}
@article {pmid41442770,
year = {2025},
author = {Liu, C and Zhang, L},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e103718},
doi = {10.1002/alz70856_103718},
pmid = {41442770},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; *Apolipoprotein E4/genetics ; Aged ; *Biomarkers ; *Alzheimer Disease/genetics/microbiology ; Feces/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: The gut-brain axis hypothesis proposes a bidirectional communication network between the gut microbiome and the central nervous system, shaping neuroinflammatory processes linked to Alzheimer's disease (AD). Although the APOE4 allele is the strongest genetic risk factor for AD-raising the likelihood of disease by two- to three-fold with even one copy-its association with the gut microbiome remains underexplored. This gap limits our full understanding of the pathways contributing to AD.<br><br>METHOD: We investigated the relationship between APOE4 status and gut microbiome composition in 114 healthy participants (average age: 77, 57% women). Stool samples underwent shotgun metagenomic sequencing. Rigorous quality control steps removed low-quality reads and human DNA contaminants. We performed taxonomic profiling and applied rarefaction to normalize sequencing depth. Alpha diversity (richness and evenness) and beta diversity (unweighted UniFrac-based principal coordinates analysis) were assessed. We then used permutational multivariate analysis of variance, adjusting for demographic and clinical variables, to identify group differences. Differential taxonomic analysis pinpointed bacterial taxa enriched in APOE4 carriers versus non-carriers.<br><br>RESULT: Alpha diversity metrics did not differ significantly between APOE4 carriers and non-carriers at the species level (p&#xa0;=&#xa0;0.070). However, beta diversity analysis showed significant differences in overall community composition after adjusted by the covariates (p&#xa0;=&#xa0;0.003), and APOE4 carrier status remained significant in PERMANOVA (p&#xa0;=&#xa0;0.039). Furthermore, subgroup analysis of APOE4 genotypes (2/4, 3/4, 4/4) also revealed significant compositional differences (p&#xa0;=&#xa0;0.030). Differential taxonomic analysis identified 21 species enriched in APOE4 carriers and 20 species enriched in non-carriers. Among non-carriers, Alistipes finegoldii (p&#xa0;=&#xa0;0.035) and Odoribacter splanchnicus (p&#xa0;=&#xa0;0.024) were more abundant. These species are involved in metabolic pathways related to short-chain fatty acid production, which can have anti-inflammatory effects. Their presence suggests a protective gut microbiome-mediated mechanism in individuals without the APOE4 allele.<br><br>CONCLUSION: Our findings suggest that APOE4 carriers have distinct gut microbiome patterns that may heighten the risk of neuroinflammation through the gut-brain axis, potentially contributing to AD onset or progression. These results highlight the interplay between genetic risk factors and gut microbial communities. They also underscore the potential for microbiome-targeted interventions to reduce AD risk in genetically susceptible individuals.},
}
@article {pmid41442682,
year = {2025},
author = {Monzón, &#xc1;RR and Ramos, JFO and Narvaez, YC and Rosales, MH},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e097688},
doi = {10.1002/alz70856_097688},
pmid = {41442682},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/metabolism ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/metabolism/microbiology ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Metabolomics ; Middle Aged ; Adult ; Aged ; Young Adult ; },
abstract = {BACKGROUND: T2DM and AD are major public health concerns characterized by metabolic and cognitive impairments, respectively, with growing evidence suggesting that gut microbiota alterations contribute to their pathogenesis. Metagenomic and metabolomic analyses provide valuable insights into the microbiota's role in glucose regulation, inflammation, and dementia risk, offering potential for early diagnosis and targeted interventions. Understanding the interplay between gut microbiota and metabolic pathways could lead to novel therapeutic strategies to improve patient outcomes.<br><br>METHOD: A descriptive study with a quantitative approach, cross-sectional observational comparative, of relational scope will be conducted. The study population will be segmented into four groups and two subgroups: Control (CTRL) (n&#xa0;=&#xa0;30), Type 2 Diabetes Mellitus (T2DM) (n&#xa0;=&#xa0;30), Alzheimer's Disease (AD) without T2DM (n&#xa0;=&#xa0;30), and AD with T2DM (n&#xa0;=&#xa0;30). Subgroups include Control (Young adults) (n&#xa0;=&#xa0;30) and T2DM (Young adults) (n&#xa0;=&#xa0;30). All groups will undergo characterization, which includes blood chemistry, and clinical, mental, nutritional, and anthropometric evaluations. We obtained urine and stool samples for DNA extraction and library preparation. We used Magnetic Resonance Mass Spectrometry (MRMS) for metabolomic analysis, which uses eluents to detect metabolites. We will apply MetaHit bioinformatics tools to assess sample diversity and perform metabolomic analysis in RStudio.<br><br>RESULT: The study revealed distinct patterns of intestinal dysbiosis and metabolic changes in patients with T2DM and AD, categorized by age. A comprehensive taxonomic and functional representation of the gut microbiome highlighted condition-specific differences. Significant correlations were found between microbiological, metabolomic, and clinical biomarkers, particularly those related to cognitive decline. Key metabolic pathways and molecular processes underlying dysbiosis were identified. Fecal metabolite analysis uncovered distinctive compounds such as (+/-)-Ethylketocyclazocine, (-)-Quebrachamine, and (-)-jasmonoyl-L-isoleucine, while urinary metabolites like (Phenylthio) acetic acid and 2,3-Diketo-L-gulonate showed disease-associated variations. These findings support the development of personalized interventions to mitigate cognitive decline through microbiota and metabolomic profile modifications.<br><br>CONCLUSION: The study identifies distinct gut microbiota and metabolic patterns linked to cognitive decline in T2DM and AD, offering insights into disease mechanisms and supporting the development of personalized therapeutic strategies to improve patient outcomes.},
}
@article {pmid41442661,
year = {2025},
author = {Ivanich, K and Yackzan, A and Chang, YH and Aware, C and Govindarajan, M and Kramer, S and Yanckello, LM and Ericsson, A and Lin, AL},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e104646},
doi = {10.1002/alz70855_104646},
pmid = {41442661},
issn = {1552-5279},
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Mice, Transgenic ; Male ; Apolipoprotein E4/genetics ; *Brain/metabolism ; Mice ; *Diet, Ketogenic ; *Alzheimer Disease/genetics/metabolism ; Apolipoprotein E3/genetics ; Metabolomics ; Disease Models, Animal ; },
abstract = {BACKGROUND: The apolipoprotein ε4 (APOE4) polymorphism is the primary genetic risk factor for Alzheimer's disease (AD). APOE4 carriers exhibit early deficits in brain metabolism and gut microbiome diversity, both elevating AD risk. This study investigated whether a ketogenic diet (KD) can restore brain metabolism and gut microbiome diversity in young, asymptomatic APOE4-positive mice, while also assessing sex-based differences, given the higher AD risk in females. Comparisons were also made with APOE3 mice, which carries a neutral AD risk, to determine genotype differences. Additionally, a correlative analysis explored relationships between microbes and brain metabolites, identifying potential therapeutic and screening targets for AD risk mitigation.<br><br>METHOD: Female and male APOE3 (n&#xa0;=&#xa0; 44) and APOE4 (n&#xa0;=&#xa0; 39) transgenic mice were randomly assigned to a control diet (5.1% fat) or a KD (75.1% fat). Mice ate ad libitum for 16 weeks, starting at 12 weeks of age. Brain tissue was collected for untargeted metabolomics (UPLC-MS/MS via Metabolon Inc.), and fecal samples were collected for 16s rRNA shotgun metagenomic sequencing (CosmosID). Gut microbiome species richness and evenness were measured using Shannon index (&#x3b1;-diversity). Bray-Curtis dissimilarity (&#x3b2;-diversity) measured intra-subject dissimilarity for pre- and post-diet gut microbiome composition, and Spearman's correlation heatmaps linked metabolites and microbes to correlations within amino acid, energy, and lipid metabolic pathways.<br><br>RESULT: The KD restored brain metabolism in APOE4 females by recovering levels of metabolites associated with mitochondrial function (Figure 1A) and glutamate metabolism (Figure 1B), while exerting variable effects on these metabolites in APOE3 mice and APOE4 males. The KD increased species' richness and evenness in APOE4 females (Figure 2A) and balanced microbiome composition in APOE4 mice, as indicated by limited changes pre- and post-dietary intervention (Figure 2B). Correlation analyses revealed that Bacteroides intestinalis, Clostridium sp. ASF502, Lachnospiraceae bacterium A4, Lactobacillus johnsonii, Lactobacillus reuteri had significant associations with metabolites involved in amino acids and energy (Figure 3A) and lipid (Figure 3B) pathways.<br><br>CONCLUSION: The KD effectively restored brain metabolism and gut microbiome diversity in APOE4 female mice. These effects were absent in APOE3 mice and APOE4 males. Correlations between microbes and metabolites provide potential targets for AD interventions and risk assessment.},
}
@article {pmid41442536,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, T and Wang, Y and Kirby, J},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e097652},
doi = {10.1002/alz70856_097652},
pmid = {41442536},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Aged ; Biomarkers ; Magnetic Resonance Imaging ; Neuropsychological Tests/statistics &amp; numerical data ; Feces/microbiology ; *Dysbiosis/microbiology ; *Cerebrovascular Circulation/physiology ; Middle Aged ; Cognition ; },
abstract = {BACKGROUND: Gut dysbiosis and cerebrovascular disease have both been implicated in Alzheimer's disease (AD) progression and pathophysiology. However, the interplay between them is unclear. The goal of this study was to identify relationships between gut microbiota (GMB), cerebrovascular functioning, and cognition in patients diagnosed with amnestic mild cognitive impairment (aMCI) compared to cognitively unimpaired older adult controls.<br><br>METHODS: Participants (N&#xa0;=&#xa0;14 aMCI and 10 controls) provided fecal samples for 16S and shotgun metagenomics GMB sequencing, underwent an MRI, and completed neuropsychological tests. For MRI, cerebral vascular reactivity (CVR), cerebral blood flow (CBF) and arterial transit time (ATT) were assessed. Spearman rho correlational analysis was used to evaluate relationships between discriminatory microbial taxa, cerebrovascular metrics, and cognition.<br><br>RESULTS: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with cognition and cerebrovascular function, whereas bacteria associated with a healthy gut microbiome had positive associations with cognitive and cerebrovascular function. For example, Alistipes indistinctus, which depletes intestinal urate levels was enriched in aMCI and had significant negative correlations with Trail Making Test-B (TMT-B; rs=-.587) and category fluency (CF) scores (rs=-.422), CVR (rs=-.437), and CBF (rs=-.546). Bilophila wadsworthia was negatively associated (trend-level) with CVR and CBF, and significantly correlated with TMT-B (rs&#xa0;=&#xa0;-.499) and category fluency (rs&#xa0;=&#xa0;-.503). The bile acid modifying bacterium, Turicibacter sp., had a significant positive correlation with CBF (rs=.423). Finally, we found that several bacteriophages had significant correlations with cognitive and cerebrovascular measures, such as a B. wadsworthia phage that was enriched in aMCI and had significant negative correlations with TMT-B (rs=-.491), delayed recall (rs=-.589), and CVR (rs=-.474). Further, this phage contained an acyl-coA synthetase capable of influencing central metabolism.<br><br>CONCLUSIONS: Consistent with previous research, we found that persons with aMCI have an altered gut microbiome relative to controls. Further, we demonstrate through metagenomics sequencing that both bacterial and viral taxa are associated with cognitive and neurovascular functioning in aMCI. Knowledge about the relationships between the microbiota, cognition, and cerebrovascular function paves the way for future studies cross-sectional and longitudinal studies.},
}
@article {pmid41441246,
year = {2025},
author = {Nikolova, R and Gatev, E and Kenarova, A and Petkova, M and Dinev, N and Baldrian, P and Radeva, G},
title = {Selective Pressure of Heavy Metals on Soil Microbial Taxa near a Smelting Area.},
journal = {Toxics},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/toxics13121025},
pmid = {41441246},
issn = {2305-6304},
support = {CZ.02.01.01/00/22_008/0004597 and LUC21352//Ministry of Education, Youth and Sports of the Czech Republic/ ; },
abstract = {Soil pollution by heavy metals (HMs) poses a major threat to soil quality and human health, with mining and smelting industries identified as key sources. Soils around smelters are often considered polluted hotspots, being generally unsuitable for agricultural activities. Although many studies have identified microbial taxa able to survive in such environments, most have focused on relatively low HM concentrations. The purpose of the study was to assess the ecological risk and to evaluate the diversity and structural shifts in microbial communities, as well as to predict key metabolic pathways associated with HM resistance in soils near Pb-Zn smelter in Bulgaria. The soils ranged from low-risk to disastrous, with cadmium (Cd) identified as the primary contributor to soil toxicity. High-throughput sequencing of 16S rRNA and ITS amplicons revealed widespread dominance of the phyla Proteobacteria, Actinobacteriota and Acidobacteriota, and Ascomycota, with the prevailing classes Acidobacteriae, Chloroflexia, and Eurotiomycetes, indicating their high tolerance to HMs. Functional predictions suggested enrichment of key pathways in the most polluted soils related to HM resistance, including efflux systems and detoxifying enzymes. These results highlight the necessity of integrating soil microbial indicators into agricultural management strategies to ensure safe food production.},
}
@article {pmid41440831,
year = {2025},
author = {Kuehn, JF and Zhang, Q and Heston, MB and Kang, JW and Harding, S and Davenport-Sis, NJ and Kerby, RL and Schiffmann, EC and Wheeler, JL and Clements, E and Shankar, S and Mickol, A and Zemberi, J and Chow, H and Zhang, E and Harpt, J and Mushtaque, A and Yoo, M and Cook, A and Carlsson, CM and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Ulland, TK and Bendlin, BB and Rey, FE},
title = {Biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e098071},
doi = {10.1002/alz70856_098071},
pmid = {41440831},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/cerebrospinal fluid ; Male ; *Alzheimer Disease/metabolism/diagnosis ; Female ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Feces/chemistry/microbiology ; Aged ; Middle Aged ; Cohort Studies ; Metagenome ; },
abstract = {BACKGROUND: Short-chain fatty acids (SCFA), including acetate, propionate, and butyrate, are abundant gut bacterial metabolites produced via the fermentation of dietary fibers and resistant starch. Several lines of evidence, particularly in preclinical mouse models, suggest a protective role of SCFA against Alzheimer's Disease (AD) pathology. In one study, supplementation of mice with tributyrin, a butyrate prodrug, significantly attenuated AD pathology. However, the relationships between SCFA, the bacterial taxa that produce them, and AD biomarkers require further elucidation in humans.<br><br>METHOD: We assessed gut metagenomes and SCFA levels in fecal samples from 213 cognitively unimpaired Microbiome Alzheimer's Risk Study (MARS) participants (Table 1). The cohort was co-enrolled in the Wisconsin Alzheimer's Disease Research Center and Wisconsin Registry for Alzheimer's Prevention, which track preclinical disease progression in middle-aged and older adults at risk for AD. We sequenced DNA extracted from 213 fecal samples (one sample per participant, 30 million reads per sample), created metagenome-assembled genomes (MAGs), and annotated their functions. We measured levels of the major SCFA in fecal samples using headspace gas chromatography. We performed multiple linear regressions between levels of cerebrospinal fluid (CSF) AD biomarkers and each SCFA or MAG, controlling for age, sex, body mass index, and APOE genotype.<br><br>RESULT: We found an inverse association between amyloid positive status (CSF A&#xa7b5;42/A&#xa7b5;40 <0.046) and MAGs encoding propionate or butyrate production pathways. Fecal acetate, propionate, and butyrate levels were reduced in females and in participants with amyloid-positive status. Mediation analysis detected a trend indicating that butyrate may mediate the inverse relationship between MAGs with butyrate production pathways and amyloid positive status.<br><br>CONCLUSION: Relative abundances of MAGs encoding enzymes for propionate and butyrate production were reduced in amyloid-positive participants in a cognitively unimpaired human cohort enriched for AD risk. These results, combined with the extensive literature in preclinical AD mouse models, suggest that SCFA may play a causal role in AD progression.},
}
@article {pmid41440703,
year = {2025},
author = {Zhang, ZF and Jiang, Y and Mao, J},
title = {Global Distribution Patterns of Dark Matter Fungi in Cold Seep: A Metagenomic Meta-Analysis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120878},
pmid = {41440703},
issn = {2309-608X},
support = {2024A04J3728//Guangzhou Science and Technology Plan Project/ ; 32400044//National Natural Science Foundation of China/ ; },
abstract = {Deep-sea cold seep ecosystems, known for their unique geochemical niches and chemosynthetic communities, harbor numerous "dark matter fungi (DMF)" that remain understudied compared to their bacterial and archaeal counterparts. Integrating 105 metagenomic datasets from 12 global cold seep sites, this study systematically elucidated the diversity, biogeography, and assembly mechanisms of cold seep fungal communities. Our analysis revealed highly diverse and abundant fungi, spanning 21 phyla and 928 genera, characterized by the absolute dominance of Ascomycota and a pervasive presence of unclassified DMF. Crucially, the fungal communities exhibited significant geographical and seep-type heterogeneity, with peak abundance notably in methane seep environments. Further analyses revealed that fungal community diversity and structure are influenced by both spatial and biological factors. Moreover, assembly exhibits multi-scale characteristics: dispersal limitation is the primary determinant globally, while local-scale structure is jointly driven by environmental variables and biological interactions with key chemosynthetic genes. These findings establish the macro-biogeographical pattern of deep-sea cold seep fungi, underscoring their tight coupling with core energy metabolism and providing essential data for future research and potential utilization.},
}
@article {pmid41440692,
year = {2025},
author = {Lv, X and Wang, H and Wang, W},
title = {Agaricus sinodeliciosus and Coprinus comatus Improve Soil Fertility and Microbial Community Structure.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120866},
pmid = {41440692},
issn = {2309-608X},
support = {41761107//National Natural Science Foundation of China/ ; 2025-ZJ-969T//The Natural Science Foundation of Qinghai Province/ ; W2412148//International (Regional) Cooperation and Exchange (ICE) Projects of the National Natural Science Foundation of China (NSFC)/ ; D23029//111 Project/ ; },
abstract = {Agaricus sinodeliciosus (A. sinodeliciosus) and Coprinus comatus (C. comatus) are precious macrofungi found in Qinghai Province, China. As decomposers, they play a crucial role in the terrestrial ecosystem. The article takes A. sinodeliciosus and C. comatus growing in the saline-alkali land of the Qaidam Basin in Qinghai Province as the research objects, and deeply analyzes the influence of the two macrofungi on soil. The results show that, compared with the control soil, the total carbon (TC) content in the soil of A. sinodeliciosus and C. comatus increased by 27.48% and 113.24%, the total nitrogen (TN) content increased by 95.16% and 108.06%, the hydrolyzable nitrogen (HN) increased by 87.36% and 97.90%, and the available potassium (AK) increased by 182.72% and 596.09%, respectively. In addition, C. comatus significantly increased the available phosphorus (AP) by 163.14%. This proves that both macrofungi can enhance soil fertility, and C. comatus has a stronger fertilization effect. In terms of soil microorganisms, A. sinodeliciosus significantly influenced the distribution of soil bacteria and fungi, increasing the abundance of Streptomyces and reducing alpha diversity. C. comatus had a greater impact on bacteria, significantly increasing the relative abundance of Pseudomonas in the soil, but had no significant effect on fungi. Additionally, there was a close relationship between soil microbial abundance and physicochemical properties. pH, AP, TC, and AK were the main factors influencing bacteria, while total salt was the main factor affecting fungi. These findings reveal that A. sinodeliciosus and C. comatus influence the soil microenvironment by regulating soil physicochemical properties and microbial communities.},
}
@article {pmid41440679,
year = {2025},
author = {Boán, J and Fernández-Ruiz, M and Aparicio-Minguijón, E and Aguado, JM},
title = {The Unnoticed Threat: Clinical Characteristics, Risk Factors, and Outcome of Mucormycosis in Solid Organ Transplantation.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120853},
pmid = {41440679},
issn = {2309-608X},
abstract = {Mucormycosis is an uncommon but life-threatening invasive fungal infection caused by molds of the order Mucorales, whose incidence has increased among solid organ transplant (SOT) recipients in recent years. Profound immunosuppression (particularly high-dose corticosteroids), T-cell-depleting therapies, diabetes mellitus, and previous episodes of graft rejection are the main predisposing conditions. This narrative review summarizes the current evidence on epidemiology, pathogenesis, risk factors, clinical presentation, diagnostic strategies, and treatment outcomes of mucormycosis in the SOT population. Pulmonary and rhino-orbital-cerebral infections are the predominant clinical forms, often characterized by rapid angioinvasive progression and mortality rates exceeding 45%. Early diagnosis remains challenging due to nonspecific clinical manifestations and the limited sensitivity of conventional diagnostic tools, although molecular techniques such as the detection of circulating Mucorales DNA in blood and metagenomic next-generation sequencing are promising. Liposomal amphotericin B remains the first-line therapy, ideally associated to surgical debridement and reduction in immunosuppression, while broad-spectrum triazoles (isavuconazole and posaconazole) represent alternative or salvage options. Despite recent advances in diagnostic methods and antifungal therapy, the prognosis of post-transplant mucormycosis remains poor, underscoring the need for multidisciplinary management and collaborative studies to inform the clinical management in this high-risk population.},
}
@article {pmid41440673,
year = {2025},
author = {Rümenapp, M and Becker, B and Pushkareva, E},
title = {Environmental Gradients Shape Fungal Diversity and Functional Traits in Arctic Biocrusts.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120847},
pmid = {41440673},
issn = {2309-608X},
support = {PU867/1-1//Deutsche Forschungsgemeinschaft/ ; Be1779///Deutsche Forschungsgemeinschaft/ ; },
abstract = {Arctic biological soil crusts (biocrusts) are known to host diverse fungal communities that facilitate nutrient cycling and soil stabilisation in these harsh environments. In this study, the diversity and composition of fungi were assessed across elevation and spatial gradients in biocrusts from Kongsfjorden (Svalbard) using metagenomic sequencing. Within the observed fungal phyla, Ascomycota was dominant across all sites, with Basidiomycota and Rozellomycota also exhibiting high abundances. Furthermore, saprotrophic fungi were most abundant, followed by mycorrhizal and parasitic guilds. Lichen-associated fungi were also detected across the samples, although their read counts were substantially lower. Additionally, the fungal genus richness and guild composition exhibited no significant variation between elevations, but location within the fjord strongly shaped community structure.},
}
@article {pmid41440348,
year = {2025},
author = {Sonets, IV and Galeeva, IS and Krivonos, DV and Pavlenko, AV and Vvedenskiy, AV and Ahmetzyanova, AA and Mikaelyan, KA and Ilina, EN and Yanushevich, OO and Revazova, ZE and Vibornaya, EI and Runova, GS and Aliamovskii, VV and Bobr, IS and Tsargasova, MO and Kalinnikova, EI and Govorun, VM},
title = {In-Depth Multi-Approach Analysis of WGS Metagenomics Data Reveals Signatures Potentially Explaining Features in Periodontitis Stage Severity.},
journal = {Dentistry journal},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/dj13120590},
pmid = {41440348},
issn = {2304-6767},
abstract = {Background: Periodontitis is a chronic inflammatory disease mostly associated with Porphyromonas gingivalis infection and characterized by progressive destruction of the supporting structures of the tooth, including the gingiva, periodontal ligament and alveolar bone. However, the impact of other members of the periodontal microbiome on stage of the severity of the periodontitis remains largely uncharacterized. Methods: This exploratory study employs whole-genome shotgun (WGS) metagenomics to characterize the periodontal microbiome in patients suffering from mild and severe periodontitis, aiming to identify microbial signatures linked to disease severity via analysis of taxonomic composition, predicted metabolic pathways and metagenome-assembled genomes (MAGs). After initial selection, 28 adult patients with a computer tomography (CT)-confirmed diagnosis of mild and severe stage of periodontitis from 2 clinics were included in the research project. Results: Taxonomic analysis confirms the presence of various commensal and pathogenic bacteria detectable at the species level, especially belonging to so-called "red, orange and green periodontal complexes"-P. gingivalis, T. forsythia, C. rectus, and Capnocytophaga spp. that may contribute to disease heterogeneity. The conducted investigation suggests that non-microbial factors such as cardiovascular diseases and antibiotic usage in the last 6 months prior to the hospital admission could explain variance of disease progression and impact on severity. Analysis of microbial functional composition revealed metabolic traits showing positive correlations with severe stage of periodontitis. Robust network analysis suggested interactions between pathogenic bacteria of the red complex and other members of the periodontal microbiome. Conclusions: These findings underscore the multifactorial nature of periodontitis pathogenesis, highlighting the need for integrated approaches combining microbial, host, and environmental data to unravel drivers of disease progression. The study provides a foundation for future large-scale investigations into personalized diagnostic or therapeutic strategies.},
}
@article {pmid41439481,
year = {2026},
author = {Zou, Y and Li, N and Li, X and Kuang, M and Xu, X and Guan, L and Li, X and Zheng, P and Li, L and Wan, J and Lu, N and Liu, J and He, C and Zhu, Y},
title = {Gut microbiota dysbiosis exacerbates acute pancreatitis via Escherichia coli-driven neutrophil heterogeneity and NETosis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606480},
doi = {10.1080/19490976.2025.2606480},
pmid = {41439481},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/microbiology/immunology/complications ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Neutrophils/immunology ; *Extracellular Traps/immunology/metabolism ; *Escherichia coli/physiology ; *Pancreatitis/microbiology/immunology/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Specific Pathogen-Free Organisms ; },
abstract = {Gut microbiota dysbiosis contributes to acute pancreatitis (AP) severity, but the specific microbes and mechanisms remain unclear. In this study, we employed both germ-free (GF) and specific-pathogen-free (SPF) murine models of AP to investigate the role of the intestinal microbiota. Our findings demonstrate that GF mice exhibited markedly attenuated pancreatic injury, inflammatory cell infiltration, and neutrophil extracellular traps (NETs) formation. Through fecal microbiota transplantation (FMT) from AP patients, differential antibiotic modulation, and single-bacterial colonization experiments, we identified Gram-negative bacteria, particularly Escherichia coli (E. coli), as critical microbial drivers of disease exacerbation. Single-cell RNA sequencing revealed that microbiota dysbiosis profoundly reprogrammed both local pancreatic and systemic immune landscapes. Specifically, dysbiosis promoted emergency granulopoiesis in the bone marrow, enhanced neutrophil mobilization and activation, and facilitated the expansion of pro-inflammatory neutrophil subpopulations (Neutrophils_2 and Neutrophils_3). These subsets exhibited upregulated signaling through NETosis-associated pathways, including TLR, NF-κB, and IL-17 axes. Conversely, in GF conditions, we observed a predominance of an anti-inflammatory neutrophil subset (Neutrophils_4), characterized by the expression of tissue repair-associated genes such as Reg1 and Reg2. Shotgun metagenomic profiling of fecal samples from patients with AP revealed an enrichment of E. coli during the acute phase, positively correlating with circulating cell-free DNA, a marker of NETosis. Together, these insights suggest that gut microbiota dysbiosis, notably increased E. coli abundance, may aggravate AP by reshaping immunity and promoting aberrant NETs formation, supporting microbiota or NETs targeted therapies.},
}
@article {pmid41439274,
year = {2026},
author = {Li, Y and Xu, C and Park, H and Omstead, AN and Anees, M and Sherry, C and Khan, AF and Grayhack, E and Weksler, B and Wagner, P and Bartlett, DL and Meltzer, SJ and Zaidi, AH and Goel, A},
title = {A machine-learning informed circulating microbial DNA signature for early diagnosis of esophageal adenocarcinoma.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604334},
doi = {10.1080/19490976.2025.2604334},
pmid = {41439274},
issn = {1949-0984},
mesh = {Humans ; *Esophageal Neoplasms/diagnosis/microbiology/blood ; *Adenocarcinoma/diagnosis/microbiology/blood ; *Machine Learning ; *Early Detection of Cancer/methods ; Barrett Esophagus/diagnosis/microbiology ; Male ; Female ; Middle Aged ; Aged ; Gastroesophageal Reflux/diagnosis/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; *DNA, Bacterial/blood/genetics ; Liquid Biopsy/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Metagenomics ; Biomarkers, Tumor/blood ; },
abstract = {Esophageal adenocarcinoma (EAC) has seen a dramatic rise in incidence in developed countries over the past three decades. Early detection of its precursors-gastroesophageal reflux disease (GERD), Barrett's esophagus (BE), and high-grade dysplasia (HGD) is critical for cancer prevention. This study presents the development and validation of a novel liquid biopsy assay based on circulating microbial DNA (cmDNA) for the early detection of EAC and HGD. Using metagenomic sequencing, we identified significant differences in microbial diversity and composition between EAC and HGD patients, as well as between BE and GERD patients. A total of 46 microbial candidates in tissue and 419 in serum were upregulated in EAC &amp; HGD, with 11 consistently elevated in both sample types. Following qRT-PCR validation and LASSO regression, a 6-marker cmDNA panel was selected. This signature was incorporated into a diagnostic model trained with the XGBoost algorithm, achieving an AUC of 0.93 in the training cohort (52 HGD &amp; EAC cases vs. 54 BE &amp; GERD controls). Importantly, the model demonstrated robust performance in an independent testing cohort (23 HGD &amp; EAC cases vs. 22 BE &amp; GERD controls), yielding AUCs of 0.91 for EAC and 0.88 for HGD. These findings highlight the diagnostic potential of cmDNA-based profiling and support its utility as a minimally invasive, accurate, and generalizable tool for early detection of esophageal adenocarcinoma.},
}
@article {pmid41439238,
year = {2026},
author = {Kumar, A and Solanki, MK and Kumar, M and Kaushik, A and Arya, A and Saikia, M and Gaur, VK and Singh, RP and Singh, SK and Singh, VK and Dufossé, L},
title = {The microbial strategies for the management of chemical pesticides: A comprehensive review.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100519},
pmid = {41439238},
issn = {2666-5174},
abstract = {Chemical pesticides considered as one of the emerging environmental contaminants that severally affect the human health and soil and water ecosystem. Despite their well-documented adverse effects on fruit quality, soil structure, the emergence of pesticide-resistant pests, and human well-being, chemical pesticides are still widely used for crop protection, particularly in developing countries. Although to manage the chemical pesticides, various traditional approaches have been employed, however the higher cost, and the generation of toxic residues have shifted research attention toward eco-friendly and sustainable bioremediation strategies. Microorganisms including the bacteria, fungi, and algae play a crucial role in pesticide degradation by transforming toxic compounds into less toxic forms. However, to optimize microbial bioremediation, a comprehensive understanding of microbial metabolism and physiology is essential. In this context, omics technologies such as genomics, metagenomics, transcriptomics, proteomics, and metabolomics, offer powerful tools for elucidating the molecular mechanisms involved in pesticide degradation. These approaches facilitate the identification of microorganism, key genes, enzymes, and metabolic pathways responsible for the breakdown of pesticide compounds and their by-products. Furthermore, advanced technology like the gene editing can enhance the efficacy of pesticides biodegradation by knocking out undesirable genes or introducing beneficial ones in the microorganisms. The Artificial intelligence also plays a significant role in analysing big data, understanding microbial communities' structure, identifying nature of pesticides and selecting or predicting the microbial species with enhanced pesticides degrading efficacy.},
}
@article {pmid41439237,
year = {2026},
author = {Wang, J and Asif, A and Gu, F and Gu, S and Ding, Y and Gu, Y and Rafiq, MS and Hao, H},
title = {A naturally isolated symbiotic Lactobacillus murinus suppresses multidrug-resistant Campylobacter jejuni via microbial metabolites.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100520},
pmid = {41439237},
issn = {2666-5174},
abstract = {Multidrug-resistant Campylobacter jejuni (MDR C. jejuni), the leading cause of food-borne gastroenteritis worldwide, poses a significant threat to public health and food safety. The intestinal microbiota prevents MDR C. jejuni colonization, but the specific mechanisms remain poorly understood. In this study, we performed a multi-omics analysis of the gut microbiota in C57BL/6 mice, combined with in vitro experiments, to investigate the role of gut microbiota in C. jejuni colonization. Treatment with tylvalosin, a new macrolide, altered the gut microbiota composition, reducing Bifidobacterium longum communities and decreasing levels of short-chain fatty acids (acetic acid, propionic acid, n-butyric acid, i-butyric acid, and i-valeric acid). This disruption of intestinal homeostasis facilitated C. jejuni colonization. Through metagenomic sequencing, we identified and isolated Lactobacillus murinus (L. murinus) from the mice's intestinal flora, which exhibited inhibitory activity against C. jejuni in vitro. Metabolomic analysis and in vitro validation further revealed the significance of L. murinus-derived metabolites. Our results indicate that L. murinus inhibits and kills C. jejuni in a co-culture system by secreting acids that synergistically induce apoptosis, leading to cell membrane disruption and the release of cellular contents.},
}
@article {pmid41439190,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Portier, SC and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf224},
pmid = {41439190},
issn = {2730-6151},
abstract = {Because accessing the small intestine is technically challenging, studies of the small intestinal microbiome are predominantly conducted in patients rather than in healthy individuals. Invasive clinical procedures, such as endoscopy or surgery, usually performed for therapeutic purposes, are typically required for sample collection. Although stomas offer a less invasive means for repeated sampling, their use remains restricted to patient populations. As a result, the small intestinal microbiome of healthy individuals remains largely understudied. This study evaluated a novel ingestible medical device for collecting luminal samples from the small intestine. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics, and culturomics were used to assess the effectiveness of the medical device in characterizing the healthy small intestinal microbiome and identifying potential biomarkers. The small intestinal microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct small intestinal metabolic footprint, with bile acids and amino acids being the most abundant metabolite classes. Host- and host/microbe-derived bile acids were particularly abundant in small intestinal samples. Using a fast culturomics approach on two small intestinal samples, we achieved species-level characterization and identified 90 bacterial species, including five potentially novel ones. This study demonstrates the efficacy of our novel sampling device in enabling comprehensive small intestinal microbiome analysis through an integrative, multi-omics approach. This approach allows distinct microbiome signatures to be identified between small intestinal and fecal samples.},
}
@article {pmid41439189,
year = {2025},
author = {Ghotbi, M and Ghotbi, M and D'Agostino, E and Kanitz, M and Needham, DM},
title = {From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf218},
pmid = {41439189},
issn = {2730-6151},
abstract = {Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can aid where 'conventional' filtrater-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural surface seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 μL of lysate from seawater microvolume extractions ranging from 100-1000 μL consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 μL lysates from 15 microvolume samples (100 μL) captured 83 high- and draft-quality, diverse bacterial genomes and 430 complete, high and medium quality viral contigs. Our approach enables scaling of rRNA gene sequencing and metagenomic library prep for high-throughput experimentation for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments by facilitating higher sample numbers and lowering sample volume needs. However, its potential bias against Gram-positive bacteria should be considered when applying to environments where these taxa are abundant.},
}
@article {pmid41439067,
year = {2025},
author = {Patel, B and Vijayan, V and Tran, K},
title = {Microbial Cell-Free DNA Sequencing in the Identification of Rhizopus Arrhizus in an Adolescent With Gastrointestinal Mucormycosis.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97426},
pmid = {41439067},
issn = {2168-8184},
abstract = {Mucormycosis is a rare and often fatal angioinvasive fungal infection, typically occurring in immunocompromised hosts. Gastrointestinal mucormycosis (GM), a rare manifestation of mucormycosis, is particularly challenging to diagnose due to its non-specific clinical presentation and overlap with other abdominal pathologies. We report the case of a previously healthy 15-year-old male with Class I obesity who presented with perforated appendicitis and developed septic shock and multi-organ failure for which he was admitted to the pediatric intensive care unit. Upon arrival, the patient was intubated and placed on mechanical ventilation. He was started on vasopressor support and intravenous antibiotics. An orogastric tube was placed for bowel decompression, but on hospital day 2, he developed profuse bloody output from the orogastric tube. Imaging revealed mixed-density debris surrounding the gastric lumen. His condition deteriorated with ongoing fevers and signs of gastrointestinal bleeding. Conventional infectious disease tests were unrevealing. Metagenomic next-generation sequencing of plasma cell-free DNA (Karius test) detected Rhizopus arrhizus, leading to the initiation of antifungal therapy with liposomal amphotericin B and posaconazole. Exploratory laparotomy revealed necrotic ulcers, extensive gastric and bowel necrosis and infarctions, confirming GM. Despite aggressive antifungal treatment and surgical debridement, the patient ultimately succumbed to his disease. This case underscores the importance of considering mucormycosis in critically ill patients without traditional risk factors and highlights the utility of microbial cell-free DNA sequencing as a non-invasive diagnostic adjunct in children with mucormycosis when tissue sampling is impractical.},
}
@article {pmid41438456,
year = {2025},
author = {Han, P and Yuan, X and Li, C and Zhang, L and Cui, J},
title = {Case Report: Pneumocystis jiroveci pneumonia: report of five children with the nephrotic syndrome and review of the literature.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1687471},
pmid = {41438456},
issn = {2296-2360},
abstract = {OBJECTIVE: To retrospectively analyze the clinical characteristics, treatment, and prognosis of five pediatric patients with nephrotic syndrome who developed Pneumocystis carinii pneumonia (PJP) after long-term use of steroids and tacrolimus.<br><br>METHODS: A review was conducted on five cases of nephrotic syndrome in children who developed Pneumocystis pneumonia after long-term treatment with steroids and tacrolimus. The initial symptoms, early clinical characteristics, and imaging changes were summarized. Among these cases, two were diagnosed through alveolar lavage fluid metagenomic testing and three through sputum metagenomic testing (BGI Genomics Co.), all indicating (pneumocystis carinii pneumonia. All five patients received early treatment with sulfa drugs, with three of them also receiving caspofungin.<br><br>RESULTS: One child died and four were discharged with symptomatic improvement.<br><br>CONCLUSION: PJP is a severe opportunistic infection that can progress rapidly and lead to life-threatening respiratory failure, particularly in immunocompromised individuals. Among children with nephrotic syndrome (NS), prolonged exposure to glucocorticoids, tacrolimus, or other immunosuppressive agents markedly increases susceptibility to PJP. Therefore, heightened clinical vigilance, early etiological diagnosis, and prompt initiation of appropriate therapy are essential to improving clinical outcomes in this population.},
}
@article {pmid41438409,
year = {2025},
author = {Carrera-Faja, L and Jasso, MV and Sarmiento, I and Cabrera-Gumbau, JM and Espunyes, J and Martínez-Urtaza, J and Cabezón, O},
title = {Metagenomic survey reveals Volzhskoe tick virus in Hyalomma ticks for the first time in western Europe, North-Eastern Spain.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101279},
pmid = {41438409},
issn = {2352-7714},
abstract = {Ticks are reservoirs and vectors of several emerging arboviruses, yet their associated virome remains poorly characterized. Using meta-transcriptomic sequencing, we surveyed Hyalomma marginatum and Rhipicephalus bursa ticks collected from areas with contrasting Crimean-Congo haemorrhagic fever virus (CCHFV) seroprevalence in wild ungulates in north-eastern Spain, a region with no reported CCHF cases in humans. While CCHFV RNA was not detected, we identified Volzhskoe tick virus (VTV), a recently described member of the class Bunyaviricetes, first identified in Russia, in H. marginatum from the Ports de Tortosa i Beseit Natural Park-making its first report of VTV in Western Europe. These findings suggest a broader distribution of VTV and raise important questions about its potential interactions with CCHFV, pathogenicity and host range. Moreover, our approach underscores the value of metagenomic surveillance for improving our understanding of tick-borne virus ecology.},
}
@article {pmid41438378,
year = {2025},
author = {Yang, W and Liu, H and Xu, R and Peng, Y and Xu, T and Yang, Y and Li, Y and Xiang, H},
title = {Integrated genomics, metagenomics and metatranscriptomics to reveal the biocontrol mechanism of Bacillus velezensis JY10 against tobacco target spot disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1707097},
pmid = {41438378},
issn = {1664-302X},
abstract = {Tobacco target spot (TTS) disease, a prevalent fungal disease caused by Rhizoctonia solani, severely reduces tobacco yield and quality, imposing substantial economic losses on the tobacco industry. In this study, we employed a biological control approach against TTS using a Bacillus velezensis JY10 isolated from healthy tobacco stems. We further elucidated the mechanism of JY10 in controlling TTS through genomics, metagenomics and metatranscriptomics. The results showed that JY10 exhibited robust inhibitory effects against R. solani, with an inhibition rate exceeding 95%, and achieved a TTS control efficacy of 68.63% in pot experiments. Whole-genome sequencing demonstrated that the JY10 genome spans 3,929,772 bp, contains 4,026 protein-coding genes, and has a GC content of 46.5%. AntiSMASH analysis predicted 12 secondary metabolite biosynthetic gene clusters, encoding antimicrobial compounds such as surfactin, fengycin, difficidin, bacillaene, bacillibactin, macrolactin H, and bacilysin. Metagenomic profiling showed that JY10 treatment had no significant influence on tobacco phyllosphere and rhizosphere microbiome structure, however, it significantly increased the relative abundance of beneficial microbes, including Bacillus, Pseudonocardia, and Pseudomonas. Metatranscriptomic analysis revealed that JY10 might enhance tobacco TTS resistance by modulating oxidative phosphorylation pathway and upregulating several antibiotics biosynthesis. Taken together, JY10 may employ a dual control strategy against TTS, involving the direct production of antifungal compounds, as well as indirectly increasing the abundance of beneficial microbes and modulating their oxidative phosphorylation and antibiotic synthesis pathways in the phyllosphere and rhizosphere of tobacco. These findings provide a theoretical foundation for understanding biocontrol mechanisms of JY10 and introduce a promising bacterial resource for the development of sustainable TTS management strategies.},
}
@article {pmid41438339,
year = {2026},
author = {Van Espen, L and Brol, MJ and Close, L and Schierwagen, R and Gu, W and Keller, MI and Balogh, B and Fullam, A and De Coninck, L and Nakamura, T and Kuhn, M and Bork, P and Laleman, W and Bajaj, JS and Papp, M and Schnabl, B and Trebicka, J and Matthijnssens, J and , },
title = {L actococcus A phages predict ACLF while Enterococcus B phages predict bacterial infection in decompensated cirrhosis.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101622},
pmid = {41438339},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: As portal hypertension progresses in cirrhosis, bacterial translocation across a compromised gut barrier leads to endotoxemia, systemic inflammation and immune dysfunction. Gut phages play a key role in these processes by influencing bacteria-host interactions. This study explores the role of the human gut virome in acute decompensation of cirrhosis and acute-on-chronic liver failure (ACLF).<br><br>METHODS: The fecal virome was longitudinally assessed by metagenomic sequencing in two independent cohorts: 93 patients (292 samples) with acute decompensation or ACLF from the PREDICT study, and 94 patients (94 samples) with decompensated cirrhosis undergoing TIPS (transjugular intrahepatic portosystemic shunt) surgery collected in a tertiary care setting. Besides descriptive analysis, phages were grouped according to their predicted bacterial host and lifestyle, and associated with clinical parameters.<br><br>RESULTS: Phage alpha-diversity was higher in patients with ACLF and correlated with ACLF severity. In the absence of ACLF, the phageome was dominated by virulent phages, but in ACLF, temperate phages became more prevalent. Genus-level analysis showed that phageomes were highly patient-specific. Lactococcus A phages were the only phage-host group predicting ACLF development (odds ratio [OR] = 14; Fisher test p = 0.0129). Enterococcus B phages (OR = 14.7; p = 0.0015; adj. p = 0.037) and their bacterial hosts (OR = 2.8; p = 0.020) were significantly more prevalent in cases of proven systemic bacterial infection. The presence of both phage families was linked to increased 90-day mortality rates.<br><br>CONCLUSION: ACLF is characterized by increased fecal virome diversity and a shift from virulent toward temperate phages at disease onset. Our study links Lactococcus A phages to ACLF development, and Enterococcus B phages to bacterial infection, while both are associated with increased 90-day mortality.<br><br>CLINICAL TRIAL NUMBER: NCT03056612.<br><br>IMPACT AND IMPLICATIONS: The human gut virome is a poorly investigated part of the human gut microbiome, especially in the context of decompensated cirrhosis and acute-on-chronic liver failure. This study identified two phage groups (Lactococcus A phages and Enterococcus B phages) with particular prognostic value. In the future, virome analysis of fecal samples could be useful for patient stratification in clinical practice.},
}
@article {pmid41437628,
year = {2025},
author = {Barth, P and Förster, F and Jaenicke, S and Thelen, F and Rossbach, O and Weber, F and Shalamova, L and Goesmann, A},
title = {PARANOiD: Pipeline for Automated read ANalysis of iCLIP Data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf673},
pmid = {41437628},
issn = {1367-4811},
abstract = {MOTIVATION: RNA-protein interactions play essential roles in every living organism, with RNA transcription, processing, and translation being just a few examples. Therefore, determining the set of RNAs that are bound by individual RNA-binding proteins, as well as the precise location of the interaction, is crucial for biological understanding. CLIP (UV-cross-linking and immunoprecipitation) is a method developed to study these interactions. Several variations of the CLIP protocol have been developed, e.g., iCLIP (individual-nucleotide resolution CLIP), which offers nucleotide-precise resolution of the cross-linking event.<br><br>RESULTS: PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations, and several additional steps, which can be used to detect specific characteristics, e.g., definite distances between cross-link events or identify binding motifs. Additionally, results are visualized as statistical plots for a quick overview and as standardized bioinformatics file formats, which can be used for further analysis steps.<br><br>AVAILABILITY: PARANOiD is published under the MIT license and is available from https://github.com/patrick-barth/PARANOiD. The documentation is available at https://paranoid.readthedocs.io/en/latest/index.html.<br><br>CONTACT: patrick.barth@computational.bio.uni-giessen.de.},
}
@article {pmid41437386,
year = {2025},
author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R},
title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02315-3},
pmid = {41437386},
issn = {2049-2618},
abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.<br><br>METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97&#x2009;&#xb1;&#x2009;0.01. Synthetic donor-recipient simulations (&#x3b1;&#x2009;=&#x2009;0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.<br><br>RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2]&#x2009;=&#x2009;0.12, p&#x2009;<&#x2009;0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC&#x2009;=&#x2009;0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC&#x2009;&#x2265;&#x2009;0.8). Entropy-based uncertainty analysis identified tipping zones (&#x3b1;&#x2009;=&#x2009;0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.<br><br>CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.},
}
@article {pmid41437205,
year = {2026},
author = {Dinesh, D and Morgan, XC and Kim, H and Scott, TM and Garelnabi, M and Lee, JS and Mangano, KM and Nguyen, LH and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Gut Microbial Variations Associated With Proton Pump Inhibitor Use in the Boston Puerto Rican Health Study.},
journal = {Pharmacology research &amp; perspectives},
volume = {14},
number = {1},
pages = {e70205},
doi = {10.1002/prp2.70205},
pmid = {41437205},
issn = {2052-1707},
support = {RF1AG075922/AG/NIA NIH HHS/United States ; P01 AG023394/NH/NIH HHS/United States ; P50 HL105185/NH/NIH HHS/United States ; R01 AG055948/NH/NIH HHS/United States ; R01 NS09772/NH/NIH HHS/United States ; //University of Massachusetts/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Aged ; Middle Aged ; Prospective Studies ; Boston ; Cross-Sectional Studies ; Puerto Rico/ethnology ; Hispanic or Latino ; Feces/microbiology ; White ; },
abstract = {Proton pump inhibitors (PPI), used to treat gastrointestinal disorders, are associated with alterations in the gut microbiome. However, this is understudied in Puerto Ricans who have unique lifestyle characteristics. Puerto Ricans, including participants of the Boston-Puerto Rican Health Study (BPRHS), report high PPI use. Therefore, we examined gut microbial variations associated with PPI use in the BPRHS. BPRHS is a prospective cohort. 309 BPRHS participants self-reported PPI use and self-collected, metagenomically profiled, stool samples. PPI use was classified as any use in the past 30 days. Cross-sectional associations between gut microbial taxa, functional pathways, and PPI use were examined using omnibus analyses, multivariate linear modeling in MaAsLin2, and random forest classifier in feature-wise analyses. We further compared our results with the non-Hispanic Health Professionals Follow-Up Study (HPFS) to validate key findings and examine ethnicity-related differences. Among 309 participants (mean age 68.8 years; female 74.6%), 112 (36%) self-reported PPI use. After adjusting for relevant covariates, we observed an enrichment of Streptococcus parasanguinis (β = 3.16, FDR p = 0.01), S. anginosus (β = 2.89, FDR p < 0.01), S. salivarius (β = 2.56, FDR p = 0.01), S. gordonii (β = 1.98, FDR p = 0.15), and Rothia mucilaginosa (β = 1.54, FDR p = 0.06), among PPI users compared to non-users. Streptococci, Lactobacilli, and Enterococci predominantly contributed to the functional pathways associated with PPI use. The observed enrichment of oral-typical taxa, such as Streptococci, among PPI users in the BPRHS suggests the potential of PPIs to alter gut microbial composition. More studies are needed to understand the impact of PPI use on the gut microbiome in different ethnicities. Trial Registration: Parent study (BPRHS) NCT01231958.},
}
@article {pmid41436743,
year = {2025},
author = {Prajapati, SK and Shukla, R and Kumar, V and Yadav, D and Lekkala, L and Szekeres, C and Ma, Y and Jain, S and Yadav, H},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e102998},
doi = {10.1002/alz70855_102998},
pmid = {41436743},
issn = {1552-5279},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/immunology ; Aged ; Female ; *Cognitive Dysfunction/immunology/microbiology ; Middle Aged ; *Alzheimer Disease/immunology/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) pathogenesis has been linked to the microbiota-immune-brain axis; however, the relationship between gut microbiota, immune activity, and cognitive impairment remains unclear. Thus, this study examines the connection between intestinal microbial composition, immune cell phenotype, and cognitive function in older adults.<br><br>METHOD: Data and biological samples were obtained from participants aged &#x2265;60 years (Control, n = 30; mild cognitive impairment (MCI), n = 30) from the MiaGB (Microbiome in Aging Gut and Brain) consortium, a multi-site, clinical study. Cognitive function was assessed using Montreal Cognitive Assessment (MoCA) scores, immunophenotyping through flow cytometry, stool microbiome analysis using whole-genome metagenomics, and bulk transcriptomics analysis was carried out.<br><br>RESULTS: The abundance of immune cells such as granulocytes, lymphocytes, T-cells, and NK cells was significantly decreased in MCI group. Interestingly, the levels of CD4+ were reduced while CD8+ cells increased in MCI participants compared to controls. Microbial profiling revealed distinct bacterial signatures, with MCI participants showing higher relative abundances of Eubacterium hallii, Parabacteroides distasonis, Eggerthella_sp_CAG_298, Dorea formicigenerans and Alistipes finegldii. Differential expression analysis of transcriptomics data identified 1632 upregulated and 240 downregulated genes. Gene ontology and pathway analysis revealed that upregulated genes are involved in several immune functions such as response to stimulus, adaptive immune response, lymphocyte, and T cell activation, while downregulated genes are linked to nervous system functions and signaling processes such as neuron projection. Transcriptomics analysis further highlighted that several downregulated genes are involved in the key pathways that participate in the neural functions.<br><br>CONCLUSION: These distinct bacteria, immune cells, and gene expression profiles suggest that alterations in immune cell populations, gene expression, and gut microbiota are associated with cognitive function in aging, highlighting potential interactions between the microbiota-immune-brain axis and cognitive impairment.},
}
@article {pmid41436649,
year = {2025},
author = {Sakurai, R and Fukuda, Y and Tada, C},
title = {Culture-independent discovery of a novel thermotolerant lipase and its producer from mesophilic anaerobic digestion sludge.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-025-13674-0},
pmid = {41436649},
issn = {1432-0614},
abstract = {Anaerobic digestion of lipid-rich wastes holds significant potential for enhanced biomethane production, due to the high energy density of lipids. However, to fully harness this potential, a deeper understanding of lipolytic microorganisms is essential, as key microbial players involved in lipid hydrolysis remain largely unidentified. In this study, we employed an integrated approach combining zymography, metaproteomics, and metagenomics to identify the lipolytic microorganisms from anaerobic digester sludge. This activity-based strategy identified a novel lipase distantly related to known lipases. Besides, although this lipase originates from a mesophilic environment, it exhibited unexpected extremophilic-like properties, with maximal activity at 97.5 °C and pH 11. We further reconstructed a metagenome-assembled genome encoding this lipase and demonstrated that it likely represents a novel genus closely related to Candidatus Scatomorpha. Metabolic reconstruction suggested that this bacterium hydrolyzes extracellular lipids and utilizes the resulting hydrolysate, glycerol, to produce lactate and ethanol. Habitat analysis revealed that this bacterium is specifically detected in anaerobic digesters, particularly those processing lipid-rich waste. These findings highlight the pivotal role of this bacterium in anaerobic lipid degradation.},
}
@article {pmid41436448,
year = {2025},
author = {Manghi, P and Antonello, G and Schiffer, L and Golzato, D and Wokaty, A and Beghini, F and Mirzayi, C and Long, K and Gravel-Pucillo, K and Piccinno, G and Gamboa-Tuz, SD and Bonetti, A and D'Amato, G and Azhar, R and Eckenrode, K and Zohra, F and Giunchiglia, V and Keller, M and Pedrotti, A and Likhotkin, I and Elsafoury, S and Geistlinger, L and Blanco-Miguez, A and Thomas, AM and Zolfo, M and Ramos, M and Valles-Colomer, M and Tamburini, S and Asnicar, F and Jones, HE and Huttenhower, C and Carey, V and Davis, S and Pasolli, E and Oh, S and Segata, N and Waldron, L},
title = {Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66888-1},
pmid = {41436448},
issn = {2041-1723},
support = {5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Large public datasets of the human microbiome now exist but combining them for large-scale analysis is difficult due to a lack of standardization. We developed curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata from 94 studies and 42 countries. This large and diverse resource allows for meta-analysis of the links between microbes and human health. Through meta-analysis, we identified hundreds of microbial species and thousands of microbial functions significantly associated with a person's sex, age, body mass index, and disease status, and catalog these as references. We developed an "oral enrichment score" (OES) based on the relative abundance of bacteria typically found in the oral cavity and not in the gut. Higher OES in the gut is a consistent feature in individuals with disease, suggesting that the relative abundance of oral bacteria in the gut is a simple and quantifiable signal of altered microbiome health. These analyses identify modest but widely shared patterns in human microbiomes, serving as a reproducible and readily updatable reference.},
}
@article {pmid41435895,
year = {2025},
author = {Zhang, PP and Cui, MY and Yang, SY and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF},
title = {Astragalus membranaceus improves blood glucose and renal function in diabetic kidney disease mice via gut microbial metabolite axis.},
journal = {Fitoterapia},
volume = {189},
number = {},
pages = {107048},
doi = {10.1016/j.fitote.2025.107048},
pmid = {41435895},
issn = {1873-6971},
abstract = {Recent studies have demonstrated the therapeutic potential of Astragalus membranaceus in diabetic kidney disease (DKD); however, the underlying mechanisms remain incompletely elucidated. In this study, we established a streptozotocin-induced DKD mouse model to evaluate the effects of A. membranaceus extract (AME) on glycemic control, renal function, gut microbiota composition, and metabolic profiles. Biochemical analyzes revealed that A. membranaceus significantly attenuated hyperglycemia and improved renal function, as indicated by reduced serum creatinine and blood urea nitrogen levels. Metagenomic sequencing demonstrated that A. membranaceus reversed microbial dysbiosis by suppressing pathogenic bacteria (e.g., Aerococcus urinaeequi) and enriching beneficial probiotics (e.g., Thomasclavelia cocleata). Furthermore, LC/MS-based metabolomics identified key metabolic pathways, including glycerophospholipid metabolism and bile acid synthesis, as potential mediators of the therapeutic effects. These findings underscore the crucial role of the gut-renal axis in DKD pathogenesis and provide a mechanistic basis for the clinical application of A. membranaceus.},
}
@article {pmid41435665,
year = {2025},
author = {Li, Y and Ma, J and Li, X and Ling, T and Zhang, Y and Xia, X},
title = {Integrating metagenomics analysis and machine learning to identify drivers of antibiotic resistance genes abundance in microplastic-contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140886},
doi = {10.1016/j.jhazmat.2025.140886},
pmid = {41435665},
issn = {1873-3336},
abstract = {Microplastics (MPs) in soil ecosystems significantly influence antibiotic resistance genes (ARGs) transmission and abundance. However, a holistic understanding of how MP characteristics interact with climatic and edaphic factors to drive ARGs fluctuations remain unclear. By integrating global metagenomic datasets, we compared divergence of soil microbial communities and antibiotic resistomes across MP types and applied interpretable machine learning (ML) techniques to explore ARG dynamics. Results revealed distinct microbial community and resistome patterns associated with MP types, explaining 31.0-36.2 % of the variation in bacterial structure and ARG profiles. Moreover, specific microbial biomarkers for 7 MP types underscore their significant role in structuring communities. Biodegradable MPs (e.g., polybutylene succinate, polyhydroxyalkanoates) exhibited reduced bacterial diversity but higher ARG abundance risk than conventional MPs. Among ML models, Gradient Boosted Decision Trees exhibited superior predictive performance for ARG abundance, with average R[2] values of 0.98 for training and 0.93 for testing. Driver importance analysis identified bacterial genera (mean contribution: 69.86 %) as the dominant factor in the abundance of primary ARG subtype, followed by climate (13.89 %), soil properties (9.55 %), and MP characteristics (6.70 %). This study provides novel insights into the environmental drivers of ARG dynamics in MP-contaminated soils, highlighting the importance of incorporating climate scenario projections into future ecological risk management strategies for MPs and ARGs.},
}
@article {pmid41435471,
year = {2025},
author = {Sun, M and Kong, L and Farooq, MA and Che, L and Tian, W and Wang, C and Wang, L and Lou, Z},
title = {Comparison of the plastisphere and surrounding waste in landfills: Bacterial community assembly and functional evolution.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128372},
doi = {10.1016/j.jenvman.2025.128372},
pmid = {41435471},
issn = {1095-8630},
abstract = {Plastic waste in landfills forms unique microbial habitats termed the plastisphere, a critical but underexplored niche in anaerobic, dark landfill environments. To advance plastisphere research in such terrestrial anaerobic settings and inform landfill management, this study employed an integrated approach of 16S rRNA sequencing and metagenomics to systematically investigate the bacterial community structure, assembly mechanisms, and metabolic functions of the plastisphere. Network analysis indicated that the plastisphere sustains a simplified yet highly modular co-occurrence network shaped by competitive niche partitioning. The plastisphere and surrounding waste exhibited no overlap in network keystone taxa. Key plastisphere taxa-including g_Devosia, g_Rummeliibacillus, and g_Dethiobacter-demonstrated enhanced carbon utilization and stress perception capabilities, playing crucial roles in community assembly and plastic degradation. Although stochastic processes dominated community assembly (73.75 %), homogeneous selection (HoS) driven by plastic properties and keystone taxa enriches pathogens (e.g., Microbacterium spp.) and nitrogen-cycling (e.g., Pseudohongiella) guilds. Metagenomic analysis confirmed the enrichment of denitrification (narB, nosZ) and sulfite reduction (sir, cysCDHIJN) genes, indicating elevated risks of N2O and H2S emissions, especially during early landfill stabilization. Redundancy analysis identified pH, biodegradable organic matter (BDM), and total Kjeldahl nitrogen (TKN) as key environmental drivers. These findings establish the landfill plastisphere as a reservoir of plastic-degrading and potentially pathogenic microorganisms, with important implications for greenhouse gas emissions, odor control, and landfill management strategies. This study provides foundational insights into the ecological consequences of anthropogenic microhabitats in terrestrial environments, bridging critical knowledge gaps in plastisphere ecosystems within landfills-an anaerobic, dark environment rich in organic matter.},
}
@article {pmid41435039,
year = {2025},
author = {Elorriaga, IT and Imatz, E and Ibarlucea, B and Cano, A and Sanmartín, E and Tueros, I and Ayala, U and de Heredia, AG and Zaldua, C and Zugaza, JL and Aleman, IT and Garcia-Sebastian, M and Martínez-Lage, P and Erramuzpe, A},
title = {Public Health.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e099250},
doi = {10.1002/alz70860_099250},
pmid = {41435039},
issn = {1552-5279},
mesh = {Humans ; Aged ; *Public Health ; Female ; Male ; Aged, 80 and over ; Biomarkers ; Middle Aged ; *Aging ; *Healthy Aging ; },
abstract = {BACKGROUND: The ITTHACA project is a collaborative initiative involving six research institutions from the Basque Country including Universities, Health, Technology and Basic Research Institutions. It builds upon the ongoing CITA GO-ON) CITA Go-On study, ClinicalTrials.gov, NCT04840030) cohort study, which adapts the Finnish FINGER [Ngandu, T., et al. 2015] model to the local context. ITTHACA focuses on enhancing healthy aging by identifying markers, prediction models and sensors for in vivo monitoring that allow the establishment and implementation of combined intervention strategies in the population.<br><br>METHOD: This one-year randomized-controlled trial (total n&#xa0;=&#xa0;250; 125 control and 125 intervention), focused on 60-85-year-old males and females at risk of dementia, adopts a multimodal approach. Biomarker identification includes proteomics and metabolomics in biological fluids (blood) and 16S metagenomics and lipidomics in the gut microbiome (stool), as well as employing a FINGER-like mice model. Biosensor technology under development includes multi-channel bioimpedance spectroscopy for tissue analysis and electrochemical sensors for real-time detection of aging markers in biofluids. Predictive modeling integrates data from these analyses and multiple domains-cognition, cardiovascular health, voice, food texture perception and habits-to generate diagnostic tools that monitor biological aging and inform early interventions. A proof-of-concept study in an older population sample, with special attention to user experience, will evaluate the potential benefits of these findings in improving the quality of life for older adults.<br><br>RESULT: Not applicable. The ITTHACA project is ongoing, with outcomes expected to include validated biomarkers, novel biosensors, and predictive models that facilitate early interventions.<br><br>CONCLUSION: ITTHACA demonstrates the power of interdisciplinary collaboration in tackling the complex multidomain challenge of aging. By leveraging the expertise of complementary Basque Country Research Centers, this initiative is poised to produce innovative resources for prolonging healthy and autonomous living. The project's outcomes are expected to support new therapeutic strategies and socio-healthcare interventions that address the rising prevalence of aging-related conditions, including cognitive decline.},
}
@article {pmid41434599,
year = {2025},
author = {Dinesh, D and Morgan, X and Scott, TM and Garelnabi, M and Mangano, KM and Noel, SE and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Public Health.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e098660},
doi = {10.1002/alz70860_098660},
pmid = {41434599},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Aged ; *Public Health ; Puerto Rico/ethnology ; Prospective Studies ; Feces/microbiology/virology ; *Cognition/physiology ; Hispanic or Latino ; Boston ; Cross-Sectional Studies ; Dysbiosis ; *Virome ; Aged, 80 and over ; Middle Aged ; Alzheimer Disease ; White ; },
abstract = {BACKGROUND: Gut bacterial variations and dysbiosis may influence cognitive function via the microbiome-gut-brain-axis. Gut viruses may also, directly or indirectly, impact cognitive function by modulating the gut bacteria. Hispanics/Latinos, who may have unique microbiome characteristics, are at a higher risk of Alzheimer's disease and related dementia. There is a lack of research on the gut microbiome and, especially, the virome in Hispanics/Latinos. Here, we examined variations in the gut bacteriome and virome associated with cognitive function in the Boston Puerto Rican Health Study (BPRHS), a prospective cohort of older Puerto Rican adults residing in the Boston area.<br><br>METHOD: This study was conducted in 316 BPRHS participants with fecal metagenomic sequencing and cognitive assessments, summarized as a composite global cognitive score (GCS). Taxonomic profiling of the gut bacteriome was performed using MetaPhlAN 4.0. Gut virome profiles from shotgun sequencing were generated using BAQLaVa 1.0. Cross-sectional associations between bacterial and viral composition and GCS were assessed using alpha (Shannon) and beta (Bray-Curtis) diversity indices. Feature-wise testing was performed using multivariate linear regression (MaAsLin2) to identify bacterial and viral taxa associated with the GCS.<br><br>RESULT: Among 316 participants (mean age 68.7 years, 70.9% female), there were no differences in overall bacterial or viral composition, measured by alpha and beta diversity, based on GCS. In feature-wise analyses, adjusted for age, sex, and BMI, among participants with higher GCS (better cognitive function), we observed an enrichment of Faecalibacterium prausnitzii bacterium (&#x3b2;&#xa0;=&#xa0;0.78, p&#xa0;=&#xa0;0.01, FDR p&#xa0;=&#xa0;0.22), and depletion of the phage Carjivirus communis (&#x3b2;&#xa0;=&#xa0;-1.07, p&#xa0;<&#xa0;0.01, FDR p&#xa0;=&#xa0;0.09).<br><br>CONCLUSION: The observed results suggest an enrichment of F. prausnitzii, a beneficial butyrate producing taxa, among participants with better cognitive function, and enrichment of Carjivirus communis, a Crassvirales dsDNA Bacteroidetes phage, among participants with worse cognitive function. A recent study reported an association between Bacteroidetes phages and amyloid &#x3b2; and Alzheimer's disease pathology. Gut viral variations may modulate gut bacteria, impacting cognitive function. Future work will test interactions of the gut bacteriome, virome and their functional pathways, as related to cognitive function in Puerto Rican adults.},
}
@article {pmid41434594,
year = {2025},
author = {Fernando, WM and Martins, RN and Rainey-Smith, SR and Sohrabi, HR and Ramachandra, S and Dissanayaka, SU},
title = {Public Health.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e096704},
doi = {10.1002/alz70860_096704},
pmid = {41434594},
issn = {1552-5279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Aged ; *Alzheimer Disease/microbiology/genetics ; *Probiotics ; Apolipoprotein E4/genetics ; *Public Health ; Feces/microbiology ; Middle Aged ; Australia ; Sex Factors ; Age Factors ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder, with evidence suggesting gut microbiota plays a critical role in its onset and progression. Shifts in probiotic communities during the preclinical phase may influence disease pathways through gut-brain interactions. This study investigates how age, sex, and APOE ε4 genotype impact probiotic composition and microbial metabolite production in cognitively unimpaired individuals.<br><br>METHOD: Stool samples from 123 participants in the Australian Imaging Biomarkers and Lifestyle (AIBL) study and WA Memory Study (WAMS) were analysed. Participants were grouped by age (<70, &#x2265;70 years), sex, and APOE &#x3b5;4 carrier status. Metagenomic sequencing assessed gut microbial composition, focusing on probiotics like Bifidobacterium and Lactobacillus. Gas-liquid chromatography measured short-chain fatty acids (SCFAs), including butyrate, propionate, and acetate.<br><br>RESULT: Gut Microbiota Composition: Dominant bacterial phyla included Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes across all groups. Age-Related Changes: Older participants (&#x2265;70 years) showed significant declines in Bacteroidetes and Firmicutes, reflecting reduced microbial diversity. Sex-Specific Differences: Females had lower Firmicutes levels, reducing butyrate production, essential for inflammation control and brain health. APOE &#x3b5;4 Carriers: Older APOE &#x3b5;4 carriers showed a decline in butyrate-producing bacteria, particularly Faecalibacterium prausnitzii, leading to reduced butyrate and elevated acetate levels. Sex and APOE &#x3b5;4: Female APOE &#x3b5;4 carriers &#x2265;70 exhibited the most pronounced butyrate decline, indicating increased vulnerability to dysbiosis and inflammation. Probiotic Alterations: Key probiotics, including Bifidobacterium and Lactobacillus, were significantly reduced in older APOE &#x3b5;4 carriers.<br><br>CONCLUSION: Age, sex, and APOE &#x3b5;4 status significantly influence gut microbiota composition and SCFA production at the preclinical stage of AD. Reduced butyrate levels, particularly in older female APOE &#x3b5;4 carriers, highlight the importance of gut health in mitigating AD risk. These findings suggest targeted probiotic interventions could restore gut balance and delay AD progression.},
}
@article {pmid41433308,
year = {2025},
author = {Konganti, K and Kase, JA and Gonzalez-Escalona, N},
title = {Centriflaken: An automated data analysis pipeline for assembly and in silico analyses of foodborne pathogens from metagenomic samples.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0329425},
doi = {10.1371/journal.pone.0329425},
pmid = {41433308},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Foodborne Diseases/microbiology ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; Food Microbiology ; Computer Simulation ; Metagenome ; Computational Biology/methods ; Data Analysis ; },
abstract = {Rapid and comprehensive analysis of metagenomic data from samples associated with foodborne outbreaks is of critical importance in food safety. Equally important is the need for automated analysis pipelines that allow the rapid and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking from metagenomic data. Here, we present centriflaken, an automated precision metagenomics pipeline for detecting and characterizing Shiga toxin-producing Escherichia coli (STEC) from metagenomic data. centriflaken streamlines the process of generating metagenome-assembled genomes (MAGs) and conducting in silico analyses of STECs, significantly reducing the time and manual effort required for comprehensive pathogen profiling. centriflaken was validated using Oxford Nanopore long-read sequencing data from agricultural water enrichments, successfully reproducing results from our previous study that involved multiple manual bioinformatics steps (Maguire et al., 2021). The tool's efficacy was further demonstrated through its application to ZymoBIOMICS microbial community standards and 21 additional irrigation water samples, completing STEC precision metagenomics analyses in less than 7 hours per sample. centriflaken's versatility allows for the analysis of user-defined taxa beyond STEC, including other foodborne pathogens like Listeria monocytogenes or Salmonella. The pipeline generates comprehensive summary plots and tables, accessible through a MultiQC HTML report. Designed for portability, centriflaken packages all software dependencies within containers and virtual environments. This open-source tool is available on GitHub under the MIT license (https://github.com/CFSAN-Biostatistics/centriflaken), offering a powerful resource for rapid, automated pathogen detection and characterization in food safety applications.},
}
@article {pmid41432724,
year = {2025},
author = {Zhang, Z and Ye, B and He, J and Xiang, L and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Li, Y and Ju, J and Liu, Y and Xia, M},
title = {Microbial metabolites associated with healthy lifestyles in relation to metabolic syndrome and vascular health: a cross-sectional study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143325},
doi = {10.1128/msystems.01433-25},
pmid = {41432724},
issn = {2379-5077},
abstract = {UNLABELLED: Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.<br><br>IMPORTANCE: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.},
}
@article {pmid41432437,
year = {2025},
author = {Bowerman, KL and Lu, Y and McRae, H and Volmer, JG and Zaugg, J and Pope, PB and Hugenholtz, P and Greening, C and Morrison, M and Soo, RM and Evans, PN},
title = {Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160825},
doi = {10.1128/msystems.01608-25},
pmid = {41432437},
issn = {2379-5077},
abstract = {Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.},
}
@article {pmid41432416,
year = {2025},
author = {Hu, B and An, L and Wu, M and Xu, J and Nie, Y and Wu, X-L},
title = {Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120425},
doi = {10.1128/msystems.01204-25},
pmid = {41432416},
issn = {2379-5077},
abstract = {UNLABELLED: Patescibacteriota is a vast lineage composed of bacteria with ultra-small size, streamlined genomes, notable defects in core metabolic potential, and symbiotic lifestyle, which are widely detected in groundwater ecosystems. Increasing attention has focused on the physiological and ecological significance of Patescibacteriota, while the potential interactions between Patescibacteriota and their phages still need more exploration. Here, we collected 82 groundwater metagenomic data sets and further derived 1,162 phages with the potential to infect 2,439 groundwater Patescibacteriota metagenome-assembled genomes (MAGs). Notably, the groundwater Patescibacteriota MAGs were predominantly infected by temperate phages, and viral operational taxonomic unit/host Patescibacteriota operational taxonomic unit (OTU) abundance ratios were significantly negatively correlated with the relative abundance of host Patescibacteriota OTUs. Intriguingly, the groundwater Patescibacteriota phages encoded various auxiliary metabolic genes (AMGs) that might promote symbiotic lifestyle and metabolic potential of host Patescibacteriota MAGs. These included AMGs associated with concanavalin A-like lectin/glucanases superfamily and O-Antigen nucleotide sugar biosynthesis, which could enhance surface adhesion of host Patescibacteriota MAGs. Moreover, AMGs related to the ABC transport system and the P-type transporter could strengthen metabolic exchange and uptake of essential nutrients from the surroundings. Additionally, AMGs involved in various metabolic pathways might alleviate metabolic deficiencies in host Patescibacteriota MAGs.<br><br>IMPORTANCE: Here, we sought phages that were capable of infecting Patescibacteriota metagenome-assembled genomes (MAGs), and further explored the diversity and novelty of Patescibacteriota phages, as well as the mechanisms underlying phage-Patescibacteriota interactions in groundwater ecosystems. The abundance profiles of phage-Patescibacteriota interactions suggested that lysogenic infection may represent a mutually adapted strategy between Patescibacteriota and their phages in groundwater ecosystems. Furthermore, the groundwater Patescibacteriota phages possessed diverse auxiliary metabolic genes which might facilitate the symbiotic associations and metabolic exchange between host Patescibacteriota MAGs and other free-living microbes and expand the metabolic capabilities of host Patescibacteriota MAGs. This study elucidated the mechanisms of phage-Patescibacteriota interactions and the potential roles of phages in modulating the physiology and ecology of Patescibacteriota within groundwater ecosystems.},
}
@article {pmid41432288,
year = {2026},
author = {Sahakyan, H and Mutz, P and Tobiasson, V and Koonin, EV},
title = {Exploring the protein universe with distant similarity detection methods.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {1},
pages = {e70397},
doi = {10.1002/pro.70397},
pmid = {41432288},
issn = {1469-896X},
support = {/NH/NIH HHS/United States ; },
mesh = {*Proteins/chemistry/genetics ; *Computational Biology/methods ; Protein Conformation ; Databases, Protein ; Sequence Analysis, Protein/methods ; Models, Molecular ; },
abstract = {During the last few years, the body of data on proteins is expanding almost exponentially with the development of advanced methods for gene sequencing, protein structure determination, particularly by cryoelectron microscopy, and structure prediction using artificial intelligence-based approaches. These developments create the potential for a comprehensive exploration of the protein universe, the entirety of the proteins existing in the biosphere. Elucidation of the relationships among proteins including the most distant ones, where only the core fold is shared, is crucial for understanding protein functions, folding mechanisms, and evolution, as well as the evolution of cellular life forms and viruses. In this brief review, we discuss methods that shaped the field of protein bioinformatics, first, through comparative sequence analysis, and the recent developments in protein structure prediction that transformed the state of the art in the comparative analysis of distantly related proteins. The combination of the rapidly growing databases of genome and metagenome sequences with sensitive methods for sequence comparison and the new generation of structure analysis tools can make charting the protein universe at the structural level a realistic goal.},
}
@article {pmid41432253,
year = {2025},
author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C},
title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf286},
pmid = {41432253},
issn = {1751-7370},
abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.},
}
@article {pmid41432242,
year = {2025},
author = {Xie, X and Chen, L and Yuan, J and Zheng, H and Zhang, L and Yu, X and Liu, X and Wei, C and Qiu, G},
title = {Metagenomic characterization of the metabolism, evolution, and global distribution of Candidatus Accumulibacter members in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf278},
pmid = {41432242},
issn = {1751-7370},
abstract = {Deciphering the genomic basis of ecological diversification in activated sludge microbiomes is essential for optimizing treatment technology and advancing microbial ecology. Here, we present a global genome-resolved investigation of Candidatus Accumulibacter, the primary functional agent of enhanced biological phosphorus removal, based on 828 metagenomes from wastewater treatment plants across six continents. We recovered 104 high-quality Candidatus Accumulibacter metagenome-assembled genomes, discovering a new clade (Clade IV), substantially expanding the known phylogenetic diversity and revealing a ubiquitous yet geographically heterogeneous global distribution. Phylogenomic and pangenome analyses uncovered extensive clade-specific gene gain and loss, particularly in nitrogen metabolism, suggesting divergent evolutionary trajectories shaped by relaxed selection and niche adaptation. Genome-wide patterns of convergent streamlining and enriched antiviral defense systems indicate selective pressures from strong competition and viral predation. Constraint-based metabolic modeling revealed pervasive amino acid autotrophies and metabolic complementarity, coupled with distinct carbon utilization strategies that support ecological specialization across operational settings. Experimental validation reconciled model-phenotype discrepancies, highlighting the importance of transporter promiscuity and gene regulation in carbon substrate assimilation. Collectively, our findings redefine Candidatus Accumulibacter as a dynamic model of microbial genome plasticity, metabolic adaptation, and ecological resilience, providing an insight for understanding how microbial communities adapt and respond under engineered environmental conditions.},
}
@article {pmid41432159,
year = {2025},
author = {Lau, KJX and Ma, A and Chen, B and Thankaraj Salammal, MS and Ramachandran, S and Naqvi, NI},
title = {Controlled irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297025},
doi = {10.1128/spectrum.02970-25},
pmid = {41432159},
issn = {2165-0497},
abstract = {The rhizosphere microbiomes of rice plants under conventional flood irrigation consist of highly complex consortia of microorganisms and, in particular, methanogens purportedly associated with methane emissions therein. Controlled irrigation has been proposed as a cultivation method of choice over continuous flooding to reduce water and fertilizer usage in an aerobic environment. However, a systematic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Using empirical analyses, we report a significant reduction in methane emissions in controlled irrigation compared to the flooded environment. Genotypic or varietal differences did not influence such methane emissions under conventional flooded cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affects the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse, was collected over 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favors microbes involved in the nitrifying-denitrifying processes, while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbiomes associated with methanogenesis were significantly reduced in drip irrigation. Several keystone taxa were evident in the co-occurrence network model related to methanogenic, methanotrophic, nitrifying, sulfur-oxidizing and sulfur-reducing activities. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota and the associated metabolic functional differences observed between the two irrigation regimes, leading up to the microbial mitigation of climate impact.IMPORTANCEUnlike previous studies in alternate wet-dry irrigation systems, this study characterized the rice microbiomes in a controlled drip irrigation setting where water levels were maintained at low levels and soil remained unflooded throughout the entire season in a greenhouse. A reduction of more than 90% in methane emissions was observed with drip irrigation compared to flood irrigation. A significant correlation was found between levels of methane emitted and mcrA gene copies detected, with a Pearson correlation coefficient R of 0.77 and P-value of 2.3e - 10. Methanogens are highly abundant in continuously flooded rice soil and are significantly reduced in drip-irrigated soil. Metagenomic profiling indicates that the shifts in microbial diversity under drip irrigation favor nitrifying microorganisms and are likely influenced by increased oxygen availability due to higher soil redox potential.},
}
@article {pmid41432156,
year = {2025},
author = {Butarelli, ACdA and Nakamura, FM and Vilela Peres, F and Modolon da Silva, F and Bendia, AG and Basti, R and Mahiques, MMd and Sumida, PYG and Pellizari, VH},
title = {Genomic insights into a versatile deep-sea methanotroph constituting the rare biosphere of a Brazilian carbonate mound complex.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0131125},
doi = {10.1128/msystems.01311-25},
pmid = {41432156},
issn = {2379-5077},
abstract = {UNLABELLED: Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions, and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Phylogenomic analysis revealed <95% of Average Nucleotide Identity (ANI) to described species, with genomic evidence of deep-sea specialization including: (i) stress adaptation through cold-shock proteins (CspA) and DNA repair systems (UvrD/LexA), (ii) metabolic versatility via complete methane oxidation (pmoABC), nitrogen fixation (nifHDK), and sulfur cycling (sox/sqr) pathways, and (iii) niche partitioning through biofilm formation (GGDEF/EAL) and heavy metal resistance (CopZ/CzcD). Comparative genomics identified a 1,234-gene deep-sea core shared with Methylotuvimicrobium sp. wino1, enriched in mobile elements (TnpA, prophages) suggesting horizontal gene transfer drives adaptation. While undetected in situ amplicon surveys, Methylotuvimicrobium crucis exhibited enrichment under methane availability, demonstrating its role as a latent methane filter. These findings contribute to the understanding of the ecological significance of aerobic methanotrophs in deep-sea systems, revealing how rare microbial taxa with genomic plasticity have the potential to influence biogeochemical cycling in deep carbonate-rich environments.<br><br>IMPORTANCE: Microbial communities in deep-sea sediments play crucial roles in global biogeochemical cycles, yet they remain poorly characterized due to the challenges of sampling and culturing under extreme conditions. This study provides a comprehensive overview of microbial diversity and functional potential in carbonate-rich deep-sea sediments, with an emphasis on methane-oxidizing bacteria. By combining high-throughput metagenomics and comparative genomics, we reconstructed high-quality genomes from previously uncharacterized microbial consortia, including novel members of the genus Methylotuvimicrobium. Our findings shed light on the ecological strategies of methanotrophs in oxygen-limited environments and expand the genomic representation of key players in carbon cycling.},
}
@article {pmid41432144,
year = {2025},
author = {Liu, J and Ni, H-B and Yu, M-Y and Qin, S-Y and Elsheikha, HM and Peng, P and Guo, L and Xie, L-H and Liang, H-R and Lei, C-C and Xu, Y and Tang, Y and Yu, H-L and Qin, Y and Liu, J and Sun, H-C and Zhang, X-X and Qiu, B},
title = {Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144325},
doi = {10.1128/msystems.01443-25},
pmid = {41432144},
issn = {2379-5077},
abstract = {UNLABELLED: Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.<br><br>IMPORTANCE: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.},
}
@article {pmid41431864,
year = {2026},
author = {Dowrick, JM and Roy, NC and Carco, C and James, SC and Heenan, PE and Frampton, CMA and Fraser, K and Young, W and Cooney, J and Trower, T and Keenan, JI and McNabb, WC and Mullaney, JA and Bayer, SB and Talley, NJ and Gearry, RB and Angeli-Gordon, TR},
title = {Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604871},
doi = {10.1080/19490976.2025.2604871},
pmid = {41431864},
issn = {1949-0984},
mesh = {Humans ; Cluster Analysis ; *Gastrointestinal Diseases/physiopathology/microbiology/classification ; Male ; Female ; *Brain/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Multiomics ; },
abstract = {Rome IV disorders of gut-brain interaction (DGBI) subtypes are known to be unstable and demonstrate high rates of non-treatment response, likely indicating patient heterogeneity. Cluster analysis, a type of unsupervised machine learning, can identify homogeneous sub-populations. Independent cluster analyses of symptom and biological data have highlighted its value in predicting patient outcomes. Integrated clustering of symptom and biological data may provide a unique multimodal perspective that better captures the complexity of DGBI. Here, integrated symptom and multi-omic cluster analysis was performed on a cohort of healthy controls and patients with lower-gastrointestinal tract DGBI. Cluster stability was assessed by considering how frequently pairs of participants appeared in the same cluster between different bootstrapped datasets. Functional enrichment analysis was performed on the biological signatures of stable DGBI-predominant clusters, implicating disrupted ammonia handling and metabolism as possible pathophysiologies present in a subset of patients with DGBI. Integrated clustering revealed subtypes that were not apparent using a singular modality, suggesting a symptom-only classification is prone to capturing heterogeneous sub-populations.},
}
@article {pmid41431647,
year = {2025},
author = {Lu, X and Dai, H and Gu, X and Xie, J and Zhong, X and Dong, X and Su, B and Su, J and Wang, L and Sun, T and Geng, L},
title = {The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20526},
pmid = {41431647},
issn = {2167-8359},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Case-Control Studies ; Biomarkers ; *Gastrointestinal Diseases/microbiology ; Clinical Relevance ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions-particularly intestinal transit and gas handling-rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.<br><br>METHODS: Fecal samples from 20 COPD &amp; FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.<br><br>RESULTS: COPD/COPD &amp; FABD patients showed significantly higher fecal microbiota &#x3b1;-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD &amp; FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. &#x3b2;-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD &amp; FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD &amp; FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04-26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).<br><br>CONCLUSION: Gut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation.},
}
@article {pmid41431641,
year = {2025},
author = {Nguyen, BN and Nguyen, LTN and Trinh, DTM and Nguyen, HT and Tran, TTT},
title = {Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20521},
pmid = {41431641},
issn = {2167-8359},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology ; Vietnam ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Pilot Projects ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; },
abstract = {In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam.},
}
@article {pmid41431463,
year = {2025},
author = {Noorian, P and Hamann, K and Hoque, MM and Espinoza-Vergara, G and To, J and Leo, D and Chari, P and Weber, G and Marial, O and Pryor, J and Duggin, IG and Lee, BB and Rice, SA and McDougald, D},
title = {A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100332},
pmid = {41431463},
issn = {2590-2075},
abstract = {Complex multispecies biofilms consistently colonise urinary catheters, causing persistent asymptomatic bacteriuria and frequent symptomatic episodes in long-term catheterized individuals. Simple single-species models often fail to capture the complexities of mixed-species interactions and lab-based organisms may not reflect the genomic diversity found in real-world infections. Additionally, growth under flow conditions promotes robust, complex-biofilm structures. Therefore, to reflect the dynamics of in vivo infections, biofilm samples from clinical indwelling catheters of spinal cord injury (SCI) participants colonised by 5-10 species were used to establish polymicrobial macro-fluidic models, in catheters. This resulted in final models of 2-4 species biofilms. Metagenomic techniques using short-read Illumina and long-read Oxford Nanopore sequencing was used to assess the taxonomic composition, in vivo to in vitro biofilms diversity shifts, single nucleotide polymorphism (SNP) analysis and complete metagenome-assembled genomes (MAGs). In silico analysis revealed a high number of varied antibiotic resistance genes, virulence factors and biofilm associated factors present in these biofilms. Antibiotic resistance testing using our models highlighted the drastic differences between planktonic bacteria, single-species and multispecies biofilms. While single-species biofilms show considerably increased tolerance to antibiotics compared to their planktonic counterparts, this resistance is even greater in multispecies biofilms. Under flow conditions, all species in the multispecies biofilm showed increased resistance, unlike static conditions where only most did. Models developed and characterised in this study are expected to facilitate testing of effective strategies to prevent and treat catheter-associated infections by enabling more accurate analysis of biofilm inhibition, disruption and microbial interactions.},
}
@article {pmid41431440,
year = {2026},
author = {Wang, W and Huang, H and Zhao, K and Lv, J and Liu, X and Xie, S and Feng, J},
title = {The Differing Responses of Chlorophyta and Bacillariophyta to Available Resources Result in Diverse Community Patterns in Lakes Situated to the East of the Hu Line During the Autumn.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {1},
pages = {e70248},
doi = {10.1002/wer.70248},
pmid = {41431440},
issn = {1554-7531},
support = {32270220//National Natural Science Foundation of China/ ; U22A20445//National Natural Science Foundation of China/ ; 2020KJ029//Excellent Achievement Cultivation Project of Higher education in Shanxi/ ; 2024-007//Research Project Supported by Shanxi Scholarship Council of China/ ; 202203021211313//Sanjin Talent Innovation Teams in Natural Sciences and Engineering Technology/ ; },
mesh = {*Lakes ; *Diatoms/genetics/physiology ; *Chlorophyta/genetics/physiology ; Seasons ; Biodiversity ; Ecosystem ; },
abstract = {Phytoplankton communities are of vital importance to the functioning of freshwater ecosystems, but the role of the metabolic capacity of the community in regulating community dynamics under natural conditions has yet to be sufficiently considered. This study investigated 26 lakes situated along the eastern section of the Hu Line, combining field surveys with metagenome-assembled analyses to ascertain the factors responsible for the divergence in Chlorophyta and Bacillariophyta communities. The results demonstrated that the diversity of Chlorophyta was markedly higher than that of Bacillariophyta whereas the abundance was significantly lower. These discrepancies in community attributes were predominantly attributable to variations in the response of the two algal groups to nutrients. The abundance and diversity of diatom metabolic genes were significantly higher than those of green algae. The greater diversity and extent of metabolic genes in Bacillariophyta confer enhanced metabolic capacity and, consequently, greater adaptive capacity. Such differences in metabolic gene composition may be attributed to the disparate evolutionary pathways that these organisms have followed.},
}
@article {pmid41431054,
year = {2025},
author = {Mei, H and Mei, J and Sun, Y and Shang, Q and Sun, P and Yang, Y and Kan, J and Chen, X and Sun, L},
title = {Antibiotics guided by metagenomic next-generation sequencing to control infection after total knee arthroplasty: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {51},
pages = {e46734},
doi = {10.1097/MD.0000000000046734},
pmid = {41431054},
issn = {1536-5964},
mesh = {Aged ; Humans ; Male ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; *Arthroplasty, Replacement, Knee/adverse effects ; Coxiella burnetii/genetics/isolation &amp; purification ; Doxycycline/therapeutic use/administration &amp; dosage ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Moxifloxacin/therapeutic use/administration &amp; dosage ; *Prosthesis-Related Infections/drug therapy/microbiology ; *Q Fever/drug therapy/diagnosis ; },
abstract = {RATIONALE: A prosthetic joint infection is a serious complication of joint surgery, with Staphylococcus aureus being the most common pathogen. In contrast, C. burnetii, the agent of Q fever, is a rare zoonotic parasite primarily found in cattle and sheep. It can be transmitted through respiratory, digestive, and cutaneous routes, destroying host cells and leading to diseases such as bone and joint infections, endocarditis, and interstitial lung disease.<br><br>PATIENT CONCERNS: A 75-year-old male patient underwent total knee arthroplasty due to degenerative disease in his left knee. After surgery, he was exposed to cattle and their feces. Fifteen months after the operation, he experienced pain, though there was no significant elevation of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and white blood cell (WBC). Oral nonsteroidal anti-inflammatory drugs (NSAIDs) were administered. The pain intensified and was accompanied by swelling. ESR and CRP were elevated, while WBC remained normal. The patient took oral Rifampicin for 28 days without improvement. The knee joint puncture culture was negative. The metagenomic next-generation sequencing (mNGS) detected C. burnetii, and oral Doxycycline for 1 week. The intravenous infusion of Doxycycline and Moxifloxacin continued for 28 days. After the above indexes stabilized, a 1-stage revision surgery was performed, and Doxycycline and Moxifloxacin were administered for 16 days until the indexes returned to normal and symptoms such as knee joint pain and swelling disappeared.<br><br>DIAGNOSES: Left knee radiography, laboratory tests, and knee cavity puncture, culture, and mNGS testing were performed to confirm the diagnosis of the pathogen.<br><br>INTERVENTIONS: According to mNGS, the left knee was revised and antibiotics were applied before and after the operation until the infection indexes returned to normal and symptoms such as knee pain and swelling disappeared.<br><br>OUTCOMES: ESR, CRP, and WBC indexes were normal. Pain and swelling disappeared. Other symptoms disappeared. Joint flexion and extension mobility was good.<br><br>LESSONS: In patients with postoperative prosthetic joint infection after total knee arthroplasty, mNGS can identify pathogenic bacteria, inform the use of antibiotics, and enable prompt surgical intervention.},
}
@article {pmid41431015,
year = {2025},
author = {Lin, B and Meng, X and Pu, K and Fu, T and Peng, N and Li, Q},
title = {Early diagnostic strategy for central nervous system bacterial infections after neurosurgery: A retrospective study.},
journal = {Medicine},
volume = {104},
number = {51},
pages = {e46635},
doi = {10.1097/MD.0000000000046635},
pmid = {41431015},
issn = {1536-5964},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Neurosurgical Procedures/adverse effects ; Adult ; Early Diagnosis ; *Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/etiology ; Aged ; *Postoperative Complications/diagnosis/cerebrospinal fluid ; ROC Curve ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Accurate diagnosis of post-neurosurgical bacterial infection of central nervous system is challenging due to the nonspecific nature of clinical signs and cerebrospinal fluid (CSF) parameters, which often overlap with sterile postoperative inflammation. This study aimed to develop and validate a stepwise diagnostic strategy integrating readily available clinical and basic laboratory indicators to improve the early identification of post-neurosurgical bacterial infection of the central nervous system. A retrospective cohort study was conducted at Tianjin Huanhu Hospital, a tertiary neurosurgical center, from October 2018 to June 2025. We enrolled 176 patients suspected of post-neurosurgical bacterial infection of the central nervous system who underwent CSF metagenomic next-generation sequencing (mNGS). Six diagnostic prediction models, combining clinical features (fever, altered mental status) and CSF parameters (white blood cell count, glucose levels), were constructed. Their diagnostic performance was evaluated against a composite reference standard (mNGS, culture, and clinical treatment response) using receiver operating characteristic analysis. The area under the curve (AUC), sensitivity, and specificity were calculated. Among the 6 models, two demonstrated superior performance. Model 5 (T > 38.0°C + [CSF white blood cell ≥ 2000 × 106/L OR CSF glucose < 2.2 mmol/L OR CSF/Blood glucose ratio < 0.4]) achieved an AUC of 0.768. Notably, Model 6 (T > 39.0°C + Altered Mental Status + Intermittent Fever), relying solely on clinical indicators, achieved a comparable AUC of 0.769. For individual parameters, a high fever threshold (T > 39.8°C) and profoundly low CSF glucose (<1.01 mmol/L) showed high specificities of 99%and 97%, respectively, for ruling in infection. A diagnostic strategy combining severe clinical manifestations (high fever and altered mental status) with high-threshold CSF parameters enables effective risk stratification for post-neurosurgical bacterial infection of the central nervous system. The high performance of a purely clinical model (Model 6) offers a valuable tool for rapid bedside assessment, especially in resource-limited settings. Future prospective, multicenter studies are recommended to validate these algorithms and further refine variable definitions for broader clinical application.},
}
@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32485-x},
pmid = {41430427},
issn = {2045-2322},
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}
@article {pmid41430301,
year = {2025},
author = {Wikki, I and Palmu, J and Kauko, A and Havulinna, A and Jousilahti, P and Lahti, L and Knight, R and Salomaa, V and Niiranen, T},
title = {Prospective association between the gut microbiota and incident pneumonia: a cohort study of 6419 individuals.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03453-w},
pmid = {41430301},
issn = {1465-993X},
support = {330887//Research Council of Finland/ ; 321351, 354447//Research Council of Finland/ ; },
abstract = {BACKGROUND: Previous animal studies have identified the protective capacity of the gut microbiota against respiratory infections. Nevertheless, the prospective association between human gut microbiota and pneumonia risk remains unknown.<br><br>OBJECTIVES: To evaluate the links between gut microbiota and incident pneumonia in a representative population sample.<br><br>METHODS: We performed shotgun metagenome sequencing on stool samples from 6419 FINRISK 2002 participants. Participants were followed up for incident pneumonia using nationwide health register data. We employed multivariable-adjusted Cox regression models and permutational multivariate analysis of variance (PERMANOVA) to assess the association of gut microbiome alpha diversity, compositional variation (beta diversity), and taxonomic composition with pneumonia risk.<br><br>RESULTS: Altogether, 685 patients (10.7%) developed pneumonia during a mean follow-up of 17.8 years. Alpha diversity was not associated with incident pneumonia (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.93&#x2009;-&#x2009;1.08), whereas community composition was (PERMANOVA R[2]&#x2009;=&#x2009;0.03%; P&#x2009;=&#x2009;0.02). We observed an inverse association between the relative abundance of butyrate-producing bacteria and incident pneumonia (HR per 1-SD increase 0.91; 95% CI 0.85-0.98). The relative abundance of Bacteroides_F pectinophilus, Eubacterium_G ventriosum, Agathobaculum butyriciproducens, Butyribacter intestini, Eubacterium_I ramulus, CAG-1427 sp000435675, and CAG-603 sp900066105 were inversely associated with pneumonia risk. The relative abundance of Clostridium_AQ innocuum was positively correlated with pneumonia risk.<br><br>CONCLUSIONS: The gut microbiota composition, and especially the relative abundance of butyrate-producing bacteria, was associated with lower pneumonia risk in the population. These findings warrant further studies to investigate whether microbiome modulation to increase short chain fatty acid production through diet, prebiotics, or probiotics could reduce pneumonia risk.},
}
@article {pmid41430289,
year = {2025},
author = {Williams, GM and Hoedt, EC and Duncanson, K and Gan, L and Prakoso, E and Talley, NJ and Beck, EJ},
title = {Inverse associations between Mediterranean diet constituents and the gut microbiota in metabolic-associated steatotic liver disease (MASLD): a case-control study.},
journal = {Nutrition &amp; metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-025-00939-8},
pmid = {41430289},
issn = {1743-7075},
abstract = {BACKGROUND: Dietary therapy, specifically for weight loss, is currently considered first-line therapy for metabolic-associated steatotic liver disease (MASLD). However, increasing recognition of the role of the gut-liver axis in MASLD highlights potential for microbiota-modulating dietary therapy to improve outcomes. This study aimed to explore dietary variables relevant to gut microbiota in MASLD.<br><br>METHODS: Twenty-five adults with MASLD and 25 healthy controls were recruited using a retrospective case-control design and characterised using 3-day dietary intake records, clinical markers, and shotgun metagenomic sequencing.<br><br>RESULTS: MASLD participants consumed less dietary fibre (p&#x2009;=&#x2009;<&#x2009;0.01), very long chain omega-3 fatty acids (p&#x2009;=&#x2009;0.02), nuts and seeds (p&#x2009;=&#x2009;0.03), whole grains (p&#x2009;<&#x2009;0.01) and vegetables (p&#x2009;=&#x2009;0.04). Participants with MASLD had lower abundance of Alistipes senegalensis (r=-0.01, p&#x2009;=&#x2009;0.04), Coprococcus eutactus (r=-0.07, p&#x2009;=&#x2009;0.006), Faecalibacterium (r=-0.02, p&#x2009;<&#x2009;0.001), and higher abundance of Ruminococcus torques (r&#x2009;=&#x2009;0.04, p&#x2009;=&#x2009;0.02), and less expression of functional pathways associated with ethanol production, methionine, folate and branched-chain amino acid metabolism. Bacterial species and functional pathways more abundant in MASLD were positively associated with intake of added sugars and saturated fat, and negatively associated with unsaturated fatty acid and dietary fibre intake.<br><br>CONCLUSIONS: Microbiota characteristics differ between individuals with and without MASLD, and this is influenced by dietary intake. Future translation-focused research investigating dietary interventions and the gut-liver-axis in MASLD are warranted.},
}
@article {pmid41429819,
year = {2025},
author = {Chen, Q and Xu, J and Yang, J and Qin, X and Fan, J and Ke, H and Yang, Z and Zheng, W and Li, X and Huang, L and Ning, W},
title = {Gut microbiota analysis in children with autism spectrum disorder and their family members.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44282},
pmid = {41429819},
issn = {2045-2322},
support = {Grant No.3502Z20214001//Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China/ ; 2022YFC2704300//National Key Research and Development Program of China/ ; 32400532//National Natural Science Foundation of China/ ; 2024GGB18//Fujian Provincial Health Technology Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology ; Child ; Male ; Female ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; Siblings ; Bifidobacterium/isolation &amp; purification/genetics ; Clostridium/isolation &amp; purification/genetics ; Bacteroides/isolation &amp; purification/genetics ; Metagenomics/methods ; Family ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication and interaction, alongside restricted, and repetitive behaviors. Emerging evidence suggests that gut microbiota alterations may contribute to ASD pathogenesis via the gut-brain axis. However, many previous studies have not adequately controlled for confounding genetic and environmental variables. In this study, we examined the gut microbiota profiles of 19 children with ASD, 8 siblings with non-ASD, and 36 parents from 17 families, providing a unique design that minimized biases related to shared genetic and familial environments. Metagenomic sequencing revealed significant differences in gut microbiota diversity and composition between groups. Specifically, children with ASD had lower abundances of Bifidobacterium and higher abundances of both Bacteroides and Clostridium species compared to their siblings, with notable dysbiosis correlated to ASD-specific symptoms. These findings highlight the potential role of microbiota alterations in ASD pathogenesis and suggest familial microbiota traits influenced by both genetic and environmental factors. Further exploration of gut microbial therapies could offer promising avenues for ASD intervention.},
}
@article {pmid41429339,
year = {2025},
author = {Li, M and Gao, S and Cheng, J and Chen, D and Li, H and Zhang, X and Wu, C and Chang, Y},
title = {Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic Analyses: A case-control study.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.026},
pmid = {41429339},
issn = {2090-1224},
abstract = {INTRODUCTION: Ascending aortic aneurysm (AsAA) is a high-risk cardiovascular condition; recent research indicates a possible association between gut microbiota, plasma metabolites, and the pathogenesis of AsAA.<br><br>OBJECTIVE: This study aims to investigate the compositional and metabolic alterations in the gut microbiota of AsAA patients to identify potential biomarkers for AsAA.<br><br>METHODS: This study enlisted 72 participants, comprising 44 individuals with AsAA and 28 healthy controls. All participants underwent examination for clinical features, and fecal and plasma samples were obtained for metagenomic and metabolomic studies.<br><br>RESULTS: Metagenomic analysis revealed a significant reduction of 23 bacterial species in AsAA patients, including Bifidobacterium adolescentis, Bifidobacterium longum, Lactiplantibacillus plantarum, Enterococcus faecalis, and Streptococcus thermophilus, while 52 bacterial species, such as Prevotella copri, Phascolarctobacterium faecium, and Eubacterium ventriosum, were found to be enriched. Furthermore, we identified seven microbial co-abundance groups (CAGs), of which three (predominantly comprising Roseburia, Agathobacter, and Prevotella) were significantly elevated in AsAA patients, whereas one (predominantly comprising Escherichia) was substantially diminished. KEGG pathway enrichment analysis indicated that the biosynthesis of unsaturated fatty acids pathway displayed the most pronounced differences between groups. Metabolomics data revealed that 22 metabolites, including ceramides, were significantly elevated, while 8 metabolites, such as threonine, were notably downregulated. Moreover, clinical indicators like C-reactive protein (CRP) and complement components C3 and C4 have shown strong correlations with specific gut microbiota (Streptococcus, Prevotella) and plasma metabolites (threonine, ceramides). These findings indicate that inflammatory responses, metabolic dysregulation, and gut microbiota imbalance are pivotal in the etiology of AsAA.<br><br>CONCLUSION: This study demonstrates substantial alterations in gut microbiota composition and plasma metabolites in patients with AsAA. Prevotella and ceramides exhibit potential as biomarkers for AsAA diagnosis. Furthermore, a synergy of Prevotella and ceramides may function as a potent disease prediction classifier, offering novel perspectives on the early diagnosis and targeted treatment of AsAA.},
}
@article {pmid41429282,
year = {2025},
author = {Akram, J and Jin, Y and Song, C and Li, C and Chen, C and Liu, G},
title = {Stimulating anaerobic degradation of biodegradable plastics by promoting direct interspecies electron transfer via conductive materials.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133850},
doi = {10.1016/j.biortech.2025.133850},
pmid = {41429282},
issn = {1873-2976},
abstract = {Although biodegradable plastics (BPs) are promoted as environmentally friendly, they exhibit low degradability and slow degradation rates under anaerobic conditions, creating challenges similar to conventional plastics. This study explores the effects of granular activated carbon and magnetite on the anaerobic digestion of BPs. Results showed that conductive materials improved digestion rates for readily degradable BPs but had no effect on recalcitrant ones unless pretreated. Magnetite increased the maximum methane production rates of cellulose diacetate, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), and thermoplastic starch by 18 %, 37 % and 15 %, respectively, at an organic loading (OL) of 8 gVS/L. Supplementation was especially effective at high OLs, where unamended controls were inhibited by excessive acidification. Metagenomic analysis revealed enrichment of direct interspecies electron transfer-capable microorganisms such as Syntrophaceticus and Methanosarcina, along with associated functional genes, in the supplemented groups. Overall, the findings suggest that conductive materials are most beneficial for readily degradable BPs, especially under high OL conditions.},
}
@article {pmid41429225,
year = {2025},
author = {Chen, J and Cao, H and Xu, Y and Chang, Y and Qin, X and Zhang, Z and Yang, W},
title = {Is light-to-moderate alcohol drinking associated with the onset of metabolic dysfunction-associated steatotic liver disease in a Chinese cohort?.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101144},
doi = {10.1016/j.ajcnut.2025.101144},
pmid = {41429225},
issn = {1938-3207},
abstract = {BACKGROUND: The association between light-to-moderate alcohol drinking (≤14 g/d for females; ≤28 g/d for males) and the risk of steatotic liver disease (SLD), including its metabolic dysfunction-associated subtype (MASLD), remains unclear, as does the role of related gut microbiota.<br><br>OBJECTIVES: We investigated the association between light-to-moderate alcohol drinking and incident SLD/MASLD, identified gut microbial species associated with such drinking, and evaluated their associations with disease risk.<br><br>METHODS: Among 1297 adults from a Chinese community-based cohort, alcohol intake was assessed by validated questionnaire, and SLD was diagnosed by vibration-controlled transient elastography. In a subset with fecal samples at follow-up (n=665), gut microbiota was profiled using shotgun metagenomic sequencing. We used the average alcohol intake from baseline and follow-up to represent long-term drinking habits. Species differentially associated with alcohol intake were identified using zero-inflated Gaussian models with false discovery rate (FDR) correction. Cox and logistic regression were used to estimate hazards ratio (HR) and odds ratio (OR) with 95% confidence interval (CI), respectively.<br><br>RESULTS: During follow-up (2020-2025), 513 incident SLD cases were identified. Light-to-moderate drinkers showed higher risks of SLD (HR=1.27, 95% CI: 1.03, 1.58) and MASLD (HR=1.27, 95% CI: 1.01, 1.59) versus abstainers. For the same comparison, liquor consumption was positively associated with SLD (HR=1.29, 95% CI: 1.01, 1.65). We identified 89 microbial species associated with alcohol intake and constructed a microbial score, which was positively associated with SLD (ORT3 vs T1=1.54, 95% CI: 1.03, 2.31, Ptrend=0.05) and MASLD (ORT3 vs T1=1.50, 95% CI: 1.00, 2.26, Ptrend=0.05). Among these species, Stenotrophomonas maltophilia AQ, Olsenella E timonensis, and Firm 11 sp., which were less abundant in drinkers, showed inverse associations with both conditions after FDR correction.<br><br>CONCLUSIONS: Light-to-moderate alcohol consumption was associated with increased risks of SLD and MASLD. A gut microbial score based on alcohol-associated species also predicted higher disease risk.},
}
@article {pmid41429195,
year = {2025},
author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C},
title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110240},
doi = {10.1016/j.jnutbio.2025.110240},
pmid = {41429195},
issn = {1873-4847},
abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/day for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multi-omics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.},
}
@article {pmid41428801,
year = {2025},
author = {Sauša, S and Zodāne, A and Kumar, S and Plūme, J and Baranova, J and Kozlova, T and , and Saušs, H and Kloviņš, J and Pīrāgs, V and Mitravinda, KS and Kistkins, S and Brīvība, M},
title = {Rapid and Selective Gut Microbiome Modulation by Polyherbal Formulation in Type 2 Diabetes.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0463},
pmid = {41428801},
issn = {2049-3614},
abstract = {BACKGROUND: Metformin, the first-line treatment for type 2 diabetes, often induces gastrointestinal side effects, affecting treatment adherence. Recent research suggests that the gut microbiome mediates both the efficacy and tolerability of metformin. This study evaluates the effect of a polyherbal formulation, used as an add-on to metformin, on the gut microbiota in patients with type 2 diabetes and metformin intolerance.<br><br>METHODS: We report preliminary findings from the first 7-day intervention phase of an ongoing randomized, placebo-controlled, crossover trial (NCT06846138) in 27 adults with type 2 diabetes. Participants received either polyherbal formulations or a placebo alongside metformin for 7 days. Stool samples were collected pre- and post-intervention for shotgun metagenomic sequencing. Microbial diversity, composition, and pathway functions were analyzed using Kraken2, Bracken, and HUMAnN3. Continuous glucose monitoring was used to assess glycemic metrics.<br><br>RESULTS: No significant alpha-diversity changes were observed; however, beta-diversity differed significantly between arms (PERMANOVA R2 = 0.04, p = 0.04). In the polyherbal formulation group, 17 species changed post-treatment (FDR < 0.25), with significant increases in six Bifidobacterium spp. (e.g., B. adolescentis, B. ruminantium). In contrast, the placebo group showed no major microbial shifts. Polyherbal formulation also altered 10 microbial pathways (FDR < 0.25). Continuous glucose monitoring revealed no short-term changes in glycemic levels.<br><br>CONCLUSION: Short-term polyherbal formulation co-administration significantly modulates gut microbiota, promoting beneficial taxa like Bifidobacterium in metformin-treated type 2 diabetes patients. This supports the potential role of the polyherbal formulation in microbiome-targeted strategies to improve metformin tolerability and effectiveness.},
}
@article {pmid41428733,
year = {2025},
author = {Yang, Z and Yu, M and Li, P and Li, Z and Teng, Y and Zhou, Y and Zhao, M and Liu, C and Zhao, Z and Wang, Z and Li, J and Jing, Y and Li, Y and Zhao, H and Song, W and Bian, C and Zhao, H and Chen, J and Xin, B and Lai, J},
title = {Casδ, an evolutionary transitional CRISPR system enables efficient genome editing across animals and plants.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1358},
pmid = {41428733},
issn = {1362-4962},
support = {//Agriculture Science and Technology/ ; 2023YFD1202900//National Key Research and Development Program of China/ ; PC2023A01004//Pinduoduo-China Agricultural University/ ; //Agriculture Science and Technology/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Humans ; Animals ; *CRISPR-Associated Proteins/genetics/metabolism/chemistry ; Genome, Plant ; RNA, Guide, CRISPR-Cas Systems/genetics ; Zea mays/genetics ; Evolution, Molecular ; Oryza/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated) adaptive immune systems provide sequence-specific mechanisms for targeting foreign DNA or RNA and have been widely used in genome editing and DNA detection. Type V CRISPR-Cas systems are characterized by a single RNA-guided RuvC domain-containing effector, Cas12. Here, through comprehensive mining of large-scale genomic and metagenomic data from microbial sources, we identified a new Class 2 CRISPR-Cas effector superfamily, designated Casδ, comprising three members with protein sizes ranging from 867 to 936 amino acids. Biochemical analyses revealed that Casδ-1 functions as a single RNA-guided endonuclease with specific recognition of 5'-RYR-3' protospacer-adjacent motifs, where R represents A or G, and Y represents T or C. Casδ-1 exhibits robust double-stranded DNA cleavage activity and target-dependent trans-cleavage activity. Casδ-1 mediates efficient genome editing across species, achieving up to 60% indel rates in human cells while generating homozygous knockout lines in two agriculturally important monocot species (Oryza sativa and Zea mays) through stable transformation. Structural and evolutionary analyses reveal Casδ as an evolutionary transitional nuclease bridging Cas12n and canonical type V systems, featuring a C-terminal loop that is essential for activity. Collectively, Casδ is an evolutionarily distinct, compact (<1000 aa), tracrRNA-free CRISPR system enabling versatile cross-kingdom genome editing.},
}
@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
doi = {10.1111/1751-7915.70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth &amp; development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}
@article {pmid41428487,
year = {2025},
author = {Deng, C and Hu, J and Chen, Q and Zhou, S and Ni, J},
title = {Expanded global groundwater microbial diversity reveals bioprospecting potential.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116760},
doi = {10.1016/j.celrep.2025.116760},
pmid = {41428487},
issn = {2211-1247},
abstract = {Although the terrestrial subsurface harbors a substantial fraction of Earth's microbial biomass, the genomic diversity of groundwater microbiomes and their potential for bioprospecting remain poorly characterized. Here, we recovered 44,320 bacterial and archaeal genomes from in-house and publicly available metagenomic datasets, establishing a large-scale groundwater microbiota catalog (GWMC) spanning 167 phyla, including four candidate phyla and over 12,000 previously uncharacterized species. This unprecedented phylogenetic diversity was accompanied by a bimodal genome size distribution (0.3-12.8 Mbp), revealing divergent strategies of genomic allocation. By mining extensive genomic resources, we found that small genomes prioritized molecular defense and redox regulation, whereas large genomes frequently harbored greater biosynthetic potential. Notably, we establish the largest selenoprotein catalog to date and highlight groundwater as an overlooked hotspot of microbial selenium metabolism. Overall, this work advances our understanding of microbial diversity in aquifers and uncovers underexplored genomic resources with potential for biotechnology and biomedicine.},
}
@article {pmid41428281,
year = {2025},
author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y},
title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {110},
pmid = {41428281},
issn = {1559-0267},
support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; },
abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.},
}
@article {pmid41427949,
year = {2025},
author = {Pan, S and Zhao, X and Shi, Q and Shen, Z and Liu, J and Li, W and Xie, Y},
title = {Significant diversity of human anelloviruses revealed by novel viral sequences identified in human metagenomic data.},
journal = {The Journal of general virology},
volume = {106},
number = {12},
pages = {},
doi = {10.1099/jgv.0.002199},
pmid = {41427949},
issn = {1465-2099},
mesh = {Humans ; Phylogeny ; Metagenomics ; *Anelloviridae/genetics/classification/isolation &amp; purification ; *Genetic Variation ; Genome, Viral ; Open Reading Frames ; Viral Proteins/genetics ; *DNA Virus Infections/virology ; },
abstract = {Human torque teno viruses are emerging infectious agents distributed globally and have increasingly been reported to be associated with human diseases. To identify potential anelloviral sequences in available metagenomic data, an in silico screening was performed mainly employing the ORF1, ORF2 and ORF3 nucleotide/protein queries of known human anelloviruses and identified 217 complete ORF1 regions. Pairwise nucleotide-identity analysis with a 69% cut-off - consistent with ICTV species demarcation - revealed 117 novel species across the 3 major human-infecting genera: 15 in Alphatorquevirus, 51 in Betatorquevirus and 51 in Gammatorquevirus. In nearly all cases, these species assignments correspond precisely to monophyletic clusters in maximum-likelihood phylogenies of ORF1 amino acid sequences. Using AlphaFold3-guided modelling together with representative ORF1 alignments, we delineated capsid motifs - the conserved jelly-roll (JR) β-sandwich core (β-strands B-I) and the outward projection domains P1/P2 - and quantified motif lengths across genera, revealing tightly constrained JR lengths with genus-specific but overlapping variation in P1/P2. A few exceptions - where pairwise-based groupings split or merge slightly differently - highlight ongoing challenges in delineating rapidly evolving viruses. Notably, the two deeply branching isolates retain the canonical JR core while exhibiting a TTMDV-like short P2, indicating preservation of key capsid architecture in the newly proposed genus. This work nearly doubles the known species richness of human anelloviruses and introduces a novel genus, underscoring the vast, hidden diversity of the gut virome and its potential impact on human health. By coupling taxonomy with structure-informed ORF1 motif analysis, our study provides biological context for these lineages and a framework for future functional and immunological investigations.},
}
@article {pmid41427872,
year = {2025},
author = {Gu, T and Chen, Z and Hutchins, DA and Sun, J},
title = {Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf281},
pmid = {41427872},
issn = {1751-7370},
abstract = {Urea is an important alternative nitrogen source to ammonium for nitrification in oligotrophic oceans, yet its role in substrate-driven nitrous oxide (N2O) production remains poorly constrained. Here, we combined N2O isotopomer profiling, 15N-tracer incubations, and metagenomics to quantify and mechanistically resolve substrate-specific archaeal nitrification in the western tropical Pacific euphotic zone. Isotopomer-based mixing and fractionation model indicated that archaeal nitrification accounted for 69.6 ± 14.1% of microbial sources of N2O in oxygenated epipelagic waters. Depth-integrated urea-driven nitrification contributed 14-41% of total nitrification and 21-39% of nitrification-derived N2O, with contributions regulated by substrate proportions. Acidification experiments showed that pH decline inhibited ammonium-driven nitrification (median 21.9%) and enhanced urea oxidation (median 61.9%), whereas N2O production increased for both substrates (median 35.9% and 38.0%). In addition, experimental acidification induced opposite shifts in hybrid versus double-labelled N2O, suggesting pH-driven shifts N-intermediate chemistry and intracellular partitioning. Metagenomic results support the globally widespread urea-type AOA. Together, these results indicate that urea-driven nitrification constitutes a non-negligible, substrate-dependent source of N2O in oligotrophic euphotic zones. We recommend that Earth-system N-cycle models represent urea and ammonium oxidation as distinct pathways with pH-sensitive yields to improve projections of marine nitrification and N2O fluxes under acidification.},
}
@article {pmid41427714,
year = {2025},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183825},
doi = {10.1128/spectrum.01838-25},
pmid = {41427714},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.<br><br>IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}
@article {pmid41427415,
year = {2025},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693354},
pmid = {41427415},
issn = {2692-8205},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug resistant Gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii . This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document potential sources of the corresponding resistance genes. This study searched for potential emerging colistin-resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments which all contained eptA genes. We confirmed their ability to confer significant colistin resistance in E. coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter strains, marking them as potential mcr genes or their precursors. This study highlights the goose fecal microbiome as a potential source for colistin resistance in the environment.},
}
@article {pmid41427287,
year = {2025},
author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW},
title = {RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.05.692407},
pmid = {41427287},
issn = {2692-8205},
abstract = {UNLABELLED: Hybridization (bait) capture combined with long-read sequencing enables targeted profiling within complex metagenomes but introduces systematic biases from bait multiplicity, sequence composition, and species abundance that existing simulators ignore. We present RAmpSim , a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing long-read simulators for modeling platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. Compared to uniform-coverage baselines, RAmpSim 's simulated coverage distributions are up to an order of magnitude closer to real data with respect to earth mover's distance. Classification analysis reveals high recall in classifying high coverage regions between simulated and experimental distributions while outperforming a uniform baseline. Supporting accurate benchmarking and bait-set evaluation, RAmpSim provides an interpretable, efficient framework for simulating capture-based metagenomic sequencing.<br><br>CODE AVAILABILITY: https://github.com/az002/RAmpSim.git.},
}
@article {pmid41427275,
year = {2025},
author = {Chen, K and Talesara, A and Thakkar, S and Shao, M},
title = {Minimum flow decomposition guided by saturating subflows.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.11.693570},
pmid = {41427275},
issn = {2692-8205},
abstract = {The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed graph (e.g., overlap graph, splice graph), where each edge has an integer weight representing the number of supporting reads. By viewing the graph as a flow network, the underlying sequences and their abundances can be extracted through decomposition into a minimum number of weighted paths. Although this problem is NP-hard, prior work has proposed an efficient heuristic that transforms the graph by identifying nontrivial equations in the flow values. However, for graphs with complex structures, many equations cannot be fully resolved by existing mechanisms, leading to suboptimal decompositions. In this study, we revisit the theoretical framework of the flow decomposition problem and extend the equation-resolving mechanisms to jointly model all equations in the graph, enabling safe merge operations that iteratively simplify the graph. Experimental results demonstrate that our new algorithm substantially improves decomposition quality over existing heuristics, achieving near-optimal solutions for complex graphs, while running several orders of magnitude faster than the ILP formulation. Source code of our algorithm is available at https://github.com/Shao-Group/catfish-LP.git .},
}
@article {pmid41426949,
year = {2025},
author = {Allshouse, T and Amendano, M and Caruso, B and Del Campo, R and Murphy, G and Shaffer, L and Steinberg, E and Sullivan, A and Stowe, E},
title = {The Microbiota of Homemade Tepache Includes Antibiotic-Resistant Microorganisms.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {41426949},
issn = {2578-9430},
abstract = {Tepache is a traditional, homemade Mexican drink made by fermenting pineapple rinds. The natural probiotic bacteria in tepache are said to promote a healthy gut microbiome. This study assessed the microbial community in homemade tepache for diversity, survival in simulated gastric fluid, and antibiotic resistance. Simulated gastric passaging reduced total community numbers but the community density was not strongly impacted by exposure to tetracycline. Metagenomic analysis reveals a community dominated by Bacillus, Meyerozyma and Talaromyces. These results indicate that consuming home fermented beverages may provide helpful probiotic bacteria but could also expose the gut microbiome to antibiotic resistance genes.},
}
@article {pmid41426737,
year = {2025},
author = {Valente, P and Sbrenna, L and Valente, F and Sbrenna, A and Mascolo, A},
title = {Drug-Induced Gingival Overgrowth Associated With Cyclosporine Therapy: A Case Report of a 23-Year Periodontal Follow-Up in a Heart Transplant Recipient.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97019},
pmid = {41426737},
issn = {2168-8184},
abstract = {Drug-induced gingival overgrowth (DIGO) is a common adverse effect of cyclosporine therapy, which is widely used as an immunosuppressive agent in solid organ transplant recipients. This case report describes the 23-year follow-up of a male patient with a history of orthotopic heart transplantation, performed two years prior to his first dental visit in 2002, who developed DIGO under long-term cyclosporine therapy. At the initial periodontal evaluation, a diagnosis of localized Stage I, Grade A periodontitis associated with gingivitis was made, and nonsurgical mechanical debridement, scaling and root planing, and tailored oral hygiene instruction were provided, yielding favorable early outcomes and long-term periodontal stability. After many years of stability, the patient returned following a three-year lapse in maintenance, presenting with marked gingival enlargement, bleeding on probing, discoloration, and migration of the maxillary central incisors, consistent with progression to Stage II, Grade B periodontitis. Nonsurgical retreatment was performed, and DNA-based metagenomic analysis of subgingival plaque and tongue biofilm revealed a dysbiotic microbial profile, including the persistence of key periodontopathogenic taxa associated with tissue destruction and alveolar bone loss. This case underscores the importance of sustained periodontal maintenance in transplant recipients receiving cyclosporine therapy and illustrates that even after decades of apparent stability, DIGO and periodontal deterioration may reemerge if maintenance care is interrupted. The integration of DNA-based metagenomic analysis provided valuable diagnostic and motivational support, reinforcing a personalized, multidisciplinary approach to long-term periodontal management in immunosuppressed patients.},
}
@article {pmid41426650,
year = {2025},
author = {Wang, C and Wei, H and Duan, R and Jin, S and Wen, J and Li, H and Cheng, A and Gao, C and Xue, H and Hou, Y},
title = {Habitat Diversity Sustains Ecosystem Functioning in Plateau Arid-Region Wetlands.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72747},
pmid = {41426650},
issn = {2045-7758},
abstract = {Plateau arid-region wetlands constitute critical ecosystems for regional ecological security, yet exhibit heightened vulnerability under multiple stressors. Current understanding of the mechanisms sustaining the functions of these systems, particularly the pivotal role of habitat diversity, remains limited. Targeting the Jinzihai Wetland (Qaidam Basin, Qinghai-Tibet Plateau), we integrated metagenomic and geochemical profiling to characterize three representative habitats: sandy meadows, peat bogs, and lake sediments. Our analyses revealed that pronounced cross-habitat physicochemical gradients drive community structure differentiation predominantly through species replacement, establishing habitat diversity as a fundamental driver of wetland biodiversity. Concurrently, community differentiation drives spatial divergence in functional gene composition, manifesting distinct functional dominance: sandy meadows govern assimilation and saline-alkaline stress response; peat bogs orchestrate nutrient enrichment and transformation; lake sediments mediate element release and burial. These functionally complementary habitats collectively catalyze biogeochemical cycling. We demonstrate that within plateau arid-region wetlands, habitat diversity stabilizes ecosystem functioning by sustaining both biodiversity and functional diversity of biogeochemical processes. Consequently, prioritizing habitat diversity conservation is imperative for safeguarding the long-term stability of these vulnerable ecosystems within management frameworks.},
}
@article {pmid41426590,
year = {2025},
author = {Zhang, J and Xu, X and Chen, L and Yang, X and Matsubara, JK and Tian, Y and Liu, J and Jin, X and Chang, H and Xu, M and Zhu, C and Wang, X and Ren, L and Xie, J and Liu, J and Liu, G and Lu, M and Wang, X and Du, L and Ma, Z and Liu, X and Zhao, H and Chen, W and Huo, X and Zheng, G and Xie, C and Xu, C and Zhang, X and Qi, W and Feng, Z},
title = {Circulating microbiome profiling in transjugular intrahepatic portosystemic shunt patients: 16S rRNA vs. shotgun sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1662837},
pmid = {41426590},
issn = {2296-858X},
abstract = {BACKGROUND AND AIM: Current efforts to characterize the circulating microbiome are constrained by the lack of standardized protocols for isolating and sequencing microbial communities in blood. To address this challenge, our study compared 16S rRNA (V3-V4 region) and shotgun metagenomic sequencing for circulating microbiome detection.<br><br>MATERIALS AND METHODS: After obtaining ethics committee approval and informed consent, samples were aseptically collected from 10 patients undergoing transjugular intrahepatic portosystemic shunt (TIPS) procedures. Shotgun metagenomic reads were taxonomically classified using the Kraken2-Bracken pipeline. 16S rRNA (V3-V4) data were analyzed through an ASV-based approach, with USEARCH for denoising and VSEARCH for taxonomic annotation. The results from both sequencing methods were then systematically compared.<br><br>RESULTS: Shotgun metagenomic sequencing generated 7,024,580,376 raw reads (mean depth: 234,152,679.2 reads/sample), while 16S rRNA sequencing produced 6,612,678 raw reads (mean depth: 220,422.6 reads/sample). 16S rRNA amplicon sequencing captured a broader range of microbial signals. Although the taxonomic profiles from both sequencing methods showed limited overlap, the core microbiota common to both were still identified. These conserved core microbial communities exhibited stable &#x3b1;- and &#x3b2;-diversity indices across separate vascular compartments.<br><br>CONCLUSION: In our study, 16S rRNA amplicon sequencing captured more diverse microbial signals than shotgun metagenomics. A stable microbial community structure was observed across vascular compartments, suggesting a homogeneous microbial composition throughout the circulatory system.},
}
@article {pmid41426580,
year = {2025},
author = {Li, S and Tian, Q and Yang, X and Zhang, M and Zheng, M and Li, D and Duan, Z and Li, Y and Qiu, Z and Liu, Z},
title = {Chronic meningoencephalomyelitis caused by Nocardia nova infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1680771},
pmid = {41426580},
issn = {2296-858X},
abstract = {A 25-year-old female zookeeper presented with 3-month history of sore throat and headache, 2-month intermittent fever, and 1-month dizziness. Neurological examination revealed bilateral nystagmus, left-sided sensory loss, ataxia, and subtle meningeal signs. Brain and cervical spinal cord MRI showed multiple enhancing lesions with central vein signs. Cerebrospinal fluid (CSF) analysis demonstrated elevated pressure (240 mmH2O) and leukocytosis (140 × 10[6]/L). Serum MOG-IgG was positive (1:32), while CSF metagenomic next-generation sequencing (mNGS) confirmed Nocardia nova infection. Initial treatment with trimethoprim-sulfamethoxazole (TMP-SMX), amikacin, and imipenem-cilastatin was followed by regimen adjustment to TMP-SMX plus minocycline at 6 weeks. One-month post-therapy, repeat CSF showed normalized pressure, reduced leukocytes, negative mNGS, and MRI evidence of lesion regression. Complete symptom resolution occurred 2 months after treatment initiation. This case exemplifies a rare presentation of N. nova-induced meningoencephalomyelitis with craniospinal involvement in an immunocompetent individual.},
}
@article {pmid41426285,
year = {2025},
author = {Ma, X and Zhang, Q and Ji, X and Xia, Y and Cao, J and Xu, X},
title = {Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluids Improves Pathogen Detection and Antimicrobial Stewardship in Lower Respiratory Tract Infections: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6611-6632},
pmid = {41426285},
issn = {1178-6973},
abstract = {PURPOSE: With the advancement of metagenomic next-generation sequencing (mNGS), its role in diagnosing lower respiratory tract infections (LRTIs) has expanded rapidly. LRTIs remain a major global health burden, particularly in critically ill patients where diagnosis is challenging. Routine microbiological testing (RMT), including culture, microscopy, antigen detection, and PCR-are limited by low sensitivity, long turnaround times, and restricted pathogen coverage. This study assesses the diagnostic performance of mNGS in LRTIs, with emphasis on pathogen detection and resistance gene prediction, and compares it with traditional methods to clarify its clinical benefits and limitations.<br><br>METHODS: This retrospective study included 367&#xa0;hospitalized patients with suspected LRTIs. All patients underwent mNGS testing, which was compared with traditional diagnostic methods. We also used mNGS to explore the pathogen spectrum characteristics in critically ill patients with pneumonia and evaluated its applicability in predicting antimicrobial resistance genes and adjusting antibiotic treatment.<br><br>RESULTS: For patients diagnosed with LRTIs, mNGS demonstrated superior microbial detection efficacy, particularly for bacteria and fungi, relative to culture (bacteria: 56.58% vs 17.37%, P < 0.0001; fungi: 49.65% vs 16.78%, P < 0.0001) and PCR (65.14% vs 45.14%, P < 0.05). In contrast to the non-severe pneumonia group, the detection rate of Enterococcus faecium was highest in the severe pneumonia group (P < 0.001), and the severe pneumonia group had more mixed infections (P < 0.001). In addition, mNGS showed high accuracy in predicting antibiotic resistance genes, with 90.57% agreement with antibiotic susceptibility testing (AST) results. Based on the mNGS results, 97.82% of patients underwent active adjustment to their antibiotic treatment regimen.<br><br>CONCLUSION: mNGS is an effective tool for diagnosing LRTIs, with significantly higher pathogen detection rates than traditional methods. mNGS also demonstrates high accuracy in predicting antimicrobial resistance, providing crucial support for clinical treatment decisions.},
}
@article {pmid41426281,
year = {2025},
author = {Yang, L and Zhang, Y and Wu, M and Zeng, F and Chen, H and Xie, D and Shi, F},
title = {Recurrent Disseminated Talaromycosis Mimicking Liver Disease in a STAT3-Mutated HIES Patient: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6605-6610},
pmid = {41426281},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is increasingly recognized in immunocompromised individuals beyond those with HIV, including patients with primary immunodeficiencies such as Hyper-IgE syndrome (HIES). However, diagnosing disseminated infection remains challenging due to nonspecific clinical manifestations and limitations of conventional diagnostic methods.<br><br>CASE PRESENTATION: We report a rare case of recurrent disseminated Talaromyces marneffei (T. marneffei) infection in a 25-year-old male with STAT3-mutated HIES. Initially presenting with abnormal liver function tests, the patient had a history of T. marneffei pulmonary infection successfully treated with itraconazole. During the current admission, he developed intermittent fever, jaundice, and splenomegaly. Initial evaluations led to a misdiagnosis of chronic drug-induced liver injury (DILI). Subsequent fever recurrence and worsening liver function prompted further investigation. Metagenomic next-generation sequencing (mNGS) and histopathology of liver revealed T. marneffei, confirming disseminated infection involving the liver. Histopathological examination of the liver showed granulomatous inflammation with IgG4-positive plasma cell infiltration, further complicating the differential diagnosis. The patient responded well to intravenous voriconazole, with significant improvement in liver function and radiological findings.<br><br>CONCLUSION: Disseminated talaromycosis should be considered in immunocompromised patients presenting with unexplained fever, hepatosplenomegaly, or organ dysfunction, even in the absence of classic symptoms. Integration of mNGS into diagnostic workflows enhances pathogen detection, and long-term antifungal prophylaxis may be necessary in patients with persistent immune deficiencies.},
}
@article {pmid41424898,
year = {2025},
author = {Chattopadhyay, P and Biswas, I and Banerjee, G},
title = {Analysing the Metagenomic Dynamics of Soil Microbiota Affected by Tea Pruning and Skiffing Methods in Tea Plantations of Dibrugarh, Assam, India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {2015-2020},
pmid = {41424898},
issn = {0046-8991},
abstract = {Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.},
}
@article {pmid41423959,
year = {2025},
author = {Bao, Y and Dolfing, J and Chen, R and Qiu, C and Zhang, J and Zhou, X and Liu, L and Wang, Y and Lin, X and Feng, Y},
title = {Phages Shape the Transformation of Organic Matter During Composting.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70291},
doi = {10.1111/1751-7915.70291},
pmid = {41423959},
issn = {1751-7915},
support = {42207365//National Natural Science Foundation of China/ ; 42177297//National Natural Science Foundation of China/ ; 42577330//National Natural Science Foundation of China/ ; 42577352//National Natural Science Foundation of China/ ; BK20221161//Natural Science Foundation of Jiangsu Province/ ; XDA28010302//Chinese Academy of Sciences (CAS) Strategic Priority Research Program/ ; },
mesh = {*Composting/methods ; *Bacteriophages/metabolism/growth &amp; development/genetics ; Manure/microbiology ; *Organic Chemicals/metabolism ; Soil Microbiology ; Biotransformation ; Animals ; Oryza ; Chickens ; Metagenomics ; Bacteria/metabolism/virology ; },
abstract = {Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)-resource acquisition (A)-stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial-/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.},
}
@article {pmid41423811,
year = {2025},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf295},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.<br><br>METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.<br><br>RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.<br><br>CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}
@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67677-6},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}
@article {pmid41423072,
year = {2025},
author = {Song, MN and Xu, HT and Liang, SM and Fang, SY and Zhang, Y and Zhang, ZZ and Jin, RC},
title = {Ultrasound-assisted breathing revives floated anammox granules by reconnecting intra‑granular metabolic interactions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133838},
doi = {10.1016/j.biortech.2025.133838},
pmid = {41423072},
issn = {1873-2976},
abstract = {The flotation of granular sludge is a critical bottleneck hindering the application of high-load anammox process. Here, we propose and validate an "assisted breathing" strategy, using non-destructive physical treatments to rapidly restore the functionality of floated granules. A systematic comparison of pressure transient (PT), mechanical shaking (MS), and ultrasonic radiation (UR) revealed that intermittent UR treatment was uniquely effective and it propelled the nitrogen removal rate (NRR) to a remarkable 7.19 kg-N m[-3] d[-1] within 60 days, far surpassing the PT, MS, and control reactors. Mechanistic investigations revealed that the efficacy of "assisted breathing" stems from a synergistic physio-ecological cascade. Physically, ultrasonication enhanced granule permeability and mass transfer efficiency by facilitating entrapped N2 gas release. Biologically, intermittent UR treatment stimulated the production of protein-rich extracellular polymeric substances (EPS), repurposing EPS from a pore-clogging obstacle into beneficial public goods. Most critically, metagenomic analysis demonstrated that UR treatment selectively enriched key heterotrophic partners, such as Ignavibacteriaceae sp. SMN043, which formed a tight syntrophic relationship with AnAOB by providing essential metabolites like folate in exchange for amino acids. Intriguingly, this led to a 14.1 % increase in SAA. These results demonstrate that targeted physical intervention can unlock superior performance by reviving and re‑linking the metabolic networks inside anammox granules. This process effectively transforms inert, floated biomass into highly active aggregates, opening a new avenue for active ecological engineering in bioreactors.},
}
@article {pmid41422804,
year = {2025},
author = {Tabuteau, S and Hervé, V and Irlinger, F and Monnet, C},
title = {Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70218},
doi = {10.1111/1462-2920.70218},
pmid = {41422804},
issn = {1462-2920},
support = {//ABIES Doctoral School/ ; //MICA Department of INRAE/ ; },
mesh = {*Cheese/microbiology ; *Iron/metabolism ; Siderophores/biosynthesis/metabolism/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; *Metagenome ; Genome, Bacterial ; },
abstract = {Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.},
}
@article {pmid41422728,
year = {2025},
author = {Xun, J and Han, Y and Liu, B and Jiang, X and Zhang, J and Hu, Z and Yang, H and Gao, Q and Wu, Z and Wang, X and Yu, X and Zhang, Q},
title = {Baihua Dangen Tang inhibits the peritoneal metastasis of colon cancer by modulating the bacterial metabolite gentisic acid to suppress MDSCs.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157720},
doi = {10.1016/j.phymed.2025.157720},
pmid = {41422728},
issn = {1618-095X},
abstract = {BACKGROUND: The treatment principle of Lingnan traditional compound Baihua Dangen Tang includes 'clearing heat and removing toxins, resolving stasis and dispersing stagnation, and dispelling wind and removing dampness', which is compatible with the pathogenesis of peritoneal cancer, which is characterized by 'dampness, heat, stasis and toxin'. Therefore, Baihua Dangen Tang may be an effective treatment for peritoneal metastasis of colon cancer.<br><br>OBJECTIVE: To systematically elucidate the effects and mechanisms of Baihua Dangen Tang in inhibiting the peritoneal metastasis of colon cancer.<br><br>METHODS: In this study, a peritoneal metastasis model of colon cancer was constructed by intraperitoneal injection of CT26/MC38 cells (1 &#xd7; 10[6]) for 14 days. Abdominal circumference, ascites volume, tumor weight and Ki67 expression were analyzed. Mass spectrometry and flow cytometry were used to analyze changes in immune cells, such as MDSCs and T-cell subsets, in ascites and peripheral blood. Changes in the fecal flora and metabolites were analyzed by macrogenomic and untargeted metabolomics to screen for key differential flora metabolites. In vitro experiments were performed to determine the effects of Baihua Dangen Tang and differential flora metabolites on tumor cell migration and invasion and MDSC function.<br><br>RESULTS: In this study, we observed that Baihua Dangen Tang significantly inhibited peritoneal metastasis of colon cancer; reduced abdominal circumference, bloody ascites content, and metastatic tumor weight; and decreased metastatic tumor Ki67 expression. Analysis of ascites and peripheral blood by mass spectrometry and flow cytometry revealed that Baihua Dangen Tang increased the numbers of CD4[+] T cells and CD8[+] T cells and decreased the number of MDSCs in ascites and peripheral blood. Combined macrogenomic and metabolomic analyses revealed that the metabolite gentisic acid, which was positively correlated with Lactobacillus spp. and negatively correlated with Desulfovibrio spp., significantly changed. In vivo experiments confirmed that gentisic acid inhibited the progression of CT26 peritoneal metastases. In vitro experiments confirmed that Baihua Dangen Tang and its regulatory bacterial colony metabolite gentisic acid inhibited the migration and invasion ability of colon cancer cells and their recruitment of MDSCs, in addition to directly inhibiting the function of MDSCs, thus enhancing T-cell activity.<br><br>CONCLUSION: Baihua Dangen Tang and its microbiota-derived metabolite gentisic acid inhibit cancer cell metastasis and MDSCs function, demonstrating multitarget suppression of colorectal cancer peritoneal metastasis.},
}
@article {pmid41422454,
year = {2025},
author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C},
title = {Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next-generation sequencing.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41422454},
issn = {1439-0973},
abstract = {A Siberian woman in her forties presented to a public hospital in northeastern Germany with chronic back pain and a paravertebral mass, initially misdiagnosed as spinal tuberculosis. Repeated biopsies and metagenomic next-generation sequencing (mNGS) ultimately confirmed vertebral alveolar echinococcosis. Haplotype analysis revealed a novel Asian-cluster variant, supporting the presumed origin of infection.},
}
@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00888-3},
pmid = {41422269},
issn = {2055-5008},
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}
@article {pmid41422081,
year = {2025},
author = {Arnaud-Haond, S and Trouche, B and Liautard-Haag, C and Alain, K and Aubé, J and Bonhomme, F and Brandt, MI and Caillarec-Joly, A and Cambon, MA and Cornette, F and Cueff-Gauchard, V and Durand, P and de Vargas, C and Felix, C and Fuchs, S and , and Günther, B and Henry, N and Hourdez, S and Jollivet, D and Le Port, AS and Lesongeur, F and Maignien, L and Comtet-Marre, S and Matabos, M and Omnes, E and Peyret, P and Pradillon, F and Sarrazin, J and Schauberger, C and Tran Lu Y, A and Ulloa, O and Vaz, S and Zeppili, D and Viard, F and Gavory, F and Gaz, S and Guy, J and Jacoby, E and Oliveira, PH and Samson, G and Aury, JM and Wincker, P and Pesant, S and Poulain, J and Belser, C},
title = {Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-025-06009-1},
pmid = {41422081},
issn = {2052-4463},
support = {ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0003//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-POCE-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; 678760//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 669947//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; },
abstract = {The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.},
}
@article {pmid41421910,
year = {2025},
author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H},
title = {Corrigendum to "Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava" [J Hazard Mater 411 (2021) 125143].},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {140878},
doi = {10.1016/j.jhazmat.2025.140878},
pmid = {41421910},
issn = {1873-3336},
}
@article {pmid41421776,
year = {2025},
author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES},
title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123595},
doi = {10.1016/j.envres.2025.123595},
pmid = {41421776},
issn = {1096-0953},
abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.},
}
@article {pmid41421745,
year = {2025},
author = {Mandelbrot, L and Kennedy, S and Rousseau, J and Goffinet, F and Landraud, L and Plainvert, C and Marcou, V and Desfrère, L and Barral, T and Allal, L and Baud, A and Grall, N and Poyart, C and Ancel, PY and Tazi, A},
title = {Predicting neonatal infection in PPROM with vaginal microbiology and metagenomics: a prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.12.042},
pmid = {41421745},
issn = {1097-6868},
abstract = {OBJECTIVE: Early-onset neonatal sepsis (EONS) due to ascending infection is a potentially preventable complication of preterm premature rupture of membranes (PPROM). Our objective was to determine whether the analysis of bacteria from vaginal swab samples is predictive of the risk of EONS in PPROM.<br><br>STUDY DESIGN: In a prospective 3-center observational cohort, patients with PPROM were enrolled between 22 and 36 weeks' gestation (WG) + 6 days. Vaginal swab samples at delivery were analyzed using two different approaches, classical bacterial cultures and shotgun metagenomic sequencing analysis. A metagenomics score was constructed combining the characterization of the vaginal microbiome and the presence of pathogens and the optimal cut-off to predict EONS was tested on a receiver operating curve.<br><br>RESULTS: 563 PPROM cases were enrolled, with 646 liveborn neonates. PPROM occurred < 32 WG in 41.9% and deliveries were < 34 WG in 41.0%. The incidence of EONS was 29/646 (4.5%). When considering all central and peripheral microbiological samples available for 26 neonates, the main pathogens isolated were Escherichia coli in 14 cases (53.8 %), other gram-negatives in 5 (19.2%), strict anaerobes in 3 (11.5%); there was a single case (3.8%) each with Group B Streptococcus (GBS), Streptococcus anginosus, Staphylococcus aureus and Ureaplasma urealyticum. We studied the prediction of EONS among 272 mothers and their 310 neonates (20 EONS, 6.4%) with both culture and metagenomic data available. A culture positive for a major or intermediate pathogen in the vaginal sample at delivery had a sensitivity of 80.0 % (95% CI=56.3-94.3) and a specificity of 37.9% (95% CI=32.3-43.8), adjusted odds ratio (aOR) of 1.6 (95 % CI [0.5-5.0]) to predict EONS. The presence of E. coli was associated with an EONS risk of 10.6% vs 4.9%, in the absence of E. coli (p=0.07). The metagenomics score was highly associated with EONS, with an area under the receiver operating curve of 0.75 (95% CI, 0.61-0.90). At the optimal cutoff value, sensitivity was 70% (95% CI, 64-95%), specificity was 85% (95% CI, 81-89%). A metagenomics score greater than 40 was associated with a significantly increased risk of EONS with an aOR of 8.9 (95 % CI [3.5; 22.3]) in multivariate analysis adjusted for latency period and gestational age, p<0.001.<br><br>CONCLUSION: In PPROM, conventional microbial culture of maternal vaginal samples was associated with EONS, but its predictive values remain insufficient to guide perinatal care. Metagenomic microbial signatures improved predictive values. This opens the perspective for a rapid point-of-care test.},
}
@article {pmid41421679,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Metabolic responses of purple phototrophic bacteria to elevated hydrogen partial pressure: Metatranscriptomic insights into biohydrogen production and consumption.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133831},
doi = {10.1016/j.biortech.2025.133831},
pmid = {41421679},
issn = {1873-2976},
abstract = {During biohydrogen production, self-generated gas accumulation can lead to elevated hydrogen partial pressure (HPP) in the headspace. However, the effects of elevated HPP on hydrogen yield in photo fermentation systems and the metabolic responses of phototrophic bacteria (PPB) under such conditions remain poorly understood. This study investigated the effects of elevated HPP on PPB-based biohydrogen production and examined the underlying metabolic responses using metagenomic and metatranscriptomic analysis. PPB maintained efficient H2 production (0.67 ± 0.09 L H2·g COD[-1]; 0.09 ± 0.01 L H2·L[-1]·d[-1]) until HPP reached about 30 %, after which both H2 production and growth declined. Transcriptomic results showed reduced nitrogenase and increased hydrogenase expression, disturbing electron allocation and redox balance and suppressing the tricarboxylic acid (TCA) cycle, gluconeogenesis, and photosynthesis. When HPP increased to about 40 %, H2 production stopped and shifted to H2 consumption, while alternative electron sinks such as the reverse TCA cycle and branched-chain amino acid synthesis were activated to partially restore metabolism. Upon headspace flushing, H2 production rapidly resumed, demonstrating the robustness of the PPB system to short-term HPP inhibition. This study provides practical insight for PF system operation, highlighting the importance of maintaining HPP below inhibitory threshold to sustain efficient H2 production.},
}
@article {pmid41421358,
year = {2025},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}
@article {pmid41421350,
year = {2025},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}
@article {pmid41421332,
year = {2025},
author = {Wang, Q and Liang, E and Xu, J and Liu, Y and Chao, C and Wan, H and Zhao, Y},
title = {Microbial self-regulation and electron transport reconstruction under Cr(VI)-4-CP stress: From synergistic inhibition to antagonistic interaction.},
journal = {Water research},
volume = {291},
number = {},
pages = {125138},
doi = {10.1016/j.watres.2025.125138},
pmid = {41421332},
issn = {1879-2448},
abstract = {Understanding how microbial communities adapt to multi-pollutant stress is crucial for efficient denitrification. Although previous studies reported the effects of heavy metals and phenolic compounds individually or in mixtures, the deep mechanisms by which combined stressors reshape microbial electron transport and community structure remain unclear. This study explored the denitrification response to combined Cr(VI) and 4-chlorophenol (4-CP) stress, revealing a temporal shift from synergistic inhibition (acute exposure) to antagonistic interaction (long-term adaptation). Acute Cr(VI)-4-CP exposure caused complete inhibition of denitrification within 18T, accompanied by the activation of dissimilatory nitrate reduction to ammonium. Cr(VI) intracellular accumulation (71.78 %) induced oxidative imbalance and 4-CP prioritized metabolism disrupted electron donor availability, collectively causing FMN decreasing, which decreased NAR electron capture efficiency. Prolonged exposure activated microbial self-regulation (denitrification efficiency recovered to 31.42 %), including extracellular Cr(III) immobilization (84.19 %), antioxidant enzyme upregulation, reshaping oxidative-antioxidant homeostasis. Concomitantly, the electron transport was remodeled via FMN/FAD complementarity, enabling partial recovery of NAR activity and suppression of N2O accumulation. Metagenomic analysis further identified functional cooperation among Microbacterium, Thermomonas, Diaphorobacter, and Acidovorax, supporting glucose/4-CP co-metabolism (COD4CP/CODglucose=1/1.26) and stabilized denitrification performance. This study established a mechanistic framework linking microbial self-regulation and electron transport remodeling, providing new insights into the resilience of denitrifiers under multi-pollutant stress.},
}
@article {pmid41421325,
year = {2025},
author = {Yang, Z and Yang, Y and Ning, D and Fan, X and Lv, Y and Zhuang, L and Wu, L},
title = {Metagenomic insights into the global distribution and functional potentials of major polyphosphate-accumulating organisms (PAOs) in activated sludge wastewater treatment plants.},
journal = {Water research},
volume = {291},
number = {},
pages = {125191},
doi = {10.1016/j.watres.2025.125191},
pmid = {41421325},
issn = {1879-2448},
abstract = {Polyphosphate accumulating organisms (PAOs) are essential for phosphorus removal in wastewater treatment plants (WWTPs); however, their global distribution patterns and potential ecological functions across diverse activated sludge systems remain poorly understood. Here, we analyzed 226 activated sludge metagenomes from 142 WWTPs across six continents, encompassing both enhanced biological phosphorus removal (EBPR) and non-EBPR processes. We reconstructed 29 near-complete PAO metagenome-assembled genomes, identifying putative members of several previously unrecognized Candidatus Accumulibacter clades. Our results revealed that Dechloromonas and Ca. Accumulibacter dominated in most WWTPs, while the former Tetrasphaera genus was prevalent in certain European samples. Furthermore, these PAOs demonstrated high metabolic versatility in carbon, nitrogen, and phosphorus cycling, though this functional potential varied significantly across genera. The link between PAOs and plant performance was process-dependent: while pollutant removal across the entire dataset showed comparable associations with both PAO abundance and the total abundance of phosphorus-cycling genes, the relationship was stronger for PAO abundance in EBPR plants. Collectively, these results represent a major expansion of the known genomic diversity of PAOs, and provide a foundational global baseline of PAO diversity that can help inform the future development of region- and process-specific optimization strategies.},
}
@article {pmid41420927,
year = {2025},
author = {Zhou, J and Yu, F and Wang, W and Zhang, D and Xie, M and Yuan, L and Zheng, J and Wang, J and Li, B and Lou, B and Han, D},
title = {Clinical metagenomics for pathogen detection in lower respiratory infections: a diagnostic study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117232},
doi = {10.1016/j.diagmicrobio.2025.117232},
pmid = {41420927},
issn = {1879-0070},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive detection of all potential pathogens in a sample. However, its diagnostic performance in various clinical settings requires further validation through real-world data.<br><br>METHODS: This retrospective study included 186 patients from the First Affiliated Hospital of Zhejiang University School of Medicine who underwent mNGS testing on respiratory samples. We compared mNGS with traditional culture method using the same samples and also assessed its performance against conventional microbiological testing combinations (CMTs) for the same patients. Additionally, we analyzed the diagnostic performance of mNGS in different disease states (immunosuppressive status and mechanical ventilation).<br><br>RESULTS: The positivity rate of mNGS was 81.2 % (151/186). In lower respiratory tract infections (LRTIs), mNGS successfully detected 84.6 % (137/162) of bacteria, 89.0 % (65/73) of fungi, 100.0 % (72/72) of viruses, 88.9 % (16/18) of Mycobacterium tuberculosis, and 100.0 % (9/9) of non-tuberculous mycobacteria. Mixed infections were the most common infection type in LRTIs in this study (69/145, 47.6 %). The detection rate of mixed infections by mNGS was significantly higher than that of CMTs (91.3 % vs 43.5 %, P < 0.01). In the comparison based on a composite LRTI diagnostic standard, mNGS showed significantly higher sensitivity than paired culture (89.0 % vs 32.4 %, P < 0.01) and CMTs (89.0 % vs 57.2 %, P < 0.01), but lower specificity (46.3 % vs 87.8 % and 46.3 % vs 82.9 %, P < 0.01). In non-mechanically ventilated patients, mNGS maintained high sensitivity (87.0 % vs 96.7 %, P = 0.19), while culture and CMTs showed significant sensitivity decline (P < 0.01).<br><br>CONCLUSION: mNGS demonstrates superior diagnostic performance for LRTIs compared to CMTs.},
}
@article {pmid41420859,
year = {2025},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}
@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}
@article {pmid41420363,
year = {2025},
author = {Babaoğlu, AS and Demirci, T and Karakaya, M and Unal, K},
title = {Assessment of bacterial and fungal profiles in fermented sucuk production using high-throughput sequencing: influence of ripening conditions and starter culture addition.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70390},
pmid = {41420363},
issn = {1097-0010},
support = {//Scientific Research Projects of Sel&#xe7;uk University/ ; },
abstract = {BACKGROUND: This study investigated the effects of various ripening conditions and starter culture additions on the microbial composition and physicochemical properties of Turkish fermented sucuk. Ripening conditions (spontaneous, controlled, and controlled with starter culture) were evaluated using metagenomic technology. Key physicochemical properties, including moisture, pH, water activity, titratable acidity, residual nitrate, residual nitrite, and color properties, were analyzed.<br><br>RESULTS: Three groups were produced: group A (spontaneous conditions); group B (controlled conditions); and group C (controlled conditions with starter culture). Microbial and physicochemical properties were assessed at three key time points: beginning (t1 - sucuk dough), middle (t2), and end (t3) of the ripening process. Physicochemical analyses showed a decrease in moisture content (from 53-54% to 39%), an increase in acidity (from 0.59% to 1%), and a reduction in nitrate levels (especially in sucuk produced with starter cultures under controlled conditions from 65.22% to 5.97%) throughout the ripening period (P&#x2009;<&#x2009;0.05). Microbial analyses revealed that Latilactobacillus sakei dominated the bacterial composition (57.9%) in group B, while the lowest bacterial diversity was observed in group C, and the highest diversity was in group A. The most detected fungal genus in the sucuk samples was Pichia, followed by Hanseniospora, Alternaria, Kluyveromyces, Cladosporium, and Monascus.<br><br>CONCLUSION: The ripening conditions and starter culture application significantly influenced both microbial and physicochemical characteristics of fermented sucuk. Controlled fermentation, particularly with starter cultures, resulted in reduced microbial diversity but enhanced the dominance of beneficial microorganisms. These findings contribute to optimizing sucuk production for improved safety and consistent quality. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid41419973,
year = {2025},
author = {Rojas, MA and Serrano, G and Torres, J and Ortega, J and Gálvez, G and Vilches, E and Parra, V and Reyes-Jara, A and Maracaja-Coutinho, V and Pizarro, L and Latorre, M and Di Genova, A},
title = {Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {153},
pmid = {41419973},
issn = {2524-6372},
support = {ACT210004//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {BACKGROUND: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community.<br><br>RESULTS: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival.<br><br>CONCLUSIONS: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.},
}
@article {pmid41419779,
year = {2025},
author = {Liu, Y and Chen, S and Li, H and Mahtab, N and Sun, Y and Li, Y and Song, J and Sun, D and Liang, M and Chen, J and Sun, J and Gong, B and Jing, J and Bu, R},
title = {Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-025-06438-y},
pmid = {41419779},
issn = {2052-4463},
support = {2024GXNSFBA010371//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069226//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069232//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; },
abstract = {Mangrove sediments, being organic-rich and anoxic, host diverse and functionally important microorganisms that play crucial roles in global biogeochemical cycling. In order to characterize this diversity at the genome-resolved level, we collected 38 sediment samples encompassing both surface (0-5 cm) and core (up to 90 cm) depths from six representative mangrove sites across Guangxi Province, China. Using a standardized pipeline for assembly, binning, and dereplication, we reconstructed 2,965 non-redundant metagenome-assembled genomes (MAGs), comprising 2,383 bacterial and 582 archaeal genomes spanning 78 microbial phyla. This dataset captures the high microbial diversity and functional potential within mangrove sediments under variable environmental conditions. It provides a valuable genomic resource for investigating the structure, metabolism, and ecological roles of sediment microbial communities in intertidal, nutrient-rich ecosystems, supporting future studies on microbial adaptation and biogeochemical cycling in global blue carbon environments.},
}
@article {pmid41419527,
year = {2025},
author = {Takeda, Y and Kato-Kogoe, N and Sakaguchi, S and Ieda, S and Tasaka, Y and Mizobata, N and Omori, M and Hamada, W and Nakamura, S and Nakano, T and Ueno, T and Matsumura, T},
title = {Characteristics of salivary IgA responses to oral microbiota in patients with oral lichen planus.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44167},
pmid = {41419527},
issn = {2045-2322},
mesh = {Humans ; *Lichen Planus, Oral/microbiology/immunology ; *Saliva/immunology/microbiology ; Female ; Male ; Middle Aged ; *Microbiota/immunology ; RNA, Ribosomal, 16S/genetics ; Adult ; *Immunoglobulin A, Secretory/immunology ; Aged ; *Immunoglobulin A/immunology ; Bacteria/genetics/classification ; Metagenomics ; Case-Control Studies ; },
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa with a risk of malignant transformation. Oral bacteria are associated with OLP development and progression; however, the immune response, especially the salivary immunoglobulin A (IgA) response to these bacteria remains poorly understood. Therefore, this study aimed to characterize the salivary microbiota in patients with OLP and evaluate the corresponding salivary IgA response. Stimulated saliva samples were collected from 21 patients with OLP and 56 control participants, and 16S rRNA metagenomic analysis was performed to characterize the composition of the microbiota. In addition, IgA-enriched and non-enriched fractions from the saliva samples were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. To evaluate differences in IgA responses to each bacterium between the two groups, we calculated the IgA index. The diversity and bacterial composition of the salivary microbiota differed considerably between the OLP and control groups. Several bacterial genera, including Leptotrichia, Fusobacterium, and Streptococcus, showed markedly lower IgA index in the OLP group than the control group. In conclusion, patients with OLP exhibited a distinctive salivary IgA response to salivary microbiota, suggesting a potential association between OLP and this altered response.},
}
@article {pmid41419481,
year = {2025},
author = {Gómez-Consarnau, L and Hassanzadeh, B and Villarreal, E and Cuevas-Cruz, M and Arístegui, J and Logares, R and Latorre, F and Lago-Lestón, A and Steindler, L and Sañudo-Wilhelmy, SA},
title = {Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67474-1},
pmid = {41419481},
issn = {2041-1723},
support = {OCE1924464//NSF | GEO | Division of Ocean Sciences (OCE)/ ; PID2023-152792NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; 2019612//United States - Israel Binational Science Foundation (BSF)/ ; },
abstract = {The surface ocean is the largest sunlit environment on Earth where marine microalgae are known as the main drivers of global productivity. However, rhodopsin phototrophs are actually the most abundant metabolic group, suggesting a major role in the biogeochemical cycles. While previous studies have shown that rhodopsin-containing bacterioplankton thrive in the most severely nutrient-depleted environments, growing evidence suggest that this type of phototrophy may also be relevant in nutrient-rich environments. To examine its role in productive waters, we investigated the monthly rhodopsin dynamics in the upwelling system of the Southern California Bight by measuring retinal-the photoreactive chromophore essential for rhodopsin function-in seawater. Unlike oligotrophic regions, rhodopsin levels peaked during the highly productive spring phytoplankton bloom, coinciding with the highest chlorophyll concentrations. Heterotrophic bacterial abundances, particularly within the order Flavobacteriales, correlated strongly with rhodopsin concentrations, allowing us to build linear models to predict rhodopsin distributions in a productive environment. Metagenomic data further showed that Flavobacteriales also dominated the rhodopsin gene pool when the highest rhodopsin levels were recorded, underscoring their key contribution to light-driven energy capture. Overall, our findings reveal that rhodopsin phototrophy plays a substantial role in productive marine systems, broadening its recognized importance far beyond oligotrophic oceans.},
}
@article {pmid41418867,
year = {2025},
author = {Ma, X and Xu, Q and Wang, Y and Lu, J and Zhu, K and Deng, J and Wu, S and Wang, Y and Wang, B and Zhang, H},
title = {Profiling of soil bio-composite pollution and driving factors in China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123578},
doi = {10.1016/j.envres.2025.123578},
pmid = {41418867},
issn = {1096-0953},
abstract = {Soil biological contamination driven by antibiotic resistance poses escalating global health threats, yet national-scale assessments remain scarce. To bridge this knowledge gap, metagenomic analysis of 300 samples spanning five ecosystems (agricultural, bare land, forest, grassland, wetland) was employed to study the diversity, co-occurrence patterns, and driving factors of the soil resistome and pathogens across China. Our analyses revealed that antibiotic resistance genes (ARGs) were ubiquitously detected (23 types; 0.03-2.6 copies/cell), with multidrug (mexF, mexW), vancomycin (vanR/S), and bacitracin (bacA) resistance dominating. Eleven major mobile genetic element (MGE) types were identified, and co-occurrence network analysis confirmed robust ARG-MGE associations. Notably, 272 ARG-carrying pathogens (APs) were identified as a severe consequence mediated by bio-composite contamination, with widely distributed genera including Enterobacter, Klebsiella, Nocardia, Pseudomonas, exhibiting potential for multidrug and vancomycin resistance. AP richness peaked in agricultural soils and was lowest in bare lands. Random forest modeling and correlation analysis revealed mean annual precipitation (MAP; ρ = 0.19, P < 0.05) and grain production (GP; ρ = 0.18, P < 0.05) were weakly but significantly associated with ARG abundance, while soil pH, organic carbon and meat production governed AP richness. These findings demonstrate nationwide soil bio-composite pollution and underscore the need for prioritized interventions in high-risk ecosystems, though further mechanistic studies are required to validate the observed correlations.},
}
@article {pmid41418855,
year = {2025},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.<br><br>METHODS: Participants provided urine and fecal samples at six weeks (6W; n=219) or twelve months (12M; n=219), a subset of whom provided samples at both (n=167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/ gene pathway relative abundance.<br><br>RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [&#x3b2;=0.07 per doubling (95%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [&#x3b2;=-0.04 per doubling (95%CI: -0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.<br><br>CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}
@article {pmid41418614,
year = {2025},
author = {Ahmed, I and Zhang, D and Farooq, MU and Sheikh, Z and Dai, X},
title = {Microplastics exacerbate antibiotic resistance by regulating microbial and functional gene dynamics in sludge and food waste composting.},
journal = {Water research},
volume = {291},
number = {},
pages = {125161},
doi = {10.1016/j.watres.2025.125161},
pmid = {41418614},
issn = {1879-2448},
abstract = {The presence of antibiotic resistance genes (ARGs) and microplastics (MPs) as co-contaminants in sewage sludge possess environmental concern. Nevertheless, the effect of specific MP types on ARGs propagation and the mechanistic drivers during composting require further elucidation. This study analyzed the impact of MPs polyethylene (PE), polypropylene (PP), and their mixture (PE+PP) on the propagation of ARGs and mobile genetic elements (MGEs) during sludge composting. Results revealed that MPs significantly increased ARGs abundance, with the highest enrichment observed in PE (2.06 log-fold), followed by PP (1.74) and PE+PP (1.65), compared to control trial. MGEs also increased by up to 1.3 log-fold in MP-treated groups. MPs altered bacterial community composition, enhancing the abundance of Brevibacterium, Microbacterium, and Streptomyces. MPs exhibited a partial reduction of up to 30.2 % during composting which modified the compost's chemical properties, elevating carbon content and depleting oxygen. Metagenomic analysis revealed MPs affected microbial functional pathways, upregulating ABC transporters, two-component regulatory systems, and the conjugation gene VirD4. Functionally, MPs enhanced denitrification and dissimilatory nitrate reduction to ammonium, inhibited assimilatory nitrate reduction, and promoted inorganic nitrogen assimilation. Redundancy analysis exhibited MGEs as the primary drivers of ARGs proliferation in MP-amended compost, while temperature was dominant in the control. Network analysis identified key bacterial hosts Staphylococcus, Weissella, Lactiplantibacillus, Sphingobacterium carrying multiple ARGs and MGEs. This study highlights the potential of MPs, even at low concentrations, to promote ARG dissemination by altering microbial communities and enhancing gene transfer, offering new insights into ecological risks associated with MP-contaminated composting systems.},
}
@article {pmid41418611,
year = {2025},
author = {Du, R and Tang, M and Cao, S and Peng, Y},
title = {Overcoming temperature and substrate limitations of anammox via partial denitrification: Stable performance, microbial structure, and N2O mitigation.},
journal = {Water research},
volume = {291},
number = {},
pages = {125186},
doi = {10.1016/j.watres.2025.125186},
pmid = {41418611},
issn = {1879-2448},
abstract = {The widespread application of the anaerobic ammonium oxidation (anammox) process remains constrained by its narrow substrate range (nitrite-to-ammonia ratio of 1.32), sensitivity to low temperatures, and difficulty in controlling nitrous oxide (N2O). This study demonstrated that under different substrate types and proportions (nitrate-nitrite, NOx[-]-N), the partial denitrification coupled with anammox (PD/A) process with high nitrogen load (1.35 kg N/m[3]/d) still maintained stable nitrogen removal efficiencies (83.5 %∼98.5 %), even at long-term continuous cooling (29.4∼11.6°C) and persistent low temperature (15.1∼9.6°C). In the presence of coexisting NO3[-]-N and NO2[-]-N (NO3[-]-N: NO2[-]-N of 1:1), carbon sources were preferentially utilized for the reduction of NO3[-]-N to NO2[-]-N, effectively circumventing the strict substrate dependence inherent to anammox. The stable nitrogen removal of the PD/A process at low temperatures was attributed to the low activation energy (35.1 kJ/mol) of partial denitrification and the cold-resistant granular sludge, ensuring a highly efficient supply of the essential NO2[-]-N for anammox. Cold-resistant granule sludge provided a spatial environment for the synergistic symbiosis of partial denitrification, anammox, and other heterotrophic bacteria, facilitating anammox adaptation to persistent low-temperature conditions. Metagenomic sequencing revealed a high relative abundance of Candidatus Brocadia (14.9 %) within the granular sludge, while Thauera (18.0 %) dominated the flocculent sludge at low temperatures. It further revealed the cross-feeding relationship of the bacterial community between granular and flocculent sludge. Notably, N2O emissions from the PD/A process can be effectively regulated by controlling the COD/NO3[-]-N ratio, achieving a balance between improving nitrogen removal efficiency and mitigating N2O emissions. This research provides a theoretical foundation for the stable operation and N2O control of non-specifically dependent PD/A process under long-term low-temperature conditions.},
}
@article {pmid41418312,
year = {2026},
author = {Braga, LPP and Wang, Y and Huang, Z and Willerslev, E and Tanentzap, AJ},
title = {The Contributions of Microbial Interactions to Abrupt Ecosystem Changes during the Late Quaternary.},
journal = {The American naturalist},
volume = {207},
number = {1},
pages = {182-195},
doi = {10.1086/738433},
pmid = {41418312},
issn = {1537-5323},
mesh = {*Soil Microbiology ; *Ecosystem ; *Climate Change ; Europe ; *Microbial Interactions ; Fungi ; Mycorrhizae/physiology ; Grassland ; Forests ; },
abstract = {AbstractAbrupt ecosystem shifts during the Late Quaternary coincided with major climatic changes and intensified human activities, but the precise causes of these shifts remain debated. Here, building on previous hypotheses and work, we propose a new hypothesis that both plant beneficial and antagonistic soil microorganisms were the proximate drivers of Late Quaternary change. We synthesized evidence from paleoecological studies and contemporary ecosystems to understand how microbes and their interactions with plants shift ecosystem function. Because relevant paleoecological data are nonexistent, we reanalyzed a contemporary survey from grasslands and woodlands across Europe to test the general role of microbial diversity versus climate in controlling ecosystem function. Our models found that the richness of different microbial groups, including Proteobacteria, mycorrhizas, and plant fungal pathogens, were more strongly associated with the magnitude of direct effects on net primary productivity than temperature and precipitation. The richness of most of these groups was also influenced by climate, supporting our hypothesis that climate change may have indirectly caused past ecosystem shifts by changing microbial composition and function. We end by highlighting the potential of environmental DNA to reconstruct the biota and conditions of past ecosystems. Ultimately, improving our understanding of how microbes drove past ecosystem shifts may improve our ability to respond to future environmental changes.},
}
@article {pmid41417461,
year = {2025},
author = {Drew, G and Kraft, CS and Mehta, N},
title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf156},
pmid = {41417461},
issn = {1530-8561},
abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.<br><br>CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.<br><br>SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.},
}
@article {pmid41416507,
year = {2025},
author = {Wang, Y and Wan, Y and Wang, H and Yan, J and Sun, J and Yang, J and Zhang, F and Cao, H and Li, D},
title = {Oral Supplementation of Indole-3-acetic Acid Alleviates High-Fat-Induced Obesity by Activating the Gpha2-Mediated Thyroid-Stimulating Hormone Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14556},
pmid = {41416507},
issn = {1520-5118},
abstract = {Obesity is a major global public health challenge. Indole-3-acetic acid (IAA), a gut microbiota-derived tryptophan metabolite, exhibits antiobesogenic potential. In this study, we found that in high-fat-diet-induced obese mice, oral IAA supplementation dose dependently attenuated body weight gain, adiposity, hepatic steatosis, and dyslipidemia while improving insulin sensitivity. Notably, intraperitoneal administration of IAA (50 mg/kg/day) paradoxically exacerbated weight gain. Metagenomic sequencing showed that oral IAA selectively enriched beneficial genera (Ileibacterium, Anaerotignum, and Clostridium) and significantly increased short-chain fatty acid (SCFA) production, particularly acetate and butyrate. In vitro experiments in Saccharomyces cerevisiae further confirmed that IAA directly suppresses de novo fatty acid biosynthesis and triacylglycerol assembly. Mechanistically, IAA upregulated hepatic Gpha2 expression, thereby activating the TSH-THR-PGC-1α-PPARγ signaling cascade and concomitantly repressing key lipogenic genes (Fasn, Acaca, and Srebp-1c). Collectively, these findings position IAA as a promising microbiota-derived metabolite with substantial preventive and therapeutic potential for obesity and related metabolic disorders.},
}
@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation &amp; purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation &amp; purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}
@article {pmid41416071,
year = {2025},
author = {Zheng, Y and Hou, J and Yang, L and Jiang, Y and Wang, S and Yu, J and Ye, X},
title = {Cavitary pulmonary tuberculosis with Orientia tsutsugamushi coinfection in a non-endemic region: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1692918},
pmid = {41416071},
issn = {2296-858X},
abstract = {INTRODUCTION: Coinfection of pulmonary tuberculosis and scrub typhus caused by Orientia tsutsugamushi is exceptionally rare. Overlapping clinical and radiologic features, together with the frequent absence of clear epidemiologic clues, complicate timely diagnosis.<br><br>CASE PRESENTATION: A 57-year-old man residing in a non-endemic region presented with a left-sided cavitary lung lesion on imaging. Computed tomography (CT)-guided percutaneous lung biopsy, acid-fast bacillus staining, and Mycobacterium tuberculosis DNA PCR established the diagnosis of active cavitary pulmonary tuberculosis. Despite initiation of a standard first-line anti-tuberculosis regimen, high-grade fever persisted. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) detected O. tsutsugamushi, which was subsequently confirmed by a positive IgM indirect immunofluorescence assay (IFA). Doxycycline was added, leading to defervescence within 48&#x202f;h and marked symptomatic improvement. On follow-up, chest CT demonstrated lesion absorption and cavity shrinkage, while new fibrotic changes emerged. The patient was started on maintenance pirfenidone and prescribed home oxygen therapy.<br><br>CONCLUSION: In patients with pulmonary tuberculosis who exhibit persistent fever or suboptimal response despite appropriate therapy-and after excluding drug resistance-scrub typhus should be included in the differential diagnosis, even in non-endemic settings without a typical exposure history. Longitudinal imaging in this case also shows that irreversible structural remodeling may occur despite microbiologic control, underscoring the need to pair prompt pathogen-directed therapy with ongoing monitoring and early strategies to preserve lung function.},
}
@article {pmid41415824,
year = {2025},
author = {Lai, W and Guo, J and Zhou, X and Luo, Y and Zheng, M and Mai, Q and Xiong, J and Luo, M},
title = {Co-infection in pediatric pertussis during 2023 and 2024 in southern China: pathogen distribution characteristic and influence on manifestation of pertussis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722003},
pmid = {41415824},
issn = {1664-302X},
abstract = {OBJECTIVE: We sought to examine the pathogen composition of co-infections in pertussis during 2023 and 2024 and assess the impacts of co-infection on pertussis.<br><br>METHODS: Clinical data of pediatric pertussis patients were retrospectively analyzed. The impact of co-infections on pertussis, the detection rate and composition of co-pathogens were analyzed. Culture, polymerase chain reaction, or metagenomic sequencing were used in pertussis or co-pathogens detection.<br><br>RESULTS: Among 620 pertussis patients, 110 patients co-infected with bacteria, 106 co-infected with virus, and 98 co-infected with both bacteria and virus. M. pneumoniae (114, 18.39%), M. catarrhalis (44, 7.1%), and H. influenzae (26, 4.19%) were the most common bacterial co-pathogens, and Rhinovirus (100, 16.12%), Cytomegalovirus (31, 5%), and Influenza virus A&amp;B (28, 4.52%) were the most common viral co-pathogens. Patients with co-infections exhibited more severe manifestations than those with pertussis alone, and the severity was associated with the type and number of pathogens. The composition of co-pathogens linked to the age and hospitalization status of the patients. M. pneumoniae (91, 21.06%), M. catarrhalis (32, 7.41%), and Influenza virus A&amp;B (22, 5.09%) primarily caused co-infections in older, non-hospitalized patients, whereas Cytomegalovirus [(19, 14.39%) non-ICU, (12, 21.43%) ICU] and Respiratory syncytial virus [(8, 6.06%) non-ICU, (8, 14.28%) ICU] were more common in younger, hospitalized patients.<br><br>CONCLUSION: Co-infections are common among pertussis and can intensify clinical symptoms. Distribution of co-infecting pathogens is associated with age and hospitalization status, and the impacts of co-infection on the manifestations of pertussis varied according to the types and number of co-pathogens.},
}
@article {pmid41415820,
year = {2025},
author = {Bao, Y and Wang, T and Adina, W and Yao, R and Chu, H and Yao, X and Meng, J and Wang, J and Ren, W and Zeng, Y},
title = {Gut microbial signatures and cardiac-microbiota axis in Yili horses with divergent exercise-induced cardiac remodeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689293},
pmid = {41415820},
issn = {1664-302X},
abstract = {This study aimed to investigate how different training outcomes affect the gut microbiota composition in racehorses. Twenty-six Yili horses underwent a 9-month conditioning training regimen under uniform husbandry and management conditions. Post-training, the horses were divided into an excellence group (D. Y group) and a general group (D. P group) based on their athletic performance, with the top 10 performers constituting the D. Y group and the bottom 10 the D. P group. Cardiac morphology and function were quantitatively assessed via echocardiography, and metagenomic sequencing was performed on fresh fecal samples. Results indicated that there were no significant differences in gut microbiota and echocardiographic parameters between the two groups prior to training. However, significant differences were observed post-training (p < 0.05). At the genus level, Parabacteroides, Bacteroides, and Prevotella exhibited significantly greater abundance n the D. Y group. LEfSe analysis showed that Prevotella was markedly enriched in the D. Y group (LDA > 4). Functional profiling indicated that multiple metabolic pathways were significantly enriched in global and overview maps, with map00534 and map00190 being particularly enriched in the D. Y group (LDA > 2). Within CAZymes genes, eight were significantly enriched in the D. Y group, including four glycoside hydrolase genes, two carbohydrate esterase genes, and two carbohydrate-binding module genes. Echocardiography revealed significant differences in seven parameters between the groups, with the D. Y group exhibiting notably higher LV_MASS_I and LVM values (p < 0.01). dbRDA analysis demonstrated a significant association between LV_MASS_I and LVM and the gut microbiota profile (p < 0.01). These findings suggest that training-induced cardiac remodeling, particularly the increase in LV_MASS_I and LVM, is closely related to alterations in gut microbiota, with Prevotella enrichment potentially serving as a marker of favorable adaptation to the training regimen. The study provides robust evidence for understanding the interaction between aerobic training, gut microbiota, and cardiac characteristics in racehorses, and highlights potential directions for optimizing athletic performance and probiotic strategies in equine athletes.},
}
@article {pmid41415819,
year = {2025},
author = {Miao, M and Ma, C and Yang, J and Yang, X and Liu, Z and Liu, A and Qian, Z and Ge, Y and Chen, Y and Yin, G and Hu, Z},
title = {BALF metagenomic next-generation sequencing for the diagnosis of pulmonary mycobacterial infection in persons with HIV: a retrospective, diagnostic accuracy study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689997},
pmid = {41415819},
issn = {1664-302X},
abstract = {Severely immunocompromised persons with HIV (PWH) are vulnerable to pulmonary mycobacterial infections (MBI), including Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM). This study aimed to assess the effectiveness of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in aiding the diagnosis of pulmonary mycobacterial infections in PWH. This study encompassed 146 hospitalized PWH who had a CD4+ T cell count of less than 200 cells/μL. We employed BALF mNGS to pinpoint the causative pathogens of pulmonary infections, with particular focus on pulmonary mycobacterial infections. We evaluated the diagnostic performance of BALF mNGS, and interpreted its clinical significance in detecting mixed infections as appropriate. The median CD4+ T cell count of the participants was 22.5 (IQR: 7.0-63.0) cells/uL. BALF mNGS analysis of 146 severely immunocompromised PWH identified Mycobacterium tuberculosis (13.0%) and M. avium complex (7.5%) as the predominant mycobacterial species, with 9.3% (4/43) of mycobacterial infections showing mixed speciation including TB-NTM co-infections or interspecies NTM coinfections. Furthermore, mNGS demonstrated 78.8% sensitivity (95% CI: 62.2%-89.3%) for proven mycobacterial infections, outperforming conventional culture (68.4% vs. 42.1%, P < 0.01), though missing 7 proven MBI cases. Finally, among 158 co-detected pathogens, Pneumocystis jirovecii (67.1%) and cytomegalovirus (63.0%) were most prevalent, demonstrating co-occurrence rates of 53.5% and 55.8%, respectively in mycobacterial-infected patients. These rates were elevated to 81.2% (P. jirovecii) and 65.3% (CMV) in the subset of 101 patients with CD4+ counts <50 cells/μL. The presence of atypical clinical presentations, along with the coexistence of multiple opportunistic pathogens in BALF, complicates the management of pulmonary MBI in PWH. In this context, mNGS has emerged as a highly promising microbiological test that could revolutionize the management of pulmonary MBI in PWH.},
}
@article {pmid41415818,
year = {2025},
author = {Wu, H and Du, X and Zheng, J and Li, X and Song, Q and Yan, Y and Ma, A and Xu, A and Li, J},
title = {Top-down enrichment of oil-degrading microbial consortia reveals functional streamlining and novel degraders.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656448},
pmid = {41415818},
issn = {1664-302X},
abstract = {INTRODUCTION: Top-down microbial enrichment is a reliable approach for understanding and designing microbiomes for crude oil remediation. Environmental variables serve as valuable determinants for selecting desired microbiomes with superior performance. However, the linkages between selection methods and the structure and function of desired microbiomes remain unclear.<br><br>METHODS: This study integrated substrate concentration gradients and cultivation patterns to investigate how selection pressures shape top-down enriched crude oil-degrading consortia. The resulting communities were analyzed using 16S rRNA gene sequencing, metagenomics, and co-occurrence network analysis. Key bacterial strains were isolated to validate their individual degradation capabilities.<br><br>RESULTS: The top-down process led to a significant reduction in phylogenetic diversity but a notable increase in the potential for xenobiotic degradation and metabolic. The final consortia, GT4, achieved a 55.72% degradation rate of crude oil at an initial concentration of 5 g/L within 7 days. Metagenomic analysis identified Microbacterium as dominant genus harboring key enzymes for the degradation of alkanes and aromatic compounds. Co-occurrence network analysis revealed Mesorhizobium as a keystone genus, showing positive associations with multiple diazotrophic bacteria and hydrocarbon degrading bacteria. Nine bacterial strains were isolated from the consortium. Among them, Microbacterium sp. WS3 and Cellulosimicrobium sp. WS9 exhibited high degradation efficiencies (57.85 and 58.60%, respectively). To the best of our knowledge, this study provides the first experimental evidence for crude oil degradation by Paracandidimonas and Caulobacter, with degradation rates of 51.19 and 40.90%, respectively.<br><br>DISCUSSION: These findings highlight the effectiveness of top-down enrichment strategy in generating functionally streamlined consortia and uncover novel oil-degrading microbes with potential for bioremediation applications.},
}
@article {pmid41415809,
year = {2025},
author = {Li, E and Wang, S and Li, Y and Liuli, A and Liang, M and Huang, J and Li, Y and Li, H and Feng, Z},
title = {Characterization of the gut microbiota in people with different levels of obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1679119},
pmid = {41415809},
issn = {1664-302X},
abstract = {PURPOSE: With the evolution of dietary habits, obesity has emerged as a significant global health issue. Numerous studies have demonstrated a close association between obesity and gut microbiota; however, the specific contribution of gut microbiota to varying degrees of obesity remains inadequately understood. Consequently, this study aims to characterize the gut microbiota of individuals across different obesity severity levels.<br><br>METHODS: We conducted a comprehensive characterization of the gut microbiome in Chinese obese patients and a healthy control group through the application of 16S rRNA gene sequencing, supplemented by metagenomic sequencing. The study cohort was stratified into five distinct categories based on body mass index (BMI): healthy, overweight, and obesity grades I, II, and III.<br><br>RESULTS: In obese populations, the gut microbiome structure shifted significantly, with beneficial genera like Faecalibacterium, Roseburia, and Ruminococcus decreasing, and potentially harmful genera such as Blautia, Collinsella, and Streptococcus increasing. These changes impacted host metabolic pathways, including ribosome synthesis, RNA polymerase activity, and DNA repair. Clinical analyses also revealed strong links between specific genera and metabolic markers like lipid metabolism and insulin resistance.<br><br>CONCLUSION: Populations with different obesity traits show unique changes in gut flora. The level of dysbiosis, or imbalance in intestinal microbiota, rises with obesity. These microbial changes are linked to host metabolism, indicating that targeting harmful bacteria and supplementing with beneficial ones from normal-weight populations could effectively reduce obesity.},
}
@article {pmid41415804,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671267},
pmid = {41415804},
issn = {1664-302X},
abstract = {Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L[-1]) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L[-1] in hypoxic vs. 66.56-255.63 μmol L[-1] in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L[-1]), and nitrate depletion (0.30-22.50 μmol L[-1]), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.},
}
@article {pmid41415514,
year = {2025},
author = {Chen, X and Wang, L and Li, J and Zhang, Y and Liu, C and Yang, J and Shi, J and Liang, S},
title = {Efficacy of Liposomal Amphotericin B in Treating Pulmonary Aspergillus flavus Infection in Nonneutropenic Adults: Cases Report and Literature Review.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71688},
pmid = {41415514},
issn = {2050-0904},
abstract = {Liposomal amphotericin B (L-AmB), as a modified formulation of traditional amphotericin B, have better targeting and lower toxicity. However, clinicians have limited experience with the use of L-AmB for the treatment of Aspergillus flavus (A. flavus) at present. We described two cases of immunocompetent adults; despite undergoing various antibacterial treatments, the symptoms were persistent. Based on the clinical characteristics and results of metagenomic next-generation sequencing and (or) pathology, pulmonary A. flavus infection was confirmed. Subsequently, L-AmB was added to the treatment. Following the initiation of antifungal therapy, the patients' symptoms and images were significantly improved. In conclusion, even in immunocompetent individuals, pathogen detection and pathological examination are crucial when treatment is not effective. In pulmonary A. flavus infection, L-AmB may deserve greater attention and confidence in clinic.},
}
@article {pmid41415494,
year = {2025},
author = {Petrov, TP and Rizzetto, M and Clagnan, E and Dell'Orto, M and De Nisi, P and D'Imporzano, G and Ovani, M and Pina, MP and Kron-Morelli, R and Adani, F},
title = {Trichoderma-Activated Granulated Digestate as an Alternative to Chemical Fertilization: Effects on Tomato Yield and Quality, and Soil Rhizospheric Communities.},
journal = {ACS agricultural science &amp; technology},
volume = {5},
number = {12},
pages = {2383-2392},
pmid = {41415494},
issn = {2692-1952},
abstract = {The use of synthetic fertilizers is always more economically and environmentally unsustainable. It is necessary to improve current agricultural practices. Bioactivated fertilizers are a promising solution to enhance digestate solid fraction's fertilizing properties with an ad hoc microbial consortium and reach yields comparable to chemical fertilization (CF), thus combining circular economy with an upgraded organic agriculture. This study designed a new granulated formulation, obtained using a vacuum drying process at the industrial level, for an improved Trichoderma-activated digestate's solid fraction. This granulation aimed to improve both management operations and Trichoderma activity. After a greenhouse experimentation, yields obtained from the activated digestate (56 ± 7 g FW plant[-1]) were similar to the one obtained with CF (62 ± 9 g FW plant[-1]). Additionally, the bioactivated digestate gave yield production that were 21-30% higher yield than that of digestate alone. Microbial activation further led to higher nutritional values with an increment in the lycopene content between 8.8% and 15.8%. A metagenomic analysis further highlighted the persistence of Trichoderma in the tomato rhizosphere and its ability to establish positive interactions with other beneficial rhizospheric microorganisms. Activated digestate showed its potential to substitute CF, while granulation resulted in a functional formulation to convey this product.},
}
@article {pmid41415413,
year = {2025},
author = {Macias Calix, K and Borges, C and do Nascimento Oliveira, AL and Albuquerque de Luna, SC and Souza Cunha, CM and de Siqueira, AM and Campelo Dos Santos, AL and DeGiorgio, M and Lindo, J and Assis, R},
title = {Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.10.693243},
pmid = {41415413},
issn = {2692-8205},
abstract = {During urban redevelopment in the historic district of a Brazilian metropolis, archaeologists uncovered a previously undocumented 17th-century cemetery, containing the closely spaced remains of over two dozen young adult males of military age. Historical records suggest the site once housed a makeshift hospital, raising questions about the origins and causes of death of those interred, particularly given the absence of skeletal evidence for violent or fatal trauma. The current study integrates bioarchaeological, historical, and genomic data to investigate the ancestry and putative disease-related mortality of nine individuals whose remains were recovered and subsequently sequenced. Population-genetic analyses revealed strong affinities with Northern European populations, particularly from Norway, Iceland, Estonia, and Czechoslovia, consistent with their likely roles as soldiers or laborers employed by the Dutch West India Company. To explore potential causes of death, we conducted a metagenomic screening with a novel pipeline optimized for degraded DNA, which revealed widespread presence of Klebsiella pneumoniae and Mycobacterium tuberculosis pathogens across all samples. Authenticity was confirmed through post-mortem damage patterns characteristic of historical samples. These findings, together with the absence of combat trauma and the collective burial context at the site, support the hypothesis of an epidemic-related mortality event. This study contributes to the growing field of historical pathogen genomics and offers a rare genomic perspective on life, mobility, and health during a period of colonial upheaval in South America.},
}
@article {pmid41415012,
year = {2025},
author = {Zhang, W and Zhang, L and Liu, H},
title = {Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1594899},
pmid = {41415012},
issn = {2296-2360},
abstract = {Congenital heart disease may increase the incidence of necrotizing enterocolitis, especially in low-birth-weight infants. We report a case of a newborn with pulmonary valve stenosis who developed neonatal necrotizing enterocolitis IIIB. The infant underwent initial cardiac surgery followed by a laparotomy. After cardiac surgery, a right atrial thrombus was found by cardiac ultrasound. Enterococcus faecium was identified using metagenomic next-generation sequencing of ascitic fluid. The infant received targeted antibiotic therapy and anticoagulant treatment and was then discharged.},
}
@article {pmid41414025,
year = {2025},
author = {Bian, J and Cao, YN and Han, YP and Liu, JG and Chen, Q and Liu, ZP and Li, MY},
title = {[Screening, Identification, and Performance of Microplastic-degrading Functional Bacteria in Saline-alkali Soil Environment].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {12},
pages = {8082-8092},
doi = {10.13227/j.hjkx.202411208},
pmid = {41414025},
issn = {0250-3301},
mesh = {*Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/isolation &amp; purification ; *Microplastics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Bacteria/metabolism/isolation &amp; purification/classification ; Alkalies ; Polyethylene Terephthalates/metabolism ; Salinity ; },
abstract = {The combined effects of salinization and microplastic pollution will have a detrimental impact on soil fertility and the ecological integrity of soil ecosystems. Three strains of salt-resistant microplastic-degrading functional bacteria were obtained from the soil of the Hetao irrigation area, which served as a source of inoculum. The strains were identified using metagenomics and were found to belong to the genera Agrobacterium, Aspergillus fumigatus, and Streptomyces. The strains were designated Agrobacterium_salinitolerans strain （A）, Aspergillus fumigatus strain （F）, and Streptomyces sudanensis strain （S）, respectively. The degradation of polyethylene （PE） and polyethylene terephthalate （PET） by single and mixed bacteria was compared using the weight loss rate of microplastics as a constraint. The findings revealed that the weight loss rates of PE and PET under the combined conditions of the three strains of functional bacteria were 21.900% and 23.800% at 60 d, which was significantly better than that of single bacteria and the mixture of two strains. Based on the growth process of functional bacteria, the characteristics of key enzyme genes, and the changes of surface morphology and functional groups during the degradation of PE and PET, the mechanism of PE and PET being degraded after long-chain depolymerization, β oxidation cycle, and tricarboxylic acid cycle under the action of mixed functional bacteria was revealed. These findings provide a theoretical basis and technical support for the control of microplastic pollution in salinized soil.},
}
@article {pmid41413769,
year = {2025},
author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F},
title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04549-5},
pmid = {41413769},
issn = {1471-2180},
support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; },
}
@article {pmid41413663,
year = {2025},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}
@article {pmid41413233,
year = {2025},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {},
number = {},
pages = {},
pmid = {41413233},
issn = {1348-4214},
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}
@article {pmid41412926,
year = {2025},
author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A},
title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.016},
pmid = {41412926},
issn = {1878-4380},
abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.},
}
@article {pmid41412727,
year = {2025},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.<br><br>OBJECTIVE: Investigate the causal role of BAs produced by 7&#x3b1;DH+ gut bacteria in CRC.<br><br>DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7&#x3b1;DH+ bacteria&#x2009;or a genetically modified strain to demonstrate causality.<br><br>RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7&#x3b1;DH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7&#x3b1;DH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.<br><br>CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7&#x3b1;DH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}
@article {pmid41412669,
year = {2026},
author = {Li, W and Chen, J and Zhang, J and Peng, Z},
title = {Multi-omics insights into the formation mechanism of aging quality in white tea (Bai Mudan) during storage: Integrating sensory evaluation, volatilomics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117996},
doi = {10.1016/j.foodres.2025.117996},
pmid = {41412669},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Food Storage ; *Tea/chemistry/microbiology ; Volatile Organic Compounds/analysis ; Taste ; *Metagenomics ; Odorants/analysis ; Humans ; *Camellia sinensis/microbiology/chemistry ; Bacteria/genetics ; Multiomics ; },
abstract = {White tea (WT) develops unique aged quality during long-term storage, characterized by progressive changes in sensory properties and chemical composition. However, integrated insights into the sensory, metabolites, and microbial contribution underlying this process remain limited. This study systematically investigated the quality evolution of Bai Mudan tea (a typical WT) over 0 to 11 years of storage using an integrated multi-omics approach. Sensory analysis revealed a flavor transition from fresh (grassy, fruity) to aged (woody, stale) characteristics. Volatilomics identified 72 volatile compounds, with cedrol and isophorone as aged characteristic aroma compounds (rOAV ≥1, VIP ≥ 1, p ≤ 0.05). Metabolomics identified 1146 non-volatile metabolites, showing accumulation of fatty acyls and flavonoids, and a decrease in amino acids. Metagenomic sequencing analysis revealed that bacterial communities (mainly Sphingomonas, Pedobacter, Methylobacterium, and Chryseobacterium) dominated during the first 7 years of storage, followed by a potential shift toward a bacterial-fungal synergy pattern in later stages as the abundances of Monascus and Aspergillus increased. KEGG annotation highlighted the roles of carbohydrate metabolism and amino acid metabolism, and flavonoid biosynthesis was activated during storage. Multi-omics correlation networks demonstrated that fungi positively regulated volatile flavors, while bacteria may be involved in taste balance. Monascus, Sphingomonas, Sphingobium, and Novosphingobium were identified as core functional taxa that may contribute to WT quality formation during storage through aged flavor synthesis, flavonoid accumulation, and lipid degradation. In conclusion, this study provides a multi-dimensional scientific basis for a comprehensive understanding of the formation mechanism of aged quality in white tea during storage.},
}
@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}
@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation &amp; purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}
@article {pmid41412435,
year = {2025},
author = {Dolci, M and Frosio, F and Signorini, L and Soggiu, A and Meroni, G and Favi, E and Alavrez, EC and Ferrante, P and Delbue, S},
title = {Human polyomavirus 6 differentially infects healthy and tumor tissue in the colon: A case report.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105865},
doi = {10.1016/j.meegid.2025.105865},
pmid = {41412435},
issn = {1567-7257},
abstract = {INTRODUCTION: Human polyomavirus 6 (HPyV6) is part of the human skin virome. Like other HPyVs, it encodes proteins with oncogenic properties.<br><br>MATERIALS AND METHODS: A 73-year-old Italian female patient with stage II right-sided colon adenocarcinoma underwent hemicolectomy; she died one month later because of bacterial sepsis. Colon tumor (T), adjacent healthy (AH) tissue, and serum samples were collected. Total nucleic acids were subjected to next-generation sequencing, followed by metagenomics analysis. HPyV detection was confirmed by real-time PCR and Rolling Circle Amplification (RCA); HPyV6 transcripts and proteins were identified by means of PCR and Western blot/mass spectrometry, respectively.<br><br>RESULTS: Viral metagenomics analysis revealed the presence of several viral genomes, mainly belonging to unclassified viruses and phages, in both AH and T tissues. HPyV6 DNA was detected in the T tissue, representing 7&#x202f;% of the viral sequences, but not in the AH tissue. Subsequent molecular analysis confirmed the presence of the HPyV6 genomes (3.3x10[6]copies/ug) as episomes, infecting 19.8&#x202f;% of the tumor cells; LT-Ag and VP1 transcripts were expressed in the T tissue, and the LT-Ag protein was expressed twice as highly in the T tissue as in the AH tissue.<br><br>CONCLUSIONS: This is the first report of the differential presence and expression of the HPyV6 genome in colon tumors but not in the AH tissue. These results are indicative of ongoing active replication of the virus, which might play a triggering role in malignant transformation.},
}
@article {pmid41412398,
year = {2025},
author = {Zhang, H and Jing, X and Gong, Y and Zheng, P and Ren, Y and Chen, R and Wu, Y and Liu, S and Zhang, L and Xu, J and Xu, Y},
title = {Single-cell phenotyping and sequencing uncover metabolically active low-abundance yeasts in thermophilic fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133803},
doi = {10.1016/j.biortech.2025.133803},
pmid = {41412398},
issn = {1873-2976},
abstract = {Microbiota-driven fermentation is a global biomanufacturing process that often operates under extreme and fluctuating temperatures. To understand how such systems maintain productivity, this study investigated the Chinese fermentation starter high-temperature Daqu (HTD) as a model system. By combining metagenomics and Raman microspectroscopy, the analysis revealed a drastic decoupling between phylogenetic composition and metabolic activity, with only 10-32 % of yeast species detected by sequencing remaining metabolically active under heat stress. Raman-activated cell sorting and culture (RACS-Culture) recovered three yeasts that consistently maintained viability throughout HTD production: Pichia kudriavzevii, Wickerhamomyces anomalus, and Saccharomycopsis fibuligera. Mono-species and synthetic-community fermentation further revealed a sophisticated mechanism of temporal niche partitioning: in the moderate-temperature early and late stages, S. fibuligera and W. anomalus dominated substrate degradation and flavor precursor biosynthesis, respectively. However, as temperatures rose above 45 °C, both species exhibited low metabolic activity and survival rates. In contrast, only P. kudriavzevii sustained robust growth at this elevated temperature. Genomic analysis revealed a remarkable expansion of heat-resistance and cell-clustering-related genes of wos2 and FLO8 in P. kudriavzevii. These genetic characteristics underpin its enhanced viability, which enables the initially low-abundance species to thrive as a primary ethanol producer and ultimately establish numerical dominance. Thus, temporally overlaying single-cell metabolic vitality profiles onto the corresponding metagenomes can unravel novel functional species and reveal their ecological roles in a complex ecosystem.},
}
@article {pmid41412053,
year = {2025},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}
@article {pmid41412046,
year = {2025},
author = {Li, X and Zhang, Y and Zhao, C and Dang, X and Li, B and Hou, S and Gao, X and Hao, J and Lyu, Z and Wang, Y and Hao, L and Zhu, T},
title = {Breaking the cycle of resistance: Hyperthermophilic composting establishes a multi-layered defense against ARG dissemination.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140801},
doi = {10.1016/j.jhazmat.2025.140801},
pmid = {41412046},
issn = {1873-3336},
abstract = {The environmental dissemination of antibiotic residues and antibiotic resistance genes (ARGs) from livestock manure poses major risks to public health. Here, we established a hyperthermophilic composting (HC, >80℃) system alongside conventional composting (CK) to elucidate the mechanisms driving antibiotic and ARG removal. By integrating metagenomics, Quantitative PCR (qPCR), and machine learning, we systematically assessed antibiotic degradation, ARG/MGE dynamics, and microbial functional shifts. HC rapidly reached 87.3 ℃ within 24 h and maintained extreme thermophilic conditions, achieving higher TOC degradation (36.58 % vs. 22.59 % in CK), accelerated humification (HA/FA=2.19 by day 15), and efficient removal of oxytetracycline, enrofloxacin, and sulfamethoxazole (98.44 %, 92.34 %, and 99.63 %, respectively), thereby shortening the selective pressure window. Metagenomics identified 796 ARGs and 128 MGEs; key ARGs (macB, bcrA, tetA(58)) declined markedly in HC, with ARG and MGE abundances strongly correlated and virulence factor genes synchronously reduced. qPCR confirmed rapid ARG/MGE attenuation in HC without the rebound observed in CK. Partial least squares path modeling (GOF=0.858) showed MGEs were the primary driver of ARG dissemination (path coefficient=0.790), while temperature exerted indirect effects by reshaping thermophilic communities, enhancing metabolism, and suppressing antibiotics and MGEs. Random forest further highlighted MGEs (integrase, transposase, IS91/ISCR) and humification indices (HA/FA/HS) as key factors, with Bacillus and Truepera as major contributors under HC. Overall, HC established a multilayered "high temperature-community restructuring-functional metabolism-MGE suppression" barrier, enabling faster, more stable and safer resistance risk control than CK. This provides a scalable pathway for safe manure valorization and ARG mitigation under the One Health framework.},
}
@article {pmid41412032,
year = {2025},
author = {You, F and Yang, S and Ding, Y and Han, J and Xing, D and Jin, C and Zhao, Y and Gao, M and Guo, L},
title = {Comparative insights into denitrification performance and microbial adaptation of heterotrophic, autotrophic, and mixotrophic systems under florfenicol stress for recirculating mariculture wastewater treatment.},
journal = {Water research},
volume = {291},
number = {},
pages = {125172},
doi = {10.1016/j.watres.2025.125172},
pmid = {41412032},
issn = {1879-2448},
abstract = {Wastewater from marine recirculating aquaculture systems (RAS) poses significant treatment challenges due to its high nitrate concentrations and low carbon-to-nitrogen ratio. The additional presence of antibiotic residues such as florfenicol creates mixed pollution that further impairs denitrification and destabilizes microbial communities. This study systematically compared the multi-scale responses of heterotrophic (HDN), sulfur-autotrophic (SADN), and mixotrophic (MDN) denitrification under 4.0 mg L[-1] florfenicol stress in synthetic recirculating mariculture wastewater (salinity = 3.5 %). The MDN system achieved the highest denitrification rate (46.83 mg NOx[-]-N h[-1] g[-1] MLVSS) and maintained nitrate removal efficiency above 98 % with minimal fluctuations under florfenicol stress. Although the HDN system exhibited high NAR/NIR activities and electron transport system activity (ETSA), nitrite accumulation occurred due to functional imbalance. The SADN system, relying on sulfur oxidation, demonstrated limited metabolic flexibility and electron supply capacity under florfenicol stress, resulting in slower nitrate reduction. Metagenomic and KEGG pathway revealed significant differences in microbial community composition and functional potential among HDN, SADN and MDN denitrification systems: HDN was dominated by biofilm-forming Proteobacteria, with broad antibiotic resistance gene (ARG) enrichment and stronger mobile genetic element co-localization; SADN showed enrichment of Campylobacterota, consistent with sulfur oxidation-based pathways, and Mantel tests confirmed tighter ARG-environment coupling; MDN showed the highest microbial diversity with elevated Planctomycetota, functional enrichment in carbohydrate and energy metabolism, and stable quorum sensing-electron transfer coupling with functional redundancy. These findings provide new insights for designing robust treatment strategies for recirculating mariculture wastewater subject to compound pollution from nitrate and antibiotics.},
}
@article {pmid41411799,
year = {2025},
author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F},
title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119554},
doi = {10.1016/j.ecoenv.2025.119554},
pmid = {41411799},
issn = {1090-2414},
abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.},
}
@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.<br><br>RECENT FINDINGS: Evidence on gut microbial &#x3b1;-diversity and &#x3b2;-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}
@article {pmid41410786,
year = {2025},
author = {Senel, E and Ramos-Barbero, MD and Santos, F and Villamor, J and Mutlu, MB and Antón, J},
title = {Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.},
journal = {Archives of virology},
volume = {171},
number = {1},
pages = {28},
pmid = {41410786},
issn = {1432-8798},
support = {208F135//the Anadolu University Research Foundation No. 1208F135. ES. was an MSc student of the Erasmus program./ ; },
mesh = {*Lakes/virology/chemistry ; Salinity ; Turkey ; Salts/chemistry ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Biodiversity ; Metagenomics ; Genome, Viral ; },
abstract = {The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).},
}
@article {pmid41410736,
year = {2025},
author = {Nath, S},
title = {Advanced microbial engineering approaches for biodegradation of pharmaceutical pollutants.},
journal = {Biodegradation},
volume = {37},
number = {1},
pages = {15},
pmid = {41410736},
issn = {1572-9729},
mesh = {*Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Pharmaceutical Preparations/metabolism ; *Metabolic Engineering/methods ; *Bacteria/metabolism/genetics ; Bioreactors/microbiology ; },
abstract = {Pharmaceutical pollutants have emerged as pervasive environmental contaminants, entering ecosystems via wastewater effluents, agricultural runoff and improper disposal. These pollutants typically belong to classes such as antiepileptics, antibiotics, analgesics, non-steroidal anti-inflammatory drugs, hormones and antiseptics. Their recalcitrance arises from their stable chemical structures, which resist degradation and pose significant challenges for conventional wastewater treatment processes, leading to their persistence in the environment and potentially harmful effects on ecosystems and human health. This study investigates microbial engineering strategies for the efficient degradation of pharmaceutical pollutants. Recent advancements in CRISPR systems, ALE, metabolic engineering, bioaugmentation and bioreactor designs have significantly improved pollutant breakdown. Additionally, novel approaches to address emerging contaminants and the application of advanced biotechnologies like synthetic biology and metagenomics are crucial for developing more effective and sustainable bioremediation strategies. These insights offer a roadmap for developing more effective and sustainable solutions for the bioremediation of pharmaceutical pollutants.},
}
@article {pmid41409983,
year = {2025},
author = {Hira, J and Mahbub, NB and Ali, J and Ahmad, R},
title = {Low-cost in-house re-formulated brain heart infusion medium for effective planktonic growth and early detection of bloodstream bacterial pathogens.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680006},
pmid = {41409983},
issn = {1664-302X},
abstract = {Sepsis, a clinically defined life-threatening condition, is a global contributor to high morbidity and mortality rates in humans. It is caused by systemic bloodstream bacterial infections, primarily involving aerobic pathogens such as Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. Rapid and accurate identification of these pathogens is a high-demand task, as prolonged diagnosis may increase the mortality rate among sepsis patients. Globally, commercial blood culture systems like the BD BACTEC™ FX blood culture system, which utilizes BD BACTEC™ PLUS Aerobic/F culture bottles (used in this study), are commonly used to detect aerobic bloodstream infections. However, due to high costs (∼$10.00-$15.00/bottle), limited availability of culture media (especially in low- and middle-income countries, and war zones), and a lack of customization for antibiotic susceptibility assay and epidemiology research, there is a need for secondary alternatives to facilitate the growth and identification of bloodborne pathogens. Therefore, we developed a low-cost (∼$4-$5/bottle) in-house culture medium with a newly improved formulation of Brain Heart Infusion media that enhances bacterial growth from spiked human blood tested on a panel of bacteria (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus faecalis). The growth dynamics of these microbes in in-house formulated BHI-Blood+ culture media coincide with those in BACTEC™ Plus Aerobic/F culture vials, which primarily suggests the compatibility of bloodborne pathogens with this media and can be flagged positive <8 h based on cellular growth rate. Additionally, conventional qPCR-based early detection (<24 h) and validation with the Oxford Nanopore MinION NGS platform highlight the value of this in-house culture media as an alternative to commercial culture media in terms of low-cost availability.},
}
@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.<br><br>METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.<br><br>RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p <&#xa0;0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p&#xa0;<&#xa0;0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p&#xa0;<&#xa0;0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.<br><br>CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}
@article {pmid41409544,
year = {2025},
author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT},
title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719025},
pmid = {41409544},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology/parasitology ; },
abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.<br><br>METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.<br><br>RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).<br><br>DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.},
}
@article {pmid41409502,
year = {2025},
author = {Pico-Tomàs, A and Sanchís, A and Mejías-Molina, C and Comas-Cufí, M and Balcázar, JL and Bofill-Mas, S and Torrell, H and Canela, N and Borrego, CM and Corominas, L},
title = {Tracking Age-Linked Antibiotic Resistance Patterns through Building-Level Wastewater Analysis.},
journal = {ACS ES&amp;T water},
volume = {5},
number = {12},
pages = {7141-7151},
pmid = {41409502},
issn = {2690-0637},
abstract = {Antimicrobial resistance (AMR) is a global health challenge, and monitoring different demographic populations can improve our understanding of its spread and prevalence in urban settlements. This study applies building-level wastewater-based epidemiology (WBE) to analyze the resistome and mobilome of age-segregated populations from an elementary school (School), a university residence (UnivRes), and an elderly care facility (ElderlyRes) all located in Girona (Catalonia, Spain). Metagenomic analyses were subsequently conducted to investigate differences in bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). The results revealed age-linked variations in the relative abundance and diversity of ARGs. The wastewater collected at the School exhibited the highest abundance of ARGs, while the ElderlyRes showed the highest diversity. Furthermore, sequences affiliated with bacterial pathogens were more prevalent in samples from both the School and the ElderlyRes, emphasizing potential public health implications. Among the 12 bacterial genera most strongly correlated with ARGs (Pearson R > 0.7), 11 were identified as members of the gut microbiota, underscoring their predominant role as reservoirs of resistance compared to bacteria of environmental origin. By integrating localized wastewater sampling with metagenomics, our study uncovers demographic-specific resistome patterns, delivering actionable evidence to strengthen AMR surveillance and intervention strategies in urban populations.},
}
@article {pmid41409175,
year = {2025},
author = {Ng, DZW and Low, A and Khairul Sani, KRB and Liu, L and Zhang, Z and Koh, XQ and Zhu, M and Mitra, K and Muthiah, M and Dan, YY and Lee, JWJ and Chan, ECY},
title = {Dysbiosis-Driven Reprogramming of Secondary Bile Acid Metabolism in Metabolic Dysfunction-Associated Steatotic Liver Disease: Insights from an Ex Vivo Human Fecal Microbiota Model.},
journal = {ACS pharmacology &amp; translational science},
volume = {8},
number = {12},
pages = {4335-4344},
pmid = {41409175},
issn = {2575-9108},
abstract = {Gut microbial dysbiosis-induced perturbations in bile acid (BA) metabolism are implicated in metabolic dysfunction-associated steatotic liver disease (MASLD), yet evidence remains largely associative. Using an optimized ex vivo fecal microbiota model, we modeled the metabolism kinetics of conjugated- and primary-BA between MASLD and healthy donors. Enzymes for known BA metabolic reactions were inferred using functional metagenomics. MASLD cultures exhibited impaired deconjugation capacity but preserved downstream primary-BA clearance and demonstrated a substrate-independent shift that favored oxidative metabolism over 7α-dehydroxylation. This was marked by increased formation clearance of 7-keto-deoxycholic acid (175%) and 3-oxo-cholic acid (51.7%) from cholic acid (CA) and 7-keto-lithocholic acid (77.9%) from chenodeoxycholic acid (CDCA). C7-oxidized BA constituted the major proportion of total BA clearance (CA = 56.0%, CDCA = 72.3%) in MASLD cultures. Enrichment of C3- and C7-hydroxysteroid dehydrogenases in MASLD compared to control corroborated the differential secondary BA profiles. Together, microbes catalyzing C7-oxidation warrants further investigation as potential pharmacological targets of MASLD.},
}
@article {pmid41408693,
year = {2025},
author = {Esener, N},
title = {Omics technologies in mastitis: text mining and topic modelling analysis of global research trends.},
journal = {The Journal of dairy research},
volume = {},
number = {},
pages = {1-11},
doi = {10.1017/S0022029925101830},
pmid = {41408693},
issn = {1469-7629},
abstract = {Mastitis, an inflammation of the mammary gland, is a disease of significant clinical and economic importance. In recent years, advances in omics technologies have provided powerful tools to unravel the complex biological mechanisms underlying mastitis. These approaches encompass diverse fields such as genomics, proteomics, transcriptomics, metagenomics, metabolomics, epigenomics, lipidomics, glycomics, pharmacogenomics, foodomics, interactomics and exposomics. However, despite the rapid growth of omics research, the thematic structure of this literature has not been systematically examined. In this study, latent dirichlet allocation (LDA) was employed to perform topic modelling on publications related to omics and mastitis retrieved from Scopus and Web of Science. The LDA analysis revealed ten distinct topics, labelled according to the most frequent terms within each cluster: 'proteomics', 'pathogen genomics', 'differential expression', 'metabolism', 'genetic selection', 'disease economy', 'molecular diagnostics', 'microbiome', 'antimicrobial resistance' and 'genetic variation.' Among these, the topics of 'genomics', 'differential expression' and 'antimicrobial resistance' accounted for the highest number of publications, while 'metabolism' emerged more recently. All topics exhibited an increasing trend in publication volume over time, likely driven by the declining costs and greater accessibility of high-throughput omics technologies. This study provides a comprehensive thematic overview of omics research on mastitis, identifies key areas of emphasis and emerging directions, and highlights knowledge gaps that may inform future investigations and the development of targeted strategies for disease control and prevention.},
}
@article {pmid41408356,
year = {2025},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites, and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.<br><br>METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.<br><br>RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae, and Parabacteroides distasonis were noticed. Conversely, P. plebeius, B. hansenii, and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and glycine, serine, and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.<br><br>CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}
@article {pmid41408316,
year = {2025},
author = {Wang, L and Remue, L and Adriaens, N and Soto, A and Verwimp, S and van Bree, J and Trappeniers, K and Delang, L},
title = {Identification of a culturable fungal species and endosymbiotic bacteria in saliva of Aedes aegypti and Culex pipiens and their impact on arbovirus infection in vitro.},
journal = {Parasites &amp; vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07158-3},
pmid = {41408316},
issn = {1756-3305},
support = {C22/18/007//KU Leuven/ ; C14/20/108//KU Leuven/ ; STG/19/008//KU Leuven/ ; },
abstract = {BACKGROUND: Mosquito saliva plays a key role in arbovirus transmission and pathogenesis. It was shown that saliva contains several molecules that are essential for blood feeding. Recently, bacteria were also reported to be present in the saliva of Aedes albopictus and Anopheles mosquitoes. Nevertheless, information on the bacterial communities in Aedes and Culex saliva is still scarce.<br><br>METHODS: This study isolated and identified culturable fungal and bacterial colonies from saliva harvested from Aedes aegypti (laboratory strain) and Culex pipiens (field-collected) mosquitoes. 16S metagenomic sequencing was performed to identify bacterial communities in saliva and mosquito organs. Furthermore, it was assessed how these microbial communities were affected upon blood feeding and upon oral treatment with antibiotics and an antifungal drug.<br><br>RESULTS: The fungal species Penicillium crustosum was identified in mosquito saliva. Culturable bacteria detected in mosquito saliva included Serratia marcescens, Serratia nematodiphila, Enterobacter spp., and Klebsiella spp., which were previously identified as mosquito or insect endosymbionts in the midgut or other organs. Analysis with 16S metagenomics showed that bacterial communities in saliva were more diverse than those in the midgut. Blood feeding did not affect the fungal or bacterial load in mosquito saliva. Oral treatment of adult mosquitoes with antibiotics or an antifungal drug resulted in a significant reduction of bacteria or fungi present in the mosquito saliva. Notably, co-incubation of the mosquito-borne Semliki Forest virus with saliva from antibiotic- or antifungal-treated mosquitoes triggered a decrease in viral infection in human skin fibroblasts compared with nontreated saliva.<br><br>CONCLUSIONS: These findings indicate that bacteria and fungi can be present in mosquito saliva and provide a foundation for further exploration of the impact of salivary fungi and bacteria on both vector competence and arbovirus infection in the mammalian host.},
}
@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04551-1},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.<br><br>METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16&#xa0;S rRNA gene sequencing or metagenomics.<br><br>RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.<br><br>CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}
@article {pmid41408023,
year = {2025},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008&#xff0c;C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.<br><br>METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.<br><br>RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.<br><br>CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points &#x2022;&#xa0;Gut microbial composition is significantly altered in SLE patients compared to healthy controls. &#x2022;&#xa0;Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. &#x2022;&#xa0;Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. &#x2022;&#xa0;The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}
@article {pmid41407999,
year = {2025},
author = {Li, Z and Yang, S and Li, C and Zhang, L and Xi, N and Li, D and Li, L},
title = {Metagenomic next-generation sequencing for the diagnosis of suspected spinal infections from biopsy samples: a novel biopsy toolkit design and real-life diagnostic value.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41407999},
issn = {1432-0932},
}
@article {pmid41407459,
year = {2025},
author = {Lin, QX and Wei, JJ and Lian, TT and Lin, BQ and Ren, JH and Zheng, XY and Wu, XQ and Li, J and Chen, H and Xie, SJ and Yang, T},
title = {[Diagnostic value of intestinal tissue metagenomic next-generation sequencing in severe diarrhea following haploidentical hematopoietic stem cell transplantation].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {11},
pages = {1020-1025},
doi = {10.3760/cma.j.cn121090-20241206-00540},
pmid = {41407459},
issn = {0253-2727},
support = {YJRC4415//Hospital talent scientific research project/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Adult ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Child, Preschool ; Adolescent ; *Diarrhea/diagnosis/etiology/microbiology ; Child ; *Metagenomics ; Young Adult ; Transplantation, Haploidentical/adverse effects ; },
abstract = {Objective: To evaluate the diagnostic value of intestinal tissue metagenomic next-generation sequencing (mNGS) in severe diarrhea following haploidentical allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: Sixteen patients who developed severe diarrhea or hematochezia after haploidentical allo-HSCT at the First Affiliated Hospital of Fujian Medical University (June 2023-August 2024) were enrolled. All underwent gastrointestinal endoscopy and mNGS for microbial detection. Clinical, endoscopic, pathological, and microbiological data were analyzed to evaluate the diagnostic value of mNGS and treatment outcomes following targeted therapy. Results: The study included 16 patients (12 males, 4 females; median age 32.5 years, range 3-60 years). Diarrhea occurred a median of 3.93 months post-transplant (range 1.63-10.40 months). Stool cultures were negative except for one case with Candida. One patient tested positive for Clostridium difficile antigen. Endoscopy revealed mucosal congestion, edema, erosion, and bleeding, with focal inflammation on pathology. mNGS detected pathogens in 87.5% (14/16) of cases, including mixed infections in 78.5% (11/14). Common pathogens were Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, Rhizopus microsporus, EBV, and CMV. Targeted treatment adjustments led to symptom improvement in 87.5% of patients. Conclusion: Allo-HSCT patients are prone to infectious diarrhea due to immunosuppression. Molecular analysis of endoscopic biopsy tissues using mNGS can accurately identify pathogens, guide targeted therapy, and improve clinical outcomes.},
}
@article {pmid41407286,
year = {2025},
author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P},
title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c14335},
pmid = {41407286},
issn = {1520-5126},
abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.},
}
@article {pmid41407095,
year = {2025},
author = {Chen, M and Cai, Y and Shi, Q and Xu, A and Tang, T and Qian, J and Yu, S and Zhu, H and Xu, J and Li, J and Shen, B},
title = {Antimicrobial management and infection outcomes of Elizabethkingia spp. co-detection in lower respiratory tract: a real-world mNGS-based observational study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108316},
doi = {10.1016/j.ijid.2025.108316},
pmid = {41407095},
issn = {1878-3511},
abstract = {OBJECTIVES: Elizabethkingia spp. infections pose a major threat to human health with high mortality. This study aimed to further understand its detection status, co-detection patterns, pathogenicity, and antimicrobial resistance in lower respiratory tract infections (LRTI) through metagenomic high throughput sequencing (mNGS)-based real-world research.<br><br>DESIGN AND METHODS: We retrospectively analyzed 105 LRTI patients positive for Elizabethkingia spp. by mNGS from July 2021 to February 2025. Pathogen profiles, antimicrobial management, and outcomes were reviewed via electronic medical records.<br><br>RESULTS: mNGS detection rates for Elizabethkingia spp. in respiratory samples were 21.5% in General Intensive Care Unit (GICU) and 11.1% in Emergency Intensive Care Unit (EICU), more sensitive than culture. Polymicrobial co-detection was ubiquitous (99%), indicating a diverse polymicrobial community. Clinical isolates exhibited variable susceptibility (74%-100%) to trimethoprim-sulfamethoxazole, ciprofloxacin, levofloxacin, doxycycline, minocycline, rifampicin, and azithromycin. Patients receiving targeted antimicrobial therapy based on mNGS indicators (Stringent Map Read Number (SMRN) rank &#x2264;2, normalized SMRN (nSMRN) &#x2265;1000, or SMRN percentage &#x2265;25%) had significantly higher effective treatment rates.<br><br>CONCLUSIONS: Elizabethkingia spp. detection rates in ICU respiratory samples are high, frequently complicated by polymicrobial co-detection. Lack of targeted therapy is a key factor in treatment failure. mNGS-derived indicators and local susceptibility databases are essential for guiding effective intervention.},
}
@article {pmid41407051,
year = {2025},
author = {Yuan, Z and Zeng, W and Zhan, M and Peng, Y},
title = {Static magnetic field enhances respiratory dissimilatory nitrate reduction to ammonium over denitrification in sulfide-based autotrophic systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133796},
doi = {10.1016/j.biortech.2025.133796},
pmid = {41407051},
issn = {1873-2976},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) represents a sustainable strategy for nitrogen resource recovery from wastewater, yet selectively enhancing DNRA over denitrification in sulfide-based autotrophic systems remains challenging. This study investigates the impact of static magnetic field (SMF, 0-100mT) on nitrate reduction pathways in sulfide-rich wastewater. SMF elevated DNRA efficiency to 41.8 % with an influent sulfide concentration of 200 mgS/L (S/N ratio of 3:1) under 30 mT, supported by nrfA upregulation (7.6 × 10[10] vs. 4.0 × 10[7] copies/g SS in control). [15]N isotope labeling and enhanced direct extracellular electron transfer via cytochrome c and conductive pili confirmed that SMF preferentially drove nitrate flux toward DNRA. Metagenomics revealed that SMF enriched DNRA taxa (Aeromonas, Shewanella) and enhanced their synergy with Thiobacillus, improving metabolic flexibility. This work unveils microbial competition mechanisms between denitrification and DNRA in sulfide-based systems and proposes an innovative SMF-assisted ammonium recovery approach, advancing the understanding of sulfide-based nitrogen removal technologies.},
}
@article {pmid41406967,
year = {2025},
author = {Liu, J and Glukhov, E and De Clerck, O and Gerwick, WH and Donia, MS},
title = {Environmentally controlled production of pagoamide A in marine macroalgae by an intracellular bacterial symbiont.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.11.023},
pmid = {41406967},
issn = {1879-0445},
abstract = {Marine algae are a rich source of diverse molecules, most of which are thought to be produced by the alga itself. We recently reported the discovery of pagoamide A from a cultured marine macroalga collected from American Samoa. Here, we found that the production of pagoamide A is conditional upon environmental temperature. Using comparative metagenomic, metatranscriptomic, and metabolomic analyses of algal cultures, we identified a nonribosomal peptide synthetase biosynthetic gene cluster (NRPS BGC) in the algal microbiome that varies in abundance between producing and non-producing conditions and whose architecture and biosynthetic logic match pagoamide A (named pag). pag belongs to a bacterium that we named "Candidatus Bryopsidiphilus pagoamidifaciens BP1," a new genus in the family Amoebophilaceae and a relative of amoeba, arthropod, and nematode endosymbionts. Ca. B. pagoamidifaciens lives intracellularly in its Bryopsis sp. algal host, harbors a reduced genome (1.7 Mbp), has lost most genes essential for free living, and is enriched in genes containing eukaryotic domains. By quantitatively monitoring longitudinal algal cultures under varying conditions for 9 weeks, we found that the abundance of both Ca. B. pagoamidifaciens and pagoamide A undergoes dramatic fluctuations in response to temperature changes. Finally, we discovered three additional strains of Ca. B. pagoamidifaciens that vary in their NRPS BGCs and eukaryotic domain-containing genes from algal samples of diverse geographical origins. Our findings suggest that symbiont-derived production of algal molecules is more common than previously anticipated and provide a unique case of environmental control of both symbiont and chemical levels in marine algae.},
}
@article {pmid41406735,
year = {2025},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, M&#xc1; and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}
@article {pmid41406531,
year = {2025},
author = {Zhao, Y and Mu, H and Hu, BX and Zhi, C and Wang, H and Huang, L and Huang, F and Han, K},
title = {Root exudates drive metabolic remodeling of microbial and resistance to facilitate sulfonamide biodegradation in karst soil-carbonate rock interface.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140829},
doi = {10.1016/j.jhazmat.2025.140829},
pmid = {41406531},
issn = {1873-3336},
abstract = {Sulfonamide antibiotics have become pervasive contaminants in karst systems, where low carbon and rapid infiltration hinder natural attenuation, leading to persistent groundwater pollution and elevated antibiotic resistance risks. Although root exudates shape soil microbial metabolism and resistance, their role at the karst soil-carbonate rock interface remains unclear. This study demonstrates that artificial root exudates (ARE) significantly boost sulfamethazine (SMZ) removal at the soil-carbonate rock interface, achieving up to 92.0 % (35.1 % higher than control). Analyses of 16S rRNA gene sequences and metagenomes reveal that ARE remodels microbial communities by enriching potential degraders and upregulating genes for carbohydrate metabolism and xenobiotic degradation. Co-occurrence networks become more modular and recruit rare taxa as connectors, enhancing resilience through cross-module connectivity. ARE also reduces antibiotic resistance risks by suppressing sul1/sul2 hosts and key integrases. Nine metabolites were identified based on RRLC-MS/MS analysis, and four transformation pathways were proposed, confirming active biodegradation. Scanning electron microscopy further shows that ARE induces mineral dissolution and organic aggregation, creating porous microhabitats that facilitate SMZ degradation. This study offers novel insights into the coupled biotic-abiotic mechanisms of root exudates-mediated sulfonamide degradation at the low-carbon karst interface and provides a framework for plant-assisted antibiotic remediation in karst systems.},
}
@article {pmid41406522,
year = {2025},
author = {Zhang, B and Hu, X and Han, L and Guo, Z and Liu, Y and Li, H and He, Y and Liu, T and Pan, Q and Mu, Y and Qu, J and Yu, H and Shen, A and Zhao, W and Ma, T and Tan, W and Zhang, Y},
title = {Unveiling the black box: Multi-omics reveal how biochar supercharges synthetic biofilms for superior bioremediation.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140816},
doi = {10.1016/j.jhazmat.2025.140816},
pmid = {41406522},
issn = {1873-3336},
abstract = {Biofilms formed by flora can be sustainably applied in a variety of fields such as bioremediation, wastewater treatment, corrosion prevention, and agricultural production. However, highly practical biofilms often result in low microbial activity, due to undesired impacts including environmental stress and microbial competition. Leveraging the advantages of carrier materials, we aimed to enhance the degradation efficiency and resilience of biofilms by integrating biochar. In this study, the biochar with excellent economic benefits and adsorption capacity was prepared and selected as the carrier material. The growth characteristics, pollutant removal performance, and nutrient cycling within biochar-based biofilms were systematically investigated. The result validated the pollutant remediation efficiency of biofilms increased by 14∼18 % after adding biochar, and found a positive nutrient cycling existing within the biochar-based biofilms. Subsequently, the enhanced remediation mechanisms of biochar-based biofilms at the molecular level were explored through metagenomic and metabolomic analyses. Our results indicate superior strengths of biochar-based biofilms in both metabolic activity and beneficial genes compared to monocultured biofilms. This study aims to improve the stability of biofilms formed by functional flora and reveal their potential in bioremediation for contaminants.},
}
@article {pmid41406519,
year = {2025},
author = {Lin, Z and Yan, Z and Kong, W and Zhou, Y and Xu, Y and Xie, J and Gu, W and Gong, B and Li, Y and Zhang, C},
title = {Unveiling the simultaneous organophosphate esters degradation mechanisms in biological wastewater nitrogen removal systems under varying phosphorus source conditions: Microbial insights and ecological interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140835},
doi = {10.1016/j.jhazmat.2025.140835},
pmid = {41406519},
issn = {1873-3336},
abstract = {The discharge of organophosphate esters (OPEs) in wastewater increasingly threatens aquatic ecosystems. Although biological nitrogen removal (BNR) system shows potential OPEs removal and the performance might be influenced by phosphorus sources, the underlying mechanisms remained poorly understood. This study investigated the synchronous OPEs and nitrogen removal under varying phosphorus source conditions, revealing the microbial insights and ecological collaboration that facilitated OPEs degradation in BNR systems. Results demonstrated that the acclimated BNR systems achieved almost complete degradation of 10 mg/L tri-n-butyl phosphate (TnBP) and tris(2-chloroethyl) phosphate (TCEP). OPEs degradation pathways mainly involved hydrolysis, hydroxylation, and dehydrogenation, while phosphorus limitation could enhance the enzymatic activities of phosphotriesterase (PTE) and alkaline phosphatase (ALP). 16S rRNA sequencing and metagenomic analysis revealed that Rhodococcus, Nitrospira, and Phaeodactylibacter were the enriched OPEs degraders, which harbored pivotal functional genes including php, phoD, glpQ, and cpdA. Moreover, molecular ecological networks analysis highlighted synergistic interactions among nitrifying bacteria, denitrifying bacteria, and OPEs degrader, suggesting the collaboration among consortia facilitated complete OPEs degradation. The microbial OPEs degrading functions and ecological interactions in BNR systems were further stimulated by phosphorus-limited condition. This study provides novel insights into the microbial mechanisms of OPEs degradation and offers a promising strategy for upgrading wastewater treatment plants to cope with emerging contaminants.},
}
@article {pmid41406442,
year = {2025},
author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B},
title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0056},
pmid = {41406442},
issn = {1480-3275},
abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4°C) and room-temperature (25°C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25°C while Bacillota increased compared to 4°C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.},
}
@article {pmid41405224,
year = {2025},
author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA},
title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0047425},
doi = {10.1128/spectrum.00474-25},
pmid = {41405224},
issn = {2165-0497},
abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.},
}
@article {pmid41404904,
year = {2025},
author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM},
title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0203625},
doi = {10.1128/spectrum.02036-25},
pmid = {41404904},
issn = {2165-0497},
abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.},
}
@article {pmid41404801,
year = {2025},
author = {Stonkus, J and Rutkienė, R and Meškienė, R and Jasiūnienė, M and Aučynaitė, A and Kalinienė, L and Lazutka, J and Balčiūnas, D and Vilkaitis, G and Meškys, R},
title = {A new role for PHYHD1 and related dioxygenases: demethylation of 2'-O-methylated nucleosides.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1379},
pmid = {41404801},
issn = {1362-4962},
support = {S-MIP-24-50//Research Council of Lithuania/ ; },
mesh = {Zebrafish/genetics/metabolism ; Animals ; *Nucleosides/metabolism ; *Dioxygenases/metabolism/genetics ; Demethylation ; Humans ; Methylation ; RNA/metabolism ; Ketoglutaric Acids/metabolism ; },
abstract = {Nucleoside 2'-O-methylation is a widespread RNA modification found across diverse RNA types in all domains of life. Although considerable progress has been made in mapping 2'-O-methylation sites and elucidating their biological roles, the enzymatic pathways responsible for the catabolism of 2'-O-methylated nucleosides remain largely unexplored. Here, we report a previously unidentified 2'-O-methylated nucleoside demethylation reaction catalyzed by a metagenome-derived bacterial dioxygenase named FJS. We further show that FJS-related enzymes, including human phytanoyl-CoA dioxygenase domain-containing protein 1 (PHYHD1), catalyze the 2-oxoglutarate-dependent demethylation of a broad range of ribose-methylated nucleosides, but do not act on modified nucleotides or 3'-terminal 2'-O-methylated RNA substrates. To determine whether the loss of PHYHD1 function affects 2'-O-methylation levels of RNA-incorporated or free nucleosides, we generated a phyhd1 knockout zebrafish line. While RNA modification levels remained unchanged, the amount of free 2'-O-methylated nucleosides was significantly elevated in both phyhd1 knockout embryos and adult zebrafish. These findings indicate that PHYHD1 does not directly demethylate RNA but instead functions in the turnover of free 2'-O-methylated nucleosides. Together, our study identifies a previously unrecognized metabolic pathway for 2'-O-methylated nucleosides and defines PHYHD1 as the key dioxygenase involved in their demethylation, providing new insights into the catabolism of modified nucleosides.},
}
@article {pmid41404617,
year = {2025},
author = {Coleman, I and Mametyarova, N and Zaznaev, A and Cai, P and Yu, L and Meydan, Y and Litman, A and Sharma, A and He, L and Simkhovich, A and Seeram, D and Park, H and Nobel, YR and Kav, AB and Pe'er, I and Uhlemann, AC and Korem, T},
title = {Comparative metagenomics using pan-metagenomic graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.24.690211},
pmid = {41404617},
issn = {2692-8205},
abstract = {Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.},
}
@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.<br><br>METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.<br><br>RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.<br><br>CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}
@article {pmid41404316,
year = {2025},
author = {, and Papić, B and Fernández, PS and Garcia-Gutierrez, E},
title = {Training in metagenomics-integrated risk assessment for food-borne pathogens in the Slovenian and Spanish meat chain (METAMEAT).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {Suppl 1},
pages = {e231115},
pmid = {41404316},
issn = {1831-4732},
abstract = {Next-generation sequencing (NGS) has become an essential tool for antimicrobial resistance (AMR) surveillance, enabling comprehensive detection of AMR determinants in both bacterial isolates and complex microbial communities. Metagenomic sequencing enables culture-independent profiling of antimicrobial resistance genes (ARGs) in different environments, while whole-genome sequencing (WGS) is widely used in AMR surveillance laboratories to predict phenotypic resistance in major food-borne pathogens. AMR risk assessment usually considers factors such as the pathogenicity of the ARG-carrying bacterial host, the abundance of ARGs and their mobility potential inferred from association with plasmids or other mobile genetic elements that facilitate horizontal gene transfer. Clinical relevance of antimicrobials and the severity of clinical outcomes can further be implemented in AMR risk assessment. Exposure assessment contextualises hazards within real-world scenarios by estimating consumer exposure to AMR bacteria or their ARGs through food or other routes. Despite challenges in fully quantitative assessments, the integration of NGS-based surveillance with risk modelling represents a critical step towards proactive AMR risk management. In this study, broiler samples from different stages of a Slovenian and a Spanish slaughterhouse were analysed using conventional microbiology, shotgun metagenomic sequencing and WGS of isolates of selected pathogenic species. A modular, semi-quantitative risk assessment model was developed that combines (meta)genomic data with key risk factors and, where available, exposure assessment. This approach prioritises AMR risks in broiler meat processing and supports evidence-based decision-making in the areas of food safety and public health.},
}
@article {pmid41404301,
year = {2025},
author = {Bucka-Kolendo, J and Fernández, PS and Garcia-Gutierrez, E},
title = {Training in metataxonomics-integrated risk assessment for foodborne pathogens in the Polish and Spanish dairy chain (DAIRYPOL).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {Suppl 1},
pages = {e231113},
pmid = {41404301},
issn = {1831-4732},
abstract = {Food safety is a key concern in the European Union, with the harmonisation of risk assessment methodologies being a strategic priority. The EU-FORA programme, coordinated by EFSA, promotes standardised approaches to microbial risk assessment across Europe. Metagenomic sequencing has advanced the understanding of microbial ecosystems in food production, with Illumina (short-reads) and Oxford Nanopore Technologies (ONT) (long-reads) playing significant roles in detecting pathogens and characterising microbial communities. These technologies differ in accuracy, read length and resolution, potentially influencing risk profiles when used in quantitative microbiological risk assessment (QMRA). This fellowship, conducted at UPCT in Spain and IBPRS-PIB in Poland, compares the two platforms in assessing microbial populations in Polish and Spanish dairy chains. It explores how sequencing strategy affects hazard identification and QMRA outcomes, while also demonstrating how metagenomic data can enhance predictive modelling and support practical improvements in food safety management.},
}
@article {pmid41403886,
year = {2025},
author = {Tarracchini, C and Bottacini, F and Mancabelli, L and Lugli, GA and Turroni, F and van Sinderen, D and Ventura, M and Milani, C},
title = {Approaches to dissect the vitamin biosynthetic network of the gut microbiota.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {37},
pmid = {41403886},
issn = {2771-5965},
abstract = {B-group vitamins and vitamin K are essential micronutrients required for numerous cellular processes in both microbial and human physiology. While traditionally considered to originate predominantly from dietary sources, the biosynthetic capacity of the human gut microbiota has recently been recognized as a valuable, though historically underappreciated, endogenous source of these vitamins. In particular, the microbial contribution to the host vitamin pool is increasingly acknowledged as a functionally relevant aspect of vitamin homeostasis, especially in the colon, where microbiota-derived vitamins may be absorbed via specific transport mechanisms. This review provides a comprehensive overview of our current understanding of the biosynthesis of B-group vitamins and vitamin K by human gut-associated bacteria, with particular emphasis on key methodologies employed to assess if, how and to what extent members of the gut microbiota supply their host with such micronutrients. Through an integrated overview of available evidence, we highlight both the progress made and the outstanding challenges in elucidating the microbial contribution to the host vitamin metabolism.},
}
@article {pmid41403881,
year = {2025},
author = {Sun, Y and Huang, Y and Li, R and Zhang, J and Fan, X and Su, X},
title = {Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {43},
pmid = {41403881},
issn = {2771-5965},
abstract = {Background: The human gut microbiome is closely linked to disease states, offering substantial potential for novel disease detection tools based on machine learning (ML). However, variations in feature types, data preprocessing strategies, feature selection strategies, and classification algorithms can all influence the model's predictive performance and robustness. Methods: To develop an optimized and systematically evaluated workflow, we conducted a comprehensive evaluation of ML methods for classifying colorectal cancer and adenoma using 4,217 fecal samples from diverse global regions. The area under the receiver operating characteristic curve was used to quantify model performance. We benchmarked 6,468 unique analytical pipelines, defined by distinct tools, parameters, and algorithms, utilizing a dual validation strategy that included both cross-validation and leave-one-dataset-out validation. Results: Our findings revealed that shotgun metagenomic (WGS) data generally outperformed 16S ribosomal RNA gene (16S) sequencing data, with features at the species-level genome bin, species, and genus levels demonstrating the greatest discriminatory power. For 16S data, Amplicon Sequence Variant-based features yielded the best disease classification performance. Furthermore, the application of specific feature selection tools, such as the Wilcoxon rank-sum test method, combined with appropriate data normalization, also optimized model performance. Finally, in the algorithm selection phase, we identified ensemble learning models (eXtreme Gradient Boosting and Random Forest) as the best-performing classifiers. Conclusion: Based on the comprehensive evaluation results, we developed an optimized Microbiome-based Detection Framework (MiDx) and validated its robust generalizability on an independent dataset, offering a systematic and practical framework for future 16S and WGS-based intestinal disease detection.},
}
@article {pmid41403880,
year = {2025},
author = {Gargari, G and Meroño, T and Peron, G and Del Bo', C and Marino, M and Cherubini, A and Andres-Lacueva, C and Kroon, PA and Riso, P and Guglielmetti, S},
title = {Effect of a polyphenol-rich dietary pattern on subjects aged ≥ 60 years with higher levels of inflammatory markers: insights into microbiome and metabolome.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {38},
pmid = {41403880},
issn = {2771-5965},
abstract = {Background: Aging may be associated with low-grade chronic inflammation ("inflammaging") and gut microbiome alterations. Dietary polyphenols have been proposed as modulators of these processes. This study aimed to explore the effects of a polyphenol-rich diet (PR-diet) on inflammatory markers, gut microbiota, and metabolomic profiles in subjects aged ≥ 60 years stratified by baseline inflammation levels. Methods: In this post-hoc analysis of the MaPLE (Microbiome mAnipulation through Polyphenols for managing Leakiness in the Elderly) randomized crossover trial, 50 subjects aged ≥ 60 years were categorized into two subgroups: high inflammation (cH) and low inflammation (cL). Participants received a PR-diet or a control diet for 8 weeks, with a washout period in between. Fecal, blood, and urine samples were analyzed using shallow shotgun metagenomics and untargeted metabolomics. Results: The PR-diet was associated with a significant reduction in key inflammatory markers [e.g., interleukin-6 (IL-6), C-reactive protein] in the cH group. Distinct microbial shifts were observed, including an increase in Blautia and Dorea and a modest improvement in microbial diversity in cH subjects. Metabolomic analysis revealed group-specific changes, notably in polyphenol-derived metabolites. Conclusion: These findings suggest that PR-diets may beneficially modulate inflammation and the gut microbial ecosystem in subjects aged ≥ 60 years with elevated baseline inflammation. Stratification by inflammatory status may improve the targeting and personalization of dietary interventions to support healthy aging.},
}
@article {pmid41403720,
year = {2025},
author = {Hong, M and Xiang, W and Kong, L and Wang, X and Fu, L and Chen, L and Liu, F},
title = {Corynebacterium Striatum Infective Endocarditis: A Systematic Review.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {17309-17318},
pmid = {41403720},
issn = {1178-7031},
abstract = {BACKGROUND: Corynebacterium striatum (CS) is an uncommon but potentially fatal pathogen of infective endocarditis (IE). The literature on the patterns and clinical progression of Corynebacterium striatum infective endocarditis (CSIE) is limited. This article aims to provide insights into the clinical presentation and management of CSIE through a retrospective analysis of documented cases.<br><br>METHODS: An electronic search was conducted across various databases including PubMed, China National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database, and Wanfang database to identify relevant articles in both English and Chinese literature documenting CSIE. Subsequently, patient-level data were extracted and subjected to analysis.<br><br>RESULTS: The systematic search yielded 38 patients from 35 articles. The median age was 68 [IQR 54, 73] years, and 63.2% of patients were men. A history of heart disease was present in 55.3% of cases, while 15.8% had a history of cardiovascular electronic device implantation. The mitral valve was the most commonly affected site, accounting for 52.8%. The misdiagnosis or missed diagnosis rate of CSIE was 28.9%. Microbiological confirmation by 16S ribosomal ribonucleic acid (16S rRNA) or metagenomic next-generation sequencing (mNGS) was present in 13.2% of cases. Vancomycin was the most effective antibiotic, with 41.7% of the CS isolates showing resistance to multiple drugs. Surgical intervention was performed in 55.3% of the CSIE patients, and the overall fatality rate was 37.8%, both of which were higher than those reported in standard IE due to common pathogens such as Staphylococcus aureus (surgical intervention rate 37.8%, fatality rate 22.4%) and viridans streptococci (surgical intervention rate 29.5%, fatality rate 36.6%).<br><br>CONCLUSION: CSIE often presents with nonspecific symptoms, making it prone to misdiagnosis or underdiagnosis. Echocardiography and blood cultures remain the primary diagnostic tools, but advanced approaches such as 16S rRNA and mNGS improve accuracy in pathogen identification. Compared to IE caused by common microorganisms (eg, Staphylococcus aureus, viridans streptococci), CSIE is associated with higher rates of surgical intervention and mortality, underscoring the urgent need for increased clinical vigilance and prompt, targeted management.},
}
@article {pmid41403708,
year = {2025},
author = {McKnight, MM and Szabolcs, N and Graham, A and Neufeld, JD},
title = {Microbial community succession of home aquarium biofilters associated with early establishment of comammox Nitrospira.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf212},
pmid = {41403708},
issn = {2730-6151},
abstract = {Nitrification in aquarium biofilters transforms toxic ammonia (NH3/NH4[+]) into less toxic nitrate (NO3[-]) via nitrite (NO2[-]). Known freshwater aquarium nitrifiers include ammonia- and nitrite-oxidizing bacteria, ammonia-oxidizing archaea (AOA), and complete ammonia-oxidizing Nitrospira (CMX), with CMX recently shown to dominate most freshwater aquarium biofilters. However, little is known about nitrifier succession during aquarium establishment in home settings. Based on CMX prevalence in mature aquariums and the rapid growth of ammonia-oxidizing bacteria (AOB), we hypothesized that AOB initially dominate before CMX establish. To test this, we monitored microbial succession and water chemistry in three home aquariums over 12 weeks, collecting weekly samples from aquarium water, biofilter beads, and sponge filters. Biofilter DNA was analyzed via 16S rRNA gene sequencing and quantitative PCR (qPCR) targeting amoA genes. Nitrification reduced ammonia and nitrite to undetectable levels by week 3 in two aquariums and by week 8 in the third. Ammonia oxidizer detection by qPCR coincided with the onset of ammonia oxidation, with AOA preferentially colonizing biofilter beads. Metagenomic profiling of week 12 biofilter samples confirmed AOA and comammox Nitrospira amoA genes in all aquariums, along with nxrB genes from both comammox and canonical Nitrospira nitrite oxidizers. These results provide insight into the establishment of ammonia oxidizers in residential aquariums. Future work should explore factors influencing nitrifier community assembly, including inoculation sources (e.g. live plants, biological supplements), fish load, and water chemistry.},
}
@article {pmid41403704,
year = {2025},
author = {Yu, QY and Liu, X and Yao, H and Lü, PP and Yang, GJ and Lü, XT and Han, XG and Guo, LD and Huang, Y},
title = {The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf215},
pmid = {41403704},
issn = {2730-6151},
abstract = {Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.},
}
@article {pmid41403505,
year = {2025},
author = {Sanjrambam, B and Sharma, D and Bakshi, RK and Deka, MB and Agarwala, S and Kalita, A},
title = {Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study.},
journal = {Journal of family medicine and primary care},
volume = {14},
number = {11},
pages = {4705-4711},
pmid = {41403505},
issn = {2249-4863},
abstract = {INTRODUCTION: Recent research highlights that the gut microbiota of pregnant women undergoes significant changes throughout pregnancy, influenced by factors such as diet, environment, and sociocultural practices. A diverse gut microbiome during pregnancy is linked to improved metabolic health and the lower risk of complications like gestational diabetes and pre-eclampsia.<br><br>OBJECTIVE: This study aimed to investigate the relationship between dietary practices of different communities of Assam and Manipur with the composition of gut microbes during pregnancy.<br><br>METHODS: A total of 18 pregnant women completed a survey assessing macronutrient consumption during the first and third trimesters. Dietary data, obtained through questionnaires, were subjected to PCoA (Principal Co-ordinate Analysis) to find similarities and dissimilarities in dietary patterns. Metagenomics analysis of stool samples was done to study the consortium of gut bacteria for the participants.<br><br>RESULTS: This study has demonstrated that higher intake of carbohydrates and fats during pregnancy results in a decrease in phylum such as Firmicutes and Actinobacteria. Phylum such as Gemmatimonadetes, Crenarchaeote, Fibrobacteres, and Fusobacteria dominated the gut of most participants.<br><br>CONCLUSION: The relationship between gut microbiota composition and dietary habits among pregnant women in Northeast India is essential for designing effective nutritional interventions aimed at improving both maternal and infant health. Future studies should prioritize longitudinal research to better understand these connections and their impact on public health in the region, with a particular focus on identifying the specific foods and dietary patterns responsible for the observed similarities.},
}
@article {pmid41403401,
year = {2025},
author = {Lin, H and Zhu, X and Zhu, J and Chen, N and Bao, W and Peng, Z},
title = {High-Throughput Sequencings Revealed That Gut Microbiota Dysbiosis is Implicated in Gouty Arthritis of Red-Crowned Crane (Grus japonensis).},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {2422900},
pmid = {41403401},
issn = {1865-1682},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Arthritis, Gouty/veterinary/microbiology ; *Dysbiosis/veterinary/microbiology/complications ; High-Throughput Nucleotide Sequencing/veterinary ; *Bird Diseases/microbiology ; Feces/microbiology ; China/epidemiology ; RNA, Ribosomal, 16S ; },
abstract = {The red-crowned crane (Grus japonensis) is one of the rarest cranes with a global population of less than 4000 individuals. The population of red-crowned crane could be influenced by health threats, including metabolic and infectious diseases. In the Wildlife Rescue Center of Suining County of Jiangsu Province, gouty arthritis (GA) was observed in all four red-crowned cranes since March 2024. A pooled fecal supernatant was first submitted to metagenomics sequencing for screening disease-associated pathogens. Enterobacteria phage phiEcoM-GJ1 was detected as the predominant virus while Escherichia coli and Aeromonas hydrophila were the dominated bacteria in the mixed fecal sample from red-crowned cranes. The 16S rRNA gene sequencing was further performed on both the mixed fecal sample and four individual samples, which showed that Escherichia-Shigella, Lactobacillus, and Enterococcus were the most abundant gut flora in both mixed and individual fecal samples. Furthermore, bacteria isolation and identification with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) confirmed that Escherichia coli was predominant (19/29 colonies, 65.52%) in the feces. Therefore, anti-uricacid and antibacteria treatments using plantain herb, doxycycline, Vitamin AD3 and multivitamin B were adopted, leading to a full behavioral recovery within 1 month. Overall, this case-based observational study provides first clue on the gut-joint axis in red-crowned cranes, supporting that gut microbiota dysbiosis is closely associated with GA in red-crowned cranes.},
}
@article {pmid41402348,
year = {2025},
author = {Liu, F and Kang, L and Li, Z and Peñuelas, J and Abbott, BW and Xu, W and Zhou, W and Liu, X and Chen, L and Qin, S and Zhang, D and Peng, Y and Yang, Y},
title = {Chemoautotrophic carbon fixation in thermokarst lakes on the Tibetan Plateau.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67478-x},
pmid = {41402348},
issn = {2041-1723},
support = {32588202, 32425004, and 32571870//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Dissolved organic carbon (DOC) derived from thermokarst lakes is usually considered to be prone to microbial degradation and releases substantial carbon dioxide to the atmosphere, potentially enhancing the positive permafrost carbon (C)-climate feedback. In contrast to this long-term standing view, here we show that dark C fixation exceeds DOC degradation in ~1/3 of the investigated thermokarst lakes on the Tibetan Plateau, based on the combination of large-scale water and sediment sampling across seasons and years, biodegradable DOC experiments and [14]C-labeling bicarbonate (NaH[14]CO3) assimilation incubation experiment. By employing qPCR, amplicon sequencing and metagenomic analyses, we find that microbial C fixation is mainly driven by nitrifying microorganisms via the Calvin-Benson-Bassham cycle carried out by the cbbL gene (encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase). These findings demonstrate that chemoautotrophic C fixation predominates in part of thermokarst lakes, which could partly offset C emissions upon permafrost thaw and thus weaken the positive permafrost C-climate feedback.},
}
@article {pmid41401858,
year = {2025},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (AN3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression, minimal weight loss, and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}
@article {pmid41401693,
year = {2025},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
doi = {10.1016/j.psj.2025.106246},
pmid = {41401693},
issn = {1525-3171},
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}
@article {pmid41401615,
year = {2025},
author = {Wu, JZ and Wang, JH and Chen, Y and Zhang, Y and Wang, L and Zhao, KL},
title = {Deciphering the microbial response and functional potential involving in cadmium-arsenic co-contaminated paddy soil remediation with silicon-magnetic biochar.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128318},
doi = {10.1016/j.jenvman.2025.128318},
pmid = {41401615},
issn = {1095-8630},
abstract = {To remediate cadmium (Cd)-arsenic (As) co-contaminated paddy soils, a novel silicon-magnetic biochar (SBC) was synthesized. Its microbial remediation mechanisms were investigated through a rice pot experiment combined with metagenomics. Results showed SBC significantly improved soil properties, including increased pH and dissolved organic carbon (DOC). This led to a drastic reduction in the rhizosphere bioavailability of Cd (by 69.9 %) and As (by 29.5 %). Consequently, SBC enhanced rice growth, with mature plant height and dry biomass increasing by 25.0 % and 46.7 %, respectively. Crucially, SBC reduced Cd and As accumulation in grains by 38.4 % and 55.6 %. Metagenomics revealed SBC enhanced microbial diversity, stability, and functional potential in both soil and phyllosphere, particularly in cellular processes and genetic information processing. SBC enriched key soil taxa linked to detoxification, such as Geobacter, Gemmatirosa, and Flaviaesturariibacter, and beneficial phyllosphere microbes like Ensifer adhaerens and Rhizobium rosettiformans. Functionally, SBC up-regulated microbial Cd efflux genes, while strong physicochemical adsorption and precipitation (with OH[-], Fe, and S[2-]) further enhanced Cd immobilization. Concurrently, it up-regulated As reduction genes while down-regulating As efflux genes, promoting microbial As(III) sequestration. These findings demonstrate SBC passivates Cd and As through synergistic physicochemical immobilization and microbial pathway modulation, which underscore its significant environmental value for restoring soil health and mitigating contamination.},
}
@article {pmid41401609,
year = {2025},
author = {Yue, H and Xu, J and Guan, X and Shen, Y},
title = {Redox-active biochar as insoluble electron acceptors for anaerobic oxidation of ammonium.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128315},
doi = {10.1016/j.jenvman.2025.128315},
pmid = {41401609},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (anammox) is a promising nitrogen removal process, but its reliance on nitrite presents operational challenges. Here, we demonstrated that redox-active pyrogenic biochar could serve as an insoluble electron acceptor for NH4[+] oxidation by anammox consortia. Through batch incubations, over 95 % total nitrogen removal was consistently achieved with biochar as the sole electron acceptor across two consecutive cycles, though at a slower rate (0.77-1.18 mmol-N·d[-1] g[-1] VSS) compared to conventional anammox reaction. Isotopic tracing confirmed the role of biochar as an electron sink, and electrochemical and spectroscopic analyses illustrated that biochar's electron-accepting capability was attributed to surface quinone-like and pyridinic N groups. High-throughput sequencing and metagenomics revealed the dominance of anammox species Candidatus Brocadia in biochar-driven NH4[+] oxidation, with upregulated genes for extracellular electron transfer (EET) associated with c-type cytochromes. Metabolic reconstruction further elucidated the hydroxylamine pathway in biochar-driven anammox, distinctively different from the canonical nitrite-dependent route. These findings underscored biochar geobatteries as an inexpensive, environmentally sustainable electron acceptor, circumventing nitrite supply limitations. This work advances the understanding of EET-mediated anammox, thereby providing the potential for developing energy-efficient nitrogen removal technologies.},
}
@article {pmid41400382,
year = {2025},
author = {Schmidt, BM and Ranjan, P and Erb-Downward, J and Dickson, RP},
title = {Microbial Dominance in Diabetic Foot Osteomyelitis using Nanopore Sequencing Techniques Predicts Positive Response to Surgical Intervention.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf617},
pmid = {41400382},
issn = {1537-6613},
abstract = {BACKGROUND: Existing tools to predict successful response to surgery for the treatment of diabetic foot osteomyelitis are lacking. Recent studies in non-bone infections have revealed that nanopore sequencing can provide real-time metagenomic identification of pathogens. In a cohort of patients with diabetic foot osteomyelitis, we tested the feasibility of generating interpretable metagenomic data from surgically-acquired osseous tissue, and compared bacterial community features (pathogen dominance) with clinical outcomes (resolution of infection). We hypothesized that nanopore-generated microbial data can be feasibly generated from surgically-acquired bone, aligns with conventional culture results, and is predictive of clinical response.<br><br>METHODS: We performed a pilot feasibility study of ten consecutive patients hospitalized with diabetic foot osteomyelitis who underwent surgery for osteomyelitis. We performed metagenomic sequencing of surgical bone samples using the MinION (Oxford Nanopore). Our primary metagenomic index was community dominance (relative abundance of most abundant species). Our primary clinical endpoint was clinical response to surgery, adjudicated at one year.<br><br>RESULTS: We successfully generated interpretable metagenomic data from all (10/10) specimens, including two specimens with negative culture growth. Among culture-positive specimens, the culture-identified pathogen was either the first or second most abundant organism in all cases. Patients with favorable clinical response exhibited greater pathogen dominance than patients with unfavorable response (p=0.002).<br><br>CONCLUSIONS: In patients with surgically treated osteomyelitis, nanopore sequencing can generate interpretable metagenomic data from bone specimens that is culture-concordant and associated with clinical response. These findings support the feasibility and plausibility of using real-time metagenomic sequencing to improve the clinical management of osteomyelitis.},
}
@article {pmid41399631,
year = {2025},
author = {Su, J and Hansen, BE and Wang, Z and Sharmenov, A and Xia, X and Broekhuizen, M and Ma, Z and Peppelenbosch, MP},
title = {Yogurt reintroduction and the circulating microbiome in healthy volunteers: protocol for a prospective, longitudinal, species-controlled crossover clinical trial (MAMI).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101579},
pmid = {41399631},
issn = {2451-8654},
abstract = {BACKGROUND: Although the gut microbiome plays a crucial role for maintaining overall host homeostasis and metabolism, it is significantly influenced by dietary changes, leading to substantial temporal variations in microbial composition within and between individuals. Despite this, incidental fecal sampling remains the standard method for microbiome assessment. Recently, the blood microbiome, defined by microbial DNA (cmDNA) circulating in the bloodstream, has emerged as a potentially more stable and integrated alternative. Preliminary data suggest that blood microbiome analysis may offer more consistent insights than fecal-based approaches, although the methodological validity of the approach has been questioned.<br><br>METHOD/DESIGN: This study aims to establish or rule-out cmDNA as a representative of the gut microbiome. In a prospective, single-arm crossover trial, effects of dairy product withdrawal and reintroduction of a yoghurt with a known consortium of bacteria will be assessed in healthy volunteers aged 18-65. Participants will first abstain from all dairy products, a phase expected to reduce yogurt-associated cmDNA in the bloodstream. Yogurt will then be reintroduced, during which reappearance of cmDNA of specific bacteria (especially LGG, LA-5 and BB-12) is anticipated. Shotgun metagenomic sequencing will be used to track cmDNA dynamics over time. This longitudinal sampling approach will provide experimental evidence supporting the existence and responsiveness of the circulating microbiome, while also revalidating the bioinformatic pipeline used for its analysis.<br><br>CONCLUSION: This pilot study will test whether blood-derived microbial DNA can serve as a valid surrogate for gut microbiome composition. If successful, this approach may provide a more stable and integrative alternative to fecal sampling and support future biomarker development and mechanistic research.<br><br>CLINICAL TRIAL REGISTRATION: NCT06944002.},
}
@article {pmid41399416,
year = {2025},
author = {Liu, Y and Zou, T and Lu, M and Li, P and Xiang, T},
title = {Delayed psychiatric sequelae following multifocal central nervous system lesions in leptospirosis: A case report.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02435},
pmid = {41399416},
issn = {2214-2509},
abstract = {Leptospirosis is a zoonotic infectious disease that can involve multiple organ systems. Neurological involvement is uncommon, and long-term neuropsychiatric sequelae have rarely been described. We report the case of a previously healthy adult who developed acute leptospiral infection complicated by multifocal central nervous system (CNS) lesions. The patient presented with fever, convulsions, altered mental status. Chest computed tomography (CT) scan revealed diffuse ground-glass opacities and patchy consolidations in both lungs. Brain magnetic resonance (MRI) demonstrated multifocal CNS lesions. Cerebrospinal fluid Metagenomic Next-generation Sequencing (mNGS) confirmed leptospiral infection. The patient received appropriate antimicrobial therapy and recovered fully, with follow-up imaging showing resolution of cortical lesions. Three years later, the patient developed new-onset psychiatric symptoms, including delusions, hallucinations, or personality changes, without evidence of recurrent infection or other organic causes. This case highlights that leptospiral infection may cause multifocal CNS lesions and lead to delayed psychiatric sequelae years after apparent recovery.},
}
@article {pmid41399344,
year = {2025},
author = {Hillman, EBM and Carson, D and Walters, JRF and Fritzsche, M and Mate, R and Chappell, KE and Chekmeneva, E and Romero, MG and Lewis, SJ and Rijpkema, S and Wellington, EMH and Arasaradnam, R and Amos, GCA},
title = {Ruminococcus gnavus and Biofilm Markers in Feces From Primary Bile Acid Diarrhea Patients Indicate New Disease Mechanisms and Potential for Diagnostic Testing.},
journal = {Gastro hep advances},
volume = {4},
number = {9},
pages = {100712},
pmid = {41399344},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Bile acid diarrhea (BAD) is a common cause of frequent loose stools, urgency, and incontinence, which is under-recognized due to limited diagnostic test availability and unclear pathogenesis. This study aimed to investigate fecal changes in well-defined subjects.<br><br>METHODS: Fecal samples were compared in BAD patients (n = 26), diagnosed by SeHCAT testing, and healthy controls (n = 21). Shotgun metagenomic sequencing was used to identify microbiome species and functional genes. An extended set of 38 bile acids was quantified by liquid chromatography mass spectrometry, including various epimers and intermediates, such as iso- (3-beta-OH), oxo (keto), allo (5-alpha), and 3-sulfated forms.<br><br>RESULTS: Alpha diversity, reflecting microbial richness, was reduced in BAD patients with severe forms of the disease, while beta diversity demonstrated distinct microbial profiles between groups. Ruminococcus gnavus (R. gnavus) was prevalent in BAD patients but rare in controls (odds ratio = 73), while Firmicutes bacterium CAG110, Eubacterium siraeum and 2 Oscillibacter species were less common in BAD (odds ratios = 25-30). Overall, 99 taxa differed significantly between groups. Bile acidtransforming genes (baiA, baiB, hdhA) were more abundant in BAD samples (P &#x2264; .0012). Most fecal bile acids, including iso-bile acids and intermediates, were higher in BAD. Elevated ursodeoxycholic acid-3-sulfate and relatively lower lithocholic acid and allo-bile acids, including isoallolithocholic acid, reflect changes in bacterial metabolism. Biofilm-associated genes (bssS, pgaA, pgaB) were markedly elevated in BAD patients (P &#x2264; .00008). SeHCAT values negatively correlated with R. gnavus (rho -0.53, P = .008) and positively with E ubacterium siraeum (rho 0.41, P = .041).<br><br>CONCLUSION: BAD may result from an overgrowth of R. gnavus, associated with intestinal biofilms and an altered bile acid metabolism.},
}
@article {pmid41399017,
year = {2025},
author = {Song, Y and Kjellander, C and Robinson, W and Öhrmalm, L and Giske, C and Gyarmati, P},
title = {Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70158},
doi = {10.1002/mbo3.70158},
pmid = {41399017},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Workflow ; *Sepsis/diagnosis/microbiology ; Hematologic Neoplasms/complications ; Bacteria/genetics/isolation &amp; purification/classification ; },
abstract = {Bloodstream infection (BSI) is a severe and often fatal condition, and a major cause of mortality in patients with hematological malignancies due to underlying conditions and anticancer therapy-induced immunodeficiency. Rapid identification of the causative pathogens is essential as BSI results in worsened prognosis, extended hospitalization, delays or dose reductions in therapy, and may progress to sepsis and septic shock if untreated. Shotgun metagenomics is a culture-independent technique capable of detecting a wide range of fungal, viral, and bacterial organisms along with their antimicrobial resistance genes. Several studies showed that shotgun metagenomics enables the diagnosis of BSI, specifically in cases where conventional methods/culture-dependent techniques fail to identify the causative pathogens. However, evaluation of the accuracy of the applied bioinformatics pipelines remains incomplete. This study aimed to compare and optimize four commonly used bioinformatics pipelines (BLAST, Kraken, Metaphlan, RTG Core) for shotgun metagenomics by assessing their accuracy in identifying pathogens in blood samples from patients with hematological malignancies and suspected BSI, with blood culture serving as the reference standard. Our work shows that the selection of bioinformatics pipelines for diagnosing BSI strongly affects the precision of the findings, and an optimized BLAST pipeline was superior to the alternatives, as it was the only method that accurately identified the causative pathogens.},
}
@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04636-7},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}
@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02260-1},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.<br><br>RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.<br><br>CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}
@article {pmid41398277,
year = {2025},
author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H},
title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-025-02490-7},
pmid = {41398277},
issn = {1741-7007},
support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&amp;D Program of China/ ; 2022YFC2805505//the National Key R&amp;D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.<br><br>RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553&#xa0;m) and sediments (3060-9232&#xa0;m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher &#x251;-diversity than the deep-sea waters and sediments (p&#x2009;<&#x2009;0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.<br><br>CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.},
}
@article {pmid41398218,
year = {2025},
author = {Huang, R and Zhang, Y and Arif, M and Song, C and Yang, L},
title = {16S rDNA sequencing of the intestinal metagenome of Wanxi White Goose (Anser cygnoides) with different egg production abilities.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-025-01401-7},
pmid = {41398218},
issn = {2730-6844},
support = {202423l10050055//Anhui Province Science and Technology Innovation Project/ ; },
}
@article {pmid41398180,
year = {2025},
author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00880-x},
pmid = {41398180},
issn = {2055-5008},
support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; },
abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.},
}
@article {pmid41398168,
year = {2025},
author = {Zhang, Y and Huang, Q and Tunçil, YE and Giriwono, PE and Xie, Z and Zhang, B},
title = {Metagenomic insights into effect of pulse cell wall integrity on gut microbiota, CAZyme gene responses and starch/protein metabolism during in vitro fecal fermentation.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00660-z},
pmid = {41398168},
issn = {2396-8370},
support = {32272342//Natural Science Foundation of China/ ; NL2024010//National Engineering Research Center of Wheat and Corn Further Processing Open Project/ ; },
abstract = {The physical structure of pulse cotyledon cells modulates gut microbiota by controlling starch and protein availability for colonic fermentation, yet the mechanisms governing the interplay between saccharolytic and proteolytic fermentation remain unclear. Here, enzymatically treated white kidney bean cotyledon cells with weakened cell walls (CWs) underwent in vitro fecal fermentations and shotgun sequencing. Impaired CWs enhanced fermentation, increased acetate and propionate production, and reduced branched-chain fatty acids (BCFAs) and ammonia. Damaged CWs upregulated CAZymes encoding genes GH4, GH15, GH126, CBM20, and CBM26, which are associated with amylase, α-glucosidases, and amyloglucosidase activities involved in starch degradation. Furthermore, amino acid pathway enrichment revealed that IhgO and csiD, involved in lysine degradation, as well as astA-E, PRODH, putA and E1.2.1.88, involved in the conversion of arginine and proline to glutamate, were upregulated. Instead, isolated protein showed the highest ammonia and BCFAs production, accompanied by elevated glutamate dehydrogenase (gudB, GLUD1_2, and E1.4.1.4), soxA and soxB, involved in serine metabolism, and DBT, involved in branched-chain amino acid degradation. These findings provide metagenomic insights into how pulse CW integrity regulates saccharolytic and proteolytic fermentation, deepening our understanding of whole pulse foods in supporting gut health.},
}
@article {pmid41330588,
year = {2025},
author = {Chen, HP and Zhu, B and Wang, XF and Zhou, XJ and Du, Y and Mu, ZL},
title = {[Nasal infection with Mycobacterium avium complex: a case report].},
journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery},
volume = {60},
number = {11},
pages = {1439-1440},
doi = {10.3760/cma.j.cn115330-20241219-00698},
pmid = {41330588},
issn = {1673-0860},
support = {82360504//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; Middle Aged ; Biopsy ; Endoscopy ; *Epistaxis/diagnosis/microbiology/therapy ; Metagenomics ; *Mycobacterium avium Complex/genetics/isolation &amp; purification ; *Mycobacterium avium-intracellulare Infection/complications/diagnosis/microbiology/therapy ; Nasal Cavity/diagnostic imaging/microbiology/pathology ; Nasal Mucosa/diagnostic imaging/microbiology/pathology ; Nasal Septum/diagnostic imaging/microbiology/pathology ; *Rhinitis/complications/diagnosis/microbiology/therapy ; },
}
@article {pmid41397341,
year = {2025},
author = {Sun, Z and Dong, D and Song, X and Wei, Y and Li, Y and Dai, H and Liu, C and Zhang, M and Li, M},
title = {Halophytes regulate microbial synergy to enhance N removal and mitigate greenhouse gas in low C/N mariculture wastewater: Revealed by isotopic &amp; metagenomics.},
journal = {Water research},
volume = {290},
number = {},
pages = {125154},
doi = {10.1016/j.watres.2025.125154},
pmid = {41397341},
issn = {1879-2448},
abstract = {Constructed wetlands (CWs) are promising for nitrogen removal from mariculture wastewater, but their efficiency under low C/N ratios remains limited by halophytes selection and unclear microbial mechanisms. Here, we investigated three halophytes (Sesuvium, Suaeda and Mangrove) in seawater CWs under C/N ratios of 5, 2.5 and 1, with unplanted controls, using metagenomics and [15]N-isotope tracing. Plants significantly enhanced total nitrogen (TN) removal under low C/N, with Sesuvium performing best (85.5% and 63.3% at C/N = 2.5 and 1), significantly surpassing Suaeda, Mangrove and controls. It also minimized greenhouse gas (GHG) emissions and reduced NH4[+]-N/NO2[-]-N accumulation. Microbial processes dominated TN removal (71.7-78.9%), whereas direct plant uptake contributed only 5.2-7.6%. Novelly, stable isotope tracing with [15]N-labeled CH4N2O confirmed that urea-N and NO3[-]-N are simultaneously removed via anammox. Under low C/N (2.5 and 1), Sesuvium selectively enriched anammox and sulfur autotrophic denitrification (SAD) taxa. Shifts in NO3[-]-N reduction pathways-from heterotrophic denitrification/dissimilatory nitrate reduction to ammonium (DNRA) under high C/N to anammox/SAD under low C/N-explained the superior performance of Sesuvium. This study highlights Sesuvium as an optimal halophyte for efficient nitrogen removal and lowest GHG emissions in low-C/N seawater CWs, providing mechanistic insights into plant-microbe interactions for mariculture wastewater treatment.},
}
@article {pmid41396836,
year = {2025},
author = {Xie, D and Tian, Y and Zheng, F and Wu, L and Xu, G and Liu, Q and Lu, G},
title = {Multi-Omics and Integrative Analytics in Natural Products Discovery.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {225},
pages = {},
doi = {10.3791/69458},
pmid = {41396836},
issn = {1940-087X},
mesh = {*Biological Products/chemistry/metabolism/analysis ; *Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Drug Discovery/methods ; Computational Biology/methods ; Multiomics ; },
abstract = {Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and isolating these compounds can be slow and often yield diminishing returns. Fortunately, advanced multi-omics and computational approaches present powerful solutions to these challenges. This review highlights innovative methodologies that integrate metabolomics, genomics, transcriptomics, and proteomics with bioinformatics and analytical chemistry to accelerate NP discovery. For instance, untargeted metabolomics platforms like high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Global Natural Products Social (GNPS) molecular networking allow for comprehensive profiling of new compounds, while targeted isotope-labeling strategies enhance this process. Additionally, genome and metagenome mining tools such as antibiotics and secondary metabolite analysis shell (antiSMASH), Deep Biosynthetic Gene Cluster (DeepBGC), and Pipeline for Reconstructing Integrated Syntheses of Metabolites (PRISM) quickly identify biosynthetic gene clusters (BGCs) in both cultured and uncultured organisms, often using heterologous expression to validate products. Transcriptomic analyses, including RNA sequencing (RNA-seq), co-expression networks, and fluxomics, help clarify how pathways are regulated, while quantitative proteomics techniques like tandem mass tags/isobaric tags for relative and absolute quantitation (TMT/iTRAQ) and label-free methods, along with chemoproteomics approaches such as cellular thermal shift assay and thermal proteome profiling (TPP), uncover molecular targets and their mechanisms of action. This review also places significant emphasis on the role of artificial intelligence (AI) and machine learning (ML) in integrating multi-omics data, spanning activities from constructing gene-metabolite correlation networks to leveraging knowledge graphs and graph neural networks for data fusion and functional prediction. Finally, this review concludes by discussing the synergistic benefits of multi-omics for natural-product discovery, addressing current technical challenges, and exploring future directions toward high-throughput, intelligent data integration for next-generation NP research.},
}
@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}
@article {pmid41396065,
year = {2025},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180625},
doi = {10.1128/spectrum.01806-25},
pmid = {41396065},
issn = {2165-0497},
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.<br><br>IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}
@article {pmid41396034,
year = {2025},
author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y},
title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04527d},
pmid = {41396034},
issn = {2042-650X},
abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.},
}
@article {pmid41395987,
year = {2025},
author = {Sun, Z and Zhang, P and Li, Y and Zhang, C and Liu, Y and Ma, B and Lan, Q and Qi, H},
title = {Microsporidia keratoconjunctivitis identified as an emerging zoonotic threat from pet parrots: Clinical and metagenomic next-generation sequencing evidence.},
journal = {Virulence},
volume = {},
number = {},
pages = {2605385},
doi = {10.1080/21505594.2025.2605385},
pmid = {41395987},
issn = {2150-5608},
abstract = {Microsporidia are opportunistic, obligate intracellular fungi capable of causing keratoconjunctivitis. Because the clinical manifestations of microsporidia keratoconjunctivitis are indistinguishable from those of other etiologies, and the organism is difficult to culture, its diagnosis is challenging. The transmission routes of microsporidia keratoconjunctivitis remain poorly defined, and zoonotic sources have long been suspected but rarely confirmed. Between September 2024 and October 2025, a total of 15 confirmed cases of microsporidia keratoconjunctivitis were identified at Peking University Third Hospital. The diagnosis was established based on Giemsa-stained corneal scrapings and/or metagenomic next-generation sequencing (mNGS) of conjunctival lavage samples. Among these 15 patients, microsporidia spores were observed in corneal scrapings from nine individuals, while 13 tested positive for Encephalitozoon hellem (E. hellem) by mNGS. Notably, all affected patients reported a history of parrot exposure. Self-reported parrot exposures included direct ocular contact (n = 3) and indirect contact (n = 12). Six patients reported that their parrots had exhibited ocular abnormalities and diarrhea before the onset of the patients' symptoms, and two patients stated that their parrots had died prior to their clinical presentation. Ocular and fecal samples from three parrots associated with four patients were collected, and all the parrots tested positive for E. hellem by mNGS. These findings provide both clinical and molecular evidence supporting pet parrots as a zoonotic source of microsporidia keratoconjunctivitis. This emerging zoonotic threat calls for greater clinical awareness and attention to animal exposure history during diagnosis.},
}
@article {pmid41395968,
year = {2025},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198525},
doi = {10.1128/aem.01985-25},
pmid = {41395968},
issn = {1098-5336},
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}
@article {pmid41395946,
year = {2025},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}
@article {pmid41395940,
year = {2025},
author = {Karamycheva, S and Wolf, YI and Koonin, EV and Makarova, KS},
title = {Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0312725},
doi = {10.1128/mbio.03127-25},
pmid = {41395940},
issn = {2150-7511},
abstract = {Evolution of prokaryotic genomes is highly dynamic, including extensive gene gain via horizontal gene transfer and gene loss, as well as different types of genome rearrangements. Most quantitative analyses of prokaryotic genome evolution are based on single-gene events, although the distribution of genes is known to be non-random at the scales of operons and various genomic islands. Here, we present a spatial-temporal phylogenomic approach for detecting arrays of genes that are likely to have been acquired as a single block. It is shown that the acquisition of multi-gene blocks makes a major contribution to prokaryotic genome evolution and that these blocks consist primarily of co-directed, functionally coherent genes. A detailed analysis of the spatial-temporal data for the genomes of multiple groups of bacteria and archaea shows that the larger blocks of co-acquired genes represent primarily mobile genetic elements (MGEs), in many cases not identified previously. For example, this includes a new group of pleolipoviruses in Haloarchaea and a group of MGEs specific for Bacteroidota with hypervariable gene content and carrying a unique RNA polymerase enzyme. We also show that some ancestral phage-related large islands correspond to previously unnoticed R-type pyocins in Proteus and Morganella genomes. Many of the smaller gene blocks prone to high genome flux are expected to comprise antivirus defense systems and toxins-antitoxins. In a pilot analysis, eight novel toxin-antitoxin and seven novel defense systems were predicted in archaea of the phylum Thermococcaceae.IMPORTANCEWith many thousands of diverse bacterial and archaeal genomes made available by the fast advancing genomic and metagenomic sequencing, methods for in-depth analysis of genome organization and evolution are essential for extracting the maximum amount of information from this wealth of genomic data. We present a spatial-temporal approach for genome analysis that detects blocks of genes that were simultaneously acquired during genome evolution and shows that genes in such blocks are mostly transcribed in the same direction and have related functions, allowing for the prediction of previously unknown functional systems. The predictive power of the approach is demonstrated by detecting multiple novel mobile genetic elements and antivirus defense systems. Unlike most other functional prediction methods, the spatial-temporal approach does not require prior knowledge of the functions of any genes and has the potential to predict hundreds of novel functional systems amenable to further in-depth study, especially for poorly characterized groups of bacteria and archaea.},
}
@article {pmid41395693,
year = {2025},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity &amp; metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestl&#xe9; Health Science/ ; //Pierre Mercier Foundation/ ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).<br><br>METHODS: In a randomised trial, patients with BMI >35&#x2009;kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.<br><br>RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.<br><br>CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}
@article {pmid41395487,
year = {2025},
author = {Bai, Z and Wang, Y and Li, Y and Xu, J and Lai, Z},
title = {The gut microbiota in liver transplantation recipients during the perioperative and postoperative recovery period.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684303},
pmid = {41395487},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic Liver Disease (CLD) is one of the frequent causes of death, especially in the developing world. Liver transplantation (LT) is an effective modality to treat end-stage liver disease. Perioperative management of liver transplantation patients and prevention of postoperative complications are the key to improving patient prognosis and quality of life, and the intestinal flora of these patients can affect postoperative complications and overall prognosis.<br><br>METHOD: We collected a total of 151 fecal samples from 59 liver transplantation patients at different stages from the First Hospital of Shanxi Medical University. Using 16S rRNA sequencing technology, we compared the characteristics and changes of their microbiota. We selected 42 samples for metagenomic sequencing using the microPITA method to further analyze the composition and functional differences of the microbiota during the perioperative period of liver transplantation across various time points.<br><br>RESULTS: After liver transplantation (LT), the diversity of gut microbiota initially decreased and then increased. Firmicutes, Proteobacteria, and Bacteroidota were the main bacterial groups during the perioperative period. Firmicutes and Proteobacteria initially decreased and then increased, while Bacteroidota exhibited the opposite process. Alpha diversity and beta diversity analyses indicated that 1 month post-transplantation was a turning point for microbiota recovery (P < 0.01). Metagenomic sequencing, analyzed using the LEfSe method, identified a total of 50 genera that played significant roles in this process. The changes in microbiota exhibited the same trend as the 16S rRNA results. KEGG pathway analysis also indicated that 1 month was a critical time point, with Ko02010 potentially being a key pathway for recovery in LT patients, and it showed a negative correlation with Bacteroidota (P < 0.05).<br><br>CONCLUSION: The diversity of intestinal flora in the perioperative period of LT patients decreased first and then increased, and the turning point of intestinal flora recovery was 1 month after LT surgery.},
}
@article {pmid41395483,
year = {2025},
author = {Lawal, OU and Parreira, VR and Rizvi, F and Precious, M and Anderson, REV and Overton, AK and Knapp, JJ and Maxwell, B and Thomas, S and Zambrano, M and Landgraff, C and Fleury, MD and Knox, NC and Charles, TC and Goodridge, L},
title = {Evaluation of sampling methods for genomic surveillance of SARS-CoV-2 variants in aircraft wastewater: advancing global early-warning systems for future pandemics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717424},
pmid = {41395483},
issn = {1664-302X},
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of aircraft wastewater was adopted at an early stage of the pandemic to track importation of emerging variants into the country. However, the acute need to determine the presence of emerging SARS-CoV-2 sublineages meant that the sampling methods utilized were not adequately validated. Here, we compared two different sampling methods for genomic surveillance of SARS-CoV-2 VOCs in aircraft sewage samples.<br><br>METHODS: Eighty-eight composite wastewater samples were collected over 9&#x202f;weeks using both autosampler and passive torpedo samplers at the same location. SARS-CoV-2 nucleic acid in the samples was quantified using RT-qPCR. RNA samples were extracted and sequenced with the MiniSeq system using the tiled-amplicon sequencing approach with ARTIC V4.1 primer sets. Raw reads were preprocessed and SARS-CoV-2 mutations, variants lineages, and other sequence metrics from the two sampling methods were compared.<br><br>RESULTS: The two sampling methods yielded comparable viral load by RT-qPCR, but the autosampler produced higher genome coverage relative to the passive samplers. The Omicron lineages identified differed by sampling method. BQ.1* and BA.5.2*, which were the predominant lineages in wastewater and clinical samples at the time, were identified as dominant in the autosampler and passive sampler, respectively. Additionally, the autosampler captured higher diversity and relative abundance of VOCs, including emerging variants (XBB* and CH.1* lineages), as well as more clinically relevant mutations (S:K444T, T22942A, S:R346T) relative to passive sampler. Overall, the passive samplers produced concordant results with the autosampler for measuring SARS-CoV-2 load with RT-qPCR in aircraft wastewater.<br><br>CONCLUSION: Taken together, our results suggest underestimation of the diversity and abundance of SARS-CoV-2 VOCs and mutations in aircraft sewage using passive torpedo samplers. These data can be used to optimize genomic surveillance approaches for SARS-CoV-2 VOCs in aircraft wastewater samples.},
}
@article {pmid41395471,
year = {2025},
author = {Cheng, YN and Chen, GT and Huang, WC and Chiu, YP and Tang, Y and Fu, PK and Lee, TY},
title = {Lung microbiome signatures and explainable predictive modeling of glucocorticoid response in severe community acquired pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706432},
pmid = {41395471},
issn = {1664-302X},
abstract = {INTRODUCTION: Systemic glucocorticoids (SG) are administered to quell hyper-inflammation in severe community acquired pneumonia (SCAP), yet trials report inconsistent efficacy and no mechanistic explanation.<br><br>METHODS: We enrolled 200 ventilated SCAP patients, whom received hydrocortisone within 48 h of ICU admission, and generated longitudinal lower-airway microbiome profiles by 16S rRNA amplicon and metagenomic sequencing on ICU Days 1, 3 and 7. Compositional data were integrated with clinical variables through a fully reproducible bioinformatics analysis workflow.<br><br>RESULTS: Baseline community structures did not differ between SG and control cohorts, but by Day 7 survivors exhibited enrichment of Actinobacteria and Gammaproteobacteria whereas non-survivors accumulated Alphaproteobacteria and Campylobacteria. A random-forest model restricted to Bacilli and Alphaproteobacteria achieved AUROC = 0.89 (sensitivity 0.83, specificity 0.81) on a patient-held-out test set, significantly outperforming conventional severity indices like APACHE II, SOFA and mNUTRIC scores.<br><br>DISCUSSION: Collectively, our results demonstrate that SG therapy imposes reproducible ecological pressures on the lung microbiome and that a two-feature microbial fingerprint can forecast treatment success with single-sample resolution. These findings show that SG therapy actively reshapes the respiratory ecosystem and that lightweight microbiome-aware machine learning can stratify treatment response, offering a tractable path toward precision corticosteroid stewardship.},
}
@article {pmid41395467,
year = {2025},
author = {Hagarová, L and Kupka, D},
title = {Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675058},
pmid = {41395467},
issn = {1664-302X},
abstract = {The Mária mine, particularly the Strieborná vein, in Rožňava, is one of the most important mines in Slovakia, containing Ag-bearing tetrahedrite (40-46 wt% Cu, 26 wt% Sb, ~1 wt% Ag), making it an important source of strategic and critical raw materials. This mine discharges a unique neutral-pH (6.9), metal-rich mine water drainage (402 mg L[-1] SO4 [2-], 4.65 mg L[-1] Fe) that has remained microbiologically uncharacterized. This study presents the first comprehensive shotgun metagenomic survey of this mine effluent, generating ~227 million high-quality reads that assembled into 157,676 contigs and 378,023 non-redundant genes. Taxonomic analysis revealed a community dominated by Betaproteobacteria (> 66%), with abundant lithotrophic genera Sulfuritalea (6.93%), Ferrigenium (5.45%), Gallionella (3.79%), and Sideroxydans (3.65%), alongside the heterotrophic genus Pseudomonas (5.2%). Among the most prevalent neutrophilic iron-oxidizing bacterial strains were Sulfuritalea hydrogenivorans (6.93%), Ferrigenium kumadai (5.45%) and Gallionella capsiferriformas (3.79%). Acidophilic genera (e.g., Thiobacillus sp. at 0.43%, Ferrovum myxofaciens, Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans) collectively accounted for <1% of the community. Functional annotation against KEGG, CAZy, COG, eggNOG, Swiss-Prot, CARD and BacMet databases demonstrated pronounced enrichment of iron cycling (e.g., the iron complex outer-membrane receptor protein TC.FEV.OM), sulfur oxidation (e.g., SoxA, SoxX, SoxB), carbon turnover (glycosyltransferase and glycoside hydrolase families) and nitrogen cycling (e.g., NifH, NifD, NirK, glnA). The antibiotic-resistance profile was dominated (> 95%) by tetracycline and fluoroquinolone determinants, while metal-resistance systems for Ni, Ag, As, Cu and Zn (including CzcD, CzcA, CznA, ArsD and AioX/AoxX) were likewise pervasive. This integrated taxonomic-functional portrait highlights a microbiome finely adapted to this unique geochemistry, combining lithotrophic metabolisms with multi-metal resistance. Our findings establish a critical baseline for long-term monitoring and highlight a high abundance of neutrophilic Fe(II)-oxidizers, suggesting they may represent promising candidates for targeted cultivation and subsequent evaluation in biotechnology applications.},
}
@article {pmid41394950,
year = {2026},
author = {Krishnan, LRA and Nair, S and Girija, D and Vishnu, BR},
title = {Unravelling the complex bacterial diversity in the rice rhizosphere of Kole lands of Thrissur through the metagenomics approach.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {27},
pmid = {41394950},
issn = {2190-572X},
abstract = {UNLABELLED: The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.},
}
@article {pmid41394910,
year = {2025},
author = {Barton, KA and Finnerty, PB and Rupasinghe, R and González-Crespo, C and Mahar, JE and Eden, JS and Meisuria, NY and Martínez-López, B and Newsome, TM and Peel, AJ and Smith, JA and Brookes, VJ},
title = {The final frontier: using carcasses for one health surveillance at the ecosystem interface.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1683110},
pmid = {41394910},
issn = {2297-1769},
abstract = {Anthropogenic activities such as agricultural intensification, urbanisation, globalisation, and climate change are accelerating disease emergence globally, yet surveillance systems have largely overlooked the critical role of vertebrate carcasses in pathogen transmission. This omission is concerning because animal mass mortality events (MMEs) are increasing in frequency and magnitude, while populations of key vertebrate scavengers, especially obligate scavengers like vultures, are declining, resulting in longer carcass persistence and altered disease risks. Carcasses serve as essential resources in food webs but also act as complex microbe transmission hubs through direct consumption, environmental contamination, vector-mediated dispersal, and increased host aggregation, facilitating cross-species and trophic spillover events. Scavengers can amplify or mitigate microbe transmission: their consumption of carcasses can remove infectious material, but their mobility and sociality may also disperse potential pathogens across large areas. Technological advances, including remote sensing, camera traps, GPS telemetry, and machine learning, now enable detailed tracking of scavenger-carcass interactions and identification of transmission hotspots. Simultaneously, metagenomic sequencing allows untargeted detection of known and novel pathogens in carcass-associated microbial communities ("necrobiome"), with portable platforms supporting field-based surveillance. Integrating carcass-based surveillance into One Health frameworks through interdisciplinary collaboration among ecologists, epidemiologists, and data scientists offers a proactive approach to early outbreak detection, improved pandemic preparedness, and ecosystem health monitoring. Given the projected increase in climate-driven mortality events, incorporating carcass-scavenger networks into disease surveillance strategies is a valuable and under-utilised complement to existing approaches, enhancing our ability to monitor and mitigate emerging infectious diseases.},
}
@article {pmid41394788,
year = {2025},
author = {Zhang, B and Wang, J and Li, Q and Ge, J and Zhang, C and Zhou, T and Guo, H and Yang, B and Jiang, H},
title = {Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing (mNGS) in Hospital-Acquired Pneumonia: A Stratified Retrospective Study of Responders and Non-Responders.},
journal = {Risk management and healthcare policy},
volume = {18},
number = {},
pages = {3803-3818},
pmid = {41394788},
issn = {1179-1594},
abstract = {INTRODUCTION: Hospital-acquired pneumonia (HAP) remains a major challenge in clinical practice, particularly due to polymicrobial infections and antimicrobial resistance. Traditional diagnostic methods, such as culture and PCR, are limited by low sensitivity, slow turnaround time, and inability to detect fastidious or novel pathogens. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to pathogen detection and may improve diagnostic accuracy and clinical decision-making.<br><br>METHODS: We conducted a retrospective study of 300 adult HAP patients admitted to Beijing Rehabilitation Hospital, China. Bronchoalveolar lavage fluid samples were analyzed using the Illumina sequencing platform for mNGS. Detection rates, pathogen spectrum, resistance gene identification, and treatment modifications were compared with conventional culture methods.<br><br>RESULTS: mNGS achieved a pathogen detection rate of 92%, significantly higher than the 72% achieved by culture. It identified a broader spectrum of bacteria, fungi, and viruses, including Pseudomonas, Klebsiella, and Aspergillus, which were often missed by culture. Polymicrobial infections were detected in 28% of cases, and antibiotic resistance genes were identified in 30% of samples. The median turnaround time for mNGS results was 48&#xa0;hours after BAL sampling. Based on mNGS findings, treatment regimens were adjusted in 26% of patients.<br><br>CONCLUSION: mNGS demonstrated superior diagnostic performance compared with culture by increasing pathogen detection rates, identifying resistance genes, and guiding treatment adjustments in HAP patients. Despite its promise for precision medicine, further studies are needed to assess cost-effectiveness and generalizability, given the retrospective and single-center design of this study.},
}
@article {pmid41394752,
year = {2025},
author = {Hillary, LS and Knotts, TA and Adams, SH and Ali, MR and Olm, MR and Emerson, JB},
title = {DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.25.690293},
pmid = {41394752},
issn = {2692-8205},
abstract = {Accurately characterising the human gut virome is critical to understanding virus-microbiome-host interactions. However, widely used methods introduce biases that complicate data interpretation and limit cross-study comparability. For instance, multiple-displacement amplification (MDA) preferentially amplifies single-stranded DNA viruses, while total metagenomes are dominated by non-viral sequences, reducing viral signal. These traditional methods have not been systematically compared to viral size-fraction metagenomes (viromes) prepared without MDA. To address this, we applied four common methods for characterising human gut viral community composition (total metagenomes, viromes with/ without DNase treatment (to remove free DNA), and MDA viromes) to a human stool sample, with technical triplicates for each approach. MDA biased viral community composition to a shocking degree: Microviridae formed ∼90% of MDA viromes compared to just 2% of non-MDA viromes. Removing ssDNA viruses from data analyses substantially reduced, but did not eliminate, MDA bias. Metagenomes were enriched for putative temperate phages and predicted Bacillota-phages , whereas predicted Bacteroidetes -phages dominated all viromes, suggesting that metagenomes and viromes select for different populations within the total viral community. DNase treatment had little-to-no effect on virome richness or community composition. This proof-of-principle experiment demonstrates that preparatory methods for viral community analysis can lead to substantially different conclusions from the same faecal sample, and we provide a comprehensive omic data analysis framework for comparing laboratory methodologies for viral ecology. With sufficient DNA yields now easily achievable from human gut viromes without the use of MDA, our results suggest that this biased amplification method should be avoided in human gut virome studies.},
}
@article {pmid41394329,
year = {2025},
author = {Yao, X and Sang, H and Gao, S and Hu, X and Yan, J and Liu, T and Chang, H and Pang, G and Dong, H and Meng, X and Jiang, L and Kong, M},
title = {Diagnostic Utility of Bronchoalveolar Lavage Metagenomic Next-Generation Sequencing for Pulmonary Mucormycosis: A Single-Center Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6469-6480},
pmid = {41394329},
issn = {1178-6973},
abstract = {BACKGROUND: Although pulmonary mucormycosis is rare, it is highly invasive and carries a significant mortality rate. Due to its nonspecific clinical manifestations, it is often misdiagnosed as other invasive fungal diseases. Bronchoalveolar lavage fluid metagenomic next-generation sequencing is a rapid, precise, and comprehensive method for pathogen detection, showing great potential in the early diagnosis of pulmonary mucormycosis in a single-center retrospective series. It provides clinicians with faster and more accurate etiological information, thereby improving patient outcomes and reducing mortality rates.<br><br>METHODS: This study conducted a retrospective analysis of the clinical data from 14 patients diagnosed with pulmonary mucormycosis between 1/6/2021 and 30/6/2024. Peripheral blood samples were collected to perform a complete blood count, measure C-reactive protein levels, and conduct 1,3-&#x3b2;-D-glucan and Galactomannan tests. Lung tissue samples were sent to the pathology laboratory for histological examination. Bronchoalveolar lavage fluid was subjected to fungal culture and metagenomic next-generation sequencing. Additionally, a three-month follow-up on the patients' survival status was carried out via telephone.<br><br>RESULTS: Males accounted for 57.14% of the cases. Diabetes mellitus was present in 12 patients (85.71%, 12/14), and fever was observed in 12 patients (85.71%, 12/14). The 14 patients were categorized as proven cases (4 cases), probable cases (4 cases), and possible cases (6 cases). Two patients (14.29%, 2/14) were diagnosed with disseminated mucormycosis. Chest Computed Tomography scans revealed cavities in half of the patients (50.00%, 7/14). Fungal hyphae were identified in all the histopathological examinations (100%, 4/4). Metagenomic next-generation sequencing detected Mucorales pathogens in all the (100%, 14/14) cases, which is higher positivity than the positive rates of the 1,3-&#x3b2;-D-glucan test (35.71%, 5/14), Galactomannan test (42.86%, 6/14) and fungal culture (7.14%, 1/14). The turnaround time for metagenomic next-generation sequencing reports is 1-3 days, which is much shorter than the time required to obtain results from fungal culture (2-5 days). Additionally, metagenomic next-generation sequencing identified bacterial and viral co-infections, with 11 patients diagnosed as having mixed infections. All patients were treated with antifungal agents targeting Aspergillus species, such as voriconazole, posaconazole, isavuconazole, or amphotericin B, resulting in 9 patients improving, 2 patients being transferred to higher-level hospitals, and 3 patients discontinuing treatment. The 90-day follow-up revealed a mortality rate of 28.57%.<br><br>CONCLUSION: Metagenomic next-generation sequencing can serve as an important complement to traditional diagnostic methods, enabling rapid and accurate differentiation of Mucorales from other fungi. This allows patients to receive timely and targeted antifungal therapy, playing a critical role in early intervention and improving prognosis.},
}
@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration &amp; dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.<br><br>AIM: This study aimed to investigate the effects of the JWC on gastric mucosal&#xa0;inflammation and the expression of drug-resistance genes in H.&#xa0;pylori-infected mice.<br><br>METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.<br><br>RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1&#x3b2;, and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.<br><br>CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}
@article {pmid41394104,
year = {2025},
author = {Xuan, F and Li, C and Zhao, H and Liu, N and Zhao, X and Zhang, B and Wu, X},
title = {Diagnosis, treatment, and monitoring of cytomegalovirus pneumonia in a hematopoietic stem cell transplantation child.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1665477},
pmid = {41394104},
issn = {2235-2988},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Child ; Female ; *Cytomegalovirus Infections/diagnosis/drug therapy ; Antiviral Agents/therapeutic use ; *Cytomegalovirus/isolation &amp; purification/genetics ; *Pneumonia, Viral/diagnosis/drug therapy/virology ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy/complications ; Bronchoalveolar Lavage Fluid/virology ; Acetates/therapeutic use ; Quinazolines/therapeutic use ; },
abstract = {BACKGROUND: Cytomegalovirus (CMV), an opportunistic pathogen, can cause severe pneumonia in Chronic myeloid leukemia (CML) children undergoing hematopoietic stem cell transplantation (HSCT), resulting in a high mortality rate.<br><br>CASE PRESENTATION: An 11-year-old girl was hospitalized with a 3-day history of fever and vomiting, presenting with anemia and massive splenomegaly. A series of diagnostic tests, including blood cell count, bone marrow analysis, flow cytometry, chromosomal examination, and genetic testing, confirmed a diagnosis of CML at blast-phase. Following a one-year course of tyrosine kinase inhibitor-based chemotherapy, the patient entered the chronic phase and underwent a 6/12 human leukocyte antigen (HLA)-matched HSCT from her father. Two weeks after HSCT, the patient developed grade III skin graft-versus-host disease and hemorrhagic cystitis, which were effectively treated and symptoms were alleviated. One month after transplantation, the patient presented with serious pneumonia and pancytopenia. Although five blood cultures and two sputum cultures were all negative, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) indicated a high abundance of CMV (16635 reads), leading to a diagnosis of CMV pneumonia. Notably, no typical resistant mutations were identified in the CMV genome. Targeted treatment with sodium phosphonoformate and letermovir was administered. As a result, the patient's condition improved remarkably with the abundance of CMV decreasing to only 12 reads. After one-year of monitoring, the primary disease was well-controlled, and no CMV reactivation was observed.<br><br>CONCLUSION: The diagnosis, treatment, and monitoring of pneumonia is crucial in post-HSCT patients. This case highlights the utility of mNGS in diagnosing and monitoring CMV pneumonia in post - HSCT patient and the effectiveness of targeted therapy in managing such infections.},
}
@article {pmid41393784,
year = {2025},
author = {Longhi, G and Tarracchini, C and Angelini, L and Anzalone, R and Viappiani, A and Ventura, M and Milani, C and Turroni, F},
title = {Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100516},
pmid = {41393784},
issn = {2666-5174},
abstract = {Traditional dry-cured hams host diverse microbial communities; however, their taxonomic composition, functional capacity, and potential interactions with the human gut remain poorly understood. This study aimed to provide a comprehensive characterization of the microbiota associated with Italian Protected Designation of Origin (PDO) dry-cured hams and to investigate their functional relevance in the food matrix and under simulated intestinal conditions. A total of 96 samples, representing different geographical origins and maturation stages, were analyzed using metagenomics approaches. A conserved microbial core dominated by Staphylococcus equorum (prevalence 80 %) was identified, accompanied by accessory taxa such as Tetragenococcus halophilus (62 %) and Leuconostoc carnosum (10 %). Cluster analyses revealed substantial variability across samples, with community structures influenced more by producer-specific factors than by product type or ripening stage. Functional metagenomics investigation highlighted the presence of metabolic pathways associated with amino acid degradation, carbohydrate metabolism, and lipid transformation, supporting a role for ham-associated microbes in flavor and texture development. Furthermore, cultivation in a simulated gut environment showed a marked reshaping of the microbial community, with low-abundance taxa, including Bacillus spp. and Lactococcus lactis, proliferating under intestinal-like conditions, while the dominance of S. equorum was reduced. Our findings showed that the microbiota of dry-cured ham not only drives key sensory qualities of the product but also comprises a reservoir of live microorganisms capable of tolerating the gut-like conditions. These results highlight the dual role of foodborne microbiota in shaping both food properties and potential interactions with the human host, underscoring the need for further in vivo investigations.},
}
@article {pmid41393342,
year = {2025},
author = {Nishimura, Y and Omae, K and Tominaga, K and Iwasaki, W},
title = {CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf182},
pmid = {41393342},
issn = {2631-9268},
mesh = {Phylogeny ; *Evolution, Molecular ; *Genome, Bacterial ; Databases, Genetic ; },
abstract = {The recent expansion of prokaryotic genomes reveals many ortholog groups (OGs) whose function cannot be inferred from conventional, sequence similarity-based annotation methods, especially in metagenome-assembled genomes. Phylogenetic profiling is one of the promising methods to annotate these OGs, by identifying functional relationships of OGs using co- or anti-occurrence of OG distributions, not sequence similarity. Here, we proposed two new phylogenetic methods for large-scale data, Ancestral State Adjustment (ASA) and Simultaneous EVolution test (SEV), which consider the ancestral state of OG presence/absence. In evaluations using three distinct prokaryotic datasets, ASA and SEV showed better or comparable performance to both established and recently proposed methods for large-scale data. We compared the functionally related OGs detected by each method and found that SEV and its predecessor can identify slowly evolving OGs, such as housekeeping genes. In contrast, ASA and its predecessors can detect functionally related OGs that tend to be gained or lost in a fixed order, indicating a strong evolutionary constraint that provides clues for functional prediction. Using matrix multiplication, we also showed that SEV is scalable in the latest genome databases.},
}
@article {pmid41393220,
year = {2026},
author = {Brown, NK and Depuydt, L and Zakeri, M and Alhadi, A and Allam, N and Begleiter, D and Kabilan Karpagavalli, NB and Khajjayam, SS and Wahed, H and Gagie, T and Langmead, B},
title = {KeBaB: k-mer based breaking for finding long MEMs.},
journal = {International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)},
volume = {16073},
number = {},
pages = {10-17},
pmid = {41393220},
abstract = {Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can often ignore much of its input, skipping matching steps which are redundant to the final output. In this paper we propose KeBaB, a fast and space efficient k-mer filtration step using a Bloom filter. This approach speeds up MEM-finders such as ropebwt3 even further by letting them ignore even more, breaking the input into substrings called "pseudo-MEMs" which are guaranteed to contain all long MEMs. We also show experimentally that KeBaB can accelerate metagenomic classification without significantly reducing accuracy, either by finding all long MEMs or by leveraging the filter to find only the long MEMs present in the t longest pseudo-MEMs.},
}
@article {pmid41392764,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}
@article {pmid41392335,
year = {2025},
author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J},
title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.},
journal = {Journal of diabetes},
volume = {17},
number = {12},
pages = {e70175},
doi = {10.1111/1753-0407.70175},
pmid = {41392335},
issn = {1753-0407},
support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).<br><br>METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.<br><br>RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-&#x3b1;, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.<br><br>CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.},
}
@article {pmid41392160,
year = {2025},
author = {Jamy, M and Huber, T and Antoine, T and Ruscheweyh, HJ and Paoli, L and Pelletier, E and O Delmont, T and Burki, F},
title = {Identification of a deep-branching lineage of algae using environmental plastid genomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67401-4},
pmid = {41392160},
issn = {2041-1723},
support = {2022-00351//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2021-04055//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; ERC consolidator grant 101044505//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Marine algae underpin entire ocean ecosystems. Yet algae in culture poorly represent their large environmental diversity, and we have a limited understanding of their convoluted evolution by endosymbiosis. Here, we perform a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental marine algae, vastly expanding plastid genome diversity within major algal groups, including many without closely related reference genomes. Notably, we recover four plastid genomes, including one near-complete, forming a deep-branching plastid lineage of nano-size algae that we informally name leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance in the Arctic. A near-complete mitochondrial genome showing strong co-occurrence with leptophyte plastids is also recovered and assigned to this group. Leptophytes encompass the enigmatic plastid group DPL2, one of the very few known plastid groups not clearly belonging to major algal groups and previously known only from 16S rDNA sequences. Comparative organellar genomics and phylogenomics indicate that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal hidden organellar diversity, and improve models of plastid evolution.},
}
@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31280-y},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}
@article {pmid41392048,
year = {2025},
author = {Liu, X and Chen, Y and Shi, Z and Shi, Z and Pu, T and Zhang, Y and He, F and Li, X and Wang, Y and Jia, J and He, B and Yang, P},
title = {Macrogenomic analysis of the previous crops effects on tobacco soil microbiomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-08640-9},
pmid = {41392048},
issn = {2045-2322},
support = {2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; 2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; (XDYC CYCX-2022-0071)//the "Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; },
abstract = {Crop rotation serves as a valuable agronomic practice for addressing succession barriers in crops, particularly in tobacco growing. The effect of different previous crops on the microbiology of soils planted with tobacco is an area that deserves further study.This study investigated the chemical properties, microbial community composition, and functional genes related to nutrient cycling in tobacco-planted soils with no preceding crop (CK), garlic (T1), or faba bean (T2) as preceding crops. The results indicated that the T1 treatment significantly decreased the contents of soil organic matter (SOM, 11.32%), total phosphorus (TP, 29.41%), total potassium (TK, 3.33%), and available potassium (AK, 46.88%), whereas the T2 treatment notably increased the content of hydrolyzable nitrogen (HN, 34.88%). Furthermore, the T2 treatment significantly enhanced the diversity of soil bacteria and fungi, particularly the bacterial Shannon index (1.49%) and fungal Chao1 (24.11%) and Shannon (7.73%) indices. In terms of microbial composition, compared to the CK, the T2 treatment enriched the relative abundance of beneficial bacterial genera (e.g., Sphingomonas, Methyloceanibacter, Rhizophagus) and reduced the relative abundance of pathogenic fungi (e.g., Fusarium). Additionally, T2 treatment increased the abundance of functional genes associated with nitrogen, phosphorus, and potassium, thereby promoting the cycling of soil nutrients. Overall, faba bean as a preceding crop was more beneficial for subsequent tobacco cultivation than fallow periods or garlic.},
}
@article {pmid41292709,
year = {2025},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the Drosophila melanogaster Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41292709},
issn = {2692-8205},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; R25 HG012702/HG/NHGRI NIH HHS/United States ; },
abstract = {The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two commercial DNA extraction kits (Qiagen and Zymo) and two lysis methods (manual pestle homogenization and bead-beating) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies, followed by bioinformatic analysis using EPI2ME for taxonomic classification and standard diversity pipelines. Our data revealed that extraction and lysis methods significantly influence microbial composition, with some protocols resulting in inflated richness in MCS samples. Pestle homogenization with the Qiagen kit yielded the highest bacterial species richness while maintaining consistent representation of both Gram-positive and Gram-negative taxa. These findings demonstrate that extraction methodology strongly affects microbial diversity estimates and emphasize the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.},
}
@article {pmid41248092,
year = {2025},
author = {Richie, T and Lee, STM},
title = {Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-18},
doi = {10.1159/000549457},
pmid = {41248092},
issn = {1421-9867},
abstract = {BACKGROUND: Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health. Having foundational knowledge of these interactions with the host is critical in understanding gastrointestinal health.<br><br>SUMMARY: This review discusses the importance of high-resolution study of the gut microbiota, which includes potential modern approaches for analyzing the gut microbiota and considers the challenges and aspects necessary for robust investigation of the gut microbiota. Here, we highlight the complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Furthermore, the review emphasizes the importance of microbial functions and products to host health outcomes in the context of inflammatory diseases.<br><br>KEY MESSAGES: Consideration for microbial functions and interactions with the gut immune system is critical for developing effective treatment strategies of inflammatory disorders. Employing high-resolution microbial techniques to investigate microbes with environmental relevance and community functions are a major challenge in the microbiome field. With new techniques and improvements on existing methodologies, investigating microbes at various community levels is feasible and becoming critical in understanding the community interactions with the host influencing the immune status and overall health outcomes.},
}
@article {pmid41391873,
year = {2025},
author = {Shen, Q and Mao, L and Shi, W and Wang, J and Ndjekadom, A and Bao, Y and Wang, X and Liu, Y and Yang, S and Ji, L and Shan, T and Zhang, W},
title = {Viral communities and identification of a parvovirus and two picornaviruses in geese with gout.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0456},
pmid = {41391873},
issn = {1347-7439},
abstract = {In recent years, an emerging infectious disease characterized by urate deposition in viscera and joints has outbreak in the goose farms of China, causing substantial economic losses. Although goose astrovirus (GoAstV) was believed to be the main causative pathogen, several studies have shown that co-infection with other viruses, such as goose parvovirus, alongside astrovirus, may exacerbate the disease condition. In our previous research, we isolated a goose astrovirus with a novel type of recombination that causes fatal gout in geese in Shanghai, China. By analyzing the viral community using viral metagenomics data of fecal, kidney and liver samples of geese with gout, we found that parvoviruses and picornaviruses occupied a substantial proportion, suggesting their potential involvement in the etiology of goose gout. To determine if there were other causative viruses present in these geese, fecal, kidney, and liver samples were deeply sequenced using viral metagenomics. The results indicated that goose parvovirus and picornavirus constituted the predominant part of all or partial viral communities. Subsequently, the genomes and genomic structures of two picornaviruses, as well as a parvovirus, were determined. Phylogenetic analysis revealed that this parvovirus, named dependoparvovirus_CH_SH01, belongs to the Parvovirinae subfamily within the family Parvoviridae, while the two picornaviruses were classified within the Megrivirus (megrivirus_CH_SH01) or Ludopivirus (ludopivirus_CH_SH01) genus within the Kodimesavirinae subfamily, respectively. Recombination analysis suggested that megrivirus_CH_SH01 was a potential recombinant virus between two megriviruses. Our study suggested that infections with viruses other than astrovirus may be associated with the occurrence of goose gout. Additionally, this work has enriched the virus sequence information for Megrivirus and picornaviruses.},
}
@article {pmid41391818,
year = {2025},
author = {Zhou, H and Gao, and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K},
title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.017},
pmid = {41391818},
issn = {2090-1224},
abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.<br><br>OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.<br><br>METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).<br><br>RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61&#x202f;% of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97&#x202f;% of the BGCs and 99.76&#x202f;% of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean&#x202f;=&#x202f;14.76, P&#x202f;=&#x202f;0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean&#x202f;=&#x202f;7.13, P&#x202f;=&#x202f;6.1e-05), Lamiaceae (mean&#x202f;=&#x202f;7, P&#x202f;=&#x202f;0.015), Ranunculaceae (mean&#x202f;=&#x202f;8.22, P&#x202f;=&#x202f;0.0053), and Rosaceae (mean&#x202f;=&#x202f;7.75, P&#x202f;=&#x202f;0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.<br><br>CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.},
}
@article {pmid41391639,
year = {2025},
author = {Yuan, F and Wang, L and Nguyen, SM and Shu, XO and Shrubsole, MJ and Wen, W and Cai, Q and Yu, D and Zheng, W},
title = {Plant-based diets, gut microbiota, blood metabolome, and risk of colorectal, liver and pancreatic cancers: results from a large prospective cohort study of predominantly low-income Americans.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101135},
doi = {10.1016/j.ajcnut.2025.101135},
pmid = {41391639},
issn = {1938-3207},
abstract = {BACKGROUND: Plant-based diets have been advertised for environmental and health benefits. Their effects on cancer risk, gut microbial and blood metabolomic profiles remain unclear.<br><br>OBJECTIVE: We investigated plant-based diets in relation to cancer incidence as well as gut microbial composition and blood metabolites in the Southern Community Cohort Study.<br><br>METHODS: Included in the analysis were 71,533 participants. Habitual dietary intake assessed at baseline (2002-2009) was used to derive overall plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Incident cancer cases were ascertained via linkage to state cancer registries and the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazards models after adjusting for potential confounders. We examined associations of the three indices with gut microbiota and blood metabolites using fecal metagenomic and blood metabolomic data from two subsets of 417 and 1,581 participants, respectively.<br><br>RESULTS: During a median follow-up time of 11.6 years, 783, 316, and 295 incident colorectal, liver, and pancreatic cancer cases were identified. High hPDI was related to a lower liver cancer risk (HR=0.67, 95% CI=0.45, 0.99 comparing extreme quartiles, Ptrend=0.03). No apparent association was observed for colorectal cancer (CRC) in the whole cohort. However, among 49,132 CRC screening-na&#xef;ve participants at baseline, PDI was inversely associated (HR=0.74, 95% CI=0.58, 0.96, Ptrend=0.01), while uPDI was positively associated (HR=1.39, 95% CI=1.06, 1.82, Ptrend=0.02) with CRC risk. No index was associated with pancreatic cancer. These diet indices were associated with microbial taxa and blood metabolites that have been implicated in the tumorigenesis of colorectum and liver.<br><br>CONCLUSIONS: A diet high in healthy plant foods and low in animal foods was inversely associated with liver cancer risk and with CRC risk among screening-na&#xef;ve participants. These associations may be partly mediated through gut microbiota and systemic metabolism.},
}
@article {pmid41391314,
year = {2025},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}
@article {pmid41391220,
year = {2025},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}
@article {pmid41391055,
year = {2025},
author = {An, X and Niu, S and Al, MA and Su, E and Chen, L and He, H and Wang, Y and Zhang, S and Yang, Y and Wang, S and Wen, Z and Xu, B and Ming, Y and Zhu, W and Zhao, Z and Wu, K and Yang, Y and Xie, W and He, Z and Yan, Q},
title = {Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).},
journal = {Advanced biotechnology},
volume = {3},
number = {4},
pages = {36},
pmid = {41391055},
issn = {2948-2801},
support = {2320004002504//Zhuhai Industry-University-Research Cooperation Project/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP002//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {The gut microbiome plays pivotal roles in the host's metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae-Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)-each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.},
}
@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30907-4},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
}
@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00858-9},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 AI151075/AI/NIAID NIH HHS/United States ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}
@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66567-1},
pmid = {41390665},
issn = {2041-1723},
support = {P30 ES007033/ES/NIEHS NIH HHS/United States ; R01AI162867//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 2127509//American Society for Engineering Education (ASEE)/ ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}
@article {pmid41390664,
year = {2025},
author = {Cao, Q and Deng, Z and Li, M and Zhu, S and Huo, Y and Dong, H and Aernouts, B and Psifidi, A and Xu, C},
title = {Integrated metagenomic and metabolomic analyses reveal tenacissoside G as a potential non-antimicrobial treatment for bovine endometritis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02264-x},
pmid = {41390664},
issn = {2049-2618},
support = {No. 2024B02016//the Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; 32125038//the National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; CARS-36//China Agriculture Research System/ ; },
abstract = {BACKGROUND: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.<br><br>RESULTS: A total of 40 Holstein dairy cows at 21&#xa0;days to 30&#xa0;days postpartum were assigned into heathy cows (n&#x2009;=&#x2009;15), subclinical endometritis cows (n&#x2009;=&#x2009;12) and clinical endometritis cows (n&#x2009;=&#x2009;13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.<br><br>CONCLUSION: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.},
}
@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07513-z},
pmid = {41390654},
issn = {1479-5876},
}
@article {pmid41387797,
year = {2025},
author = {Fu, W and Deng, ZW and Wang, P and Zhu, ZW and Xie, ZB and Li, YZ and Zhang, HQ and Yu, HY},
title = {HIV infection complicated with talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis and non-Hodgkin lymphoma: a complex case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1714},
pmid = {41387797},
issn = {1471-2334},
support = {2023JJ50447//the Natural Science Foundation of Hunan Province, CN/ ; 2024JJ7349//the Natural Science Foundation of Hunan Province, CN/ ; 2022YLT002//Hunan Provincial People's Hospital Medical Association Special Scientific Research Fund Project, CN/ ; QNJJ202503//Hunan University of Medicine General Hospital Youth Scientific Research Fund/ ; },
abstract = {BACKGROUND: Due to severe immunosuppression, human immunodeficiency virus (HIV) infected individuals are prone to multiple opportunistic infections and malignancies. This report presents a complex case of a 62-year-old male HIV patient who was diagnosed with co-infections of Talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis (HLH), and ultimately non-Hodgkin B-cell lymphoma. This case provides valuable insights for clinical diagnosis and treatment.<br><br>CASE SUMMARY: The patient was admitted with complaints of &#x201c;poor appetite, weight loss, and diarrhea for two weeks, accompanied by fever for four days.&#x201d; Upon admission, the patient was diagnosed with HIV infection, with a CD4&#x2009;+&#x2009;T-cell count of only 25/&#xb5;L. Pathological examination of cervical lymph node aspiration and metagenomic next-generation sequencing (mNGS) confirmed infections with Talaromyces marneffei, Mycobacterium tuberculosis, and Aspergillus species. During treatment, the patient developed persistent high fever, pancytopenia, decreased fibrinogen, and significantly elevated ferritin levels. Abdominal computed tomography (CT) revealed splenomegaly. Further bone marrow examination confirmed HLH, and symptoms improved after treatment with glucocorticoids and immunoglobulin. However, the patient&#x2019;s condition further deteriorated, and positron emission tomography computed tomography (PET-CT) along with repeat lymph node biopsy confirmed the diagnosis of non-Hodgkin B-cell lymphoma. Under combined antifungal, anti-tuberculosis, antiretroviral therapy (ART), and chemotherapy, the patient showed clinical improvement.<br><br>CONCLUSION: This case highlights the complexity and challenges in diagnosing and managing multiple opportunistic infections and malignancies in advanced HIV patients. It underscores the importance of multidisciplinary collaboration and provides valuable experience for the clinical management of HIV-related opportunistic infections and malignancies.},
}
@article {pmid41390498,
year = {2025},
author = {Freel, KC and Tucker, SJ and Freel, EB and Stingl, U and Giovannoni, SJ and Eren, AM and Rappé, MS},
title = {New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67043-6},
pmid = {41390498},
issn = {2041-1723},
abstract = {The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.},
}
@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07175-9},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.<br><br>METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906&#xa0;million paired-end reads per specimen.<br><br>RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.<br><br>CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}
@article {pmid41389850,
year = {2025},
author = {Petrov, VA and Schade, S and Laczny, CC and Hallqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids and a reduction of opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}
@article {pmid41389417,
year = {2025},
author = {Gong, L and Yao, L and Gu, L and Qu, Y and Gao, X and Wang, W and Huang, W and Peng, Y},
title = {Beyond traditional biological nutrient removal limits: achieving ultra-low effluent nitrogen via an anaerobic/Oxic/Anoxic (AOA) process in a pilot-scale system treating municipal wastewater.},
journal = {Water research},
volume = {290},
number = {},
pages = {125123},
doi = {10.1016/j.watres.2025.125123},
pmid = {41389417},
issn = {1879-2448},
abstract = {Developing low-cost and high-efficiency biological nutrient removal (BNR) process remains a major challenge in wastewater treatment plants (WWTPs). In this study, a pilot-scale anaerobic/oxic/anoxic (AOA) process with a treatment capacity of 100 m[3]/day was established and operated continuously for 335 days using real municipal wastewater. Without external carbon addition, the system achieved an average effluent total nitrogen (TN) concentration of 1.2 mg/L, with 90 % of values below 1.8 mg/L. Total phosphorus (TP) and chemical oxygen demand (COD) removal efficiencies reached 92.8 % and 94.1 %, respectively. A sufficient influent organic load (C/N ratio of 8.6) and extremely low nitrate concentrations enabled effective carbon storage in the anaerobic zone. Precise aeration control in the aerobic zone maintained low residual ammonium concentration, minimizing the consumption of internal carbon sources. Therefore, the anoxic zone in the AOA system fully utilized internal carbon sources for denitrification, resulting in ultra-low effluent total nitrogen concentrations. Metagenomic analysis revealed that multiple unclassified microorganisms, such as Unclassified Saccharimonadales, Unclassified Saprospiraceae, and Unclassified Myxococcales, encoded complete Gly and polyhydroxyalkanoate (PHA) metabolism as well as denitrification genes, and potentially contributed to endogenous denitrification. The AOA system overcame the nitrogen removal limitations of conventional processes by eliminating internal nitrate recirculation, while simultaneously reducing chemical dosing and energy consumption. This finding providing a scalable, energy-efficient, and economically viable strategy for next-generation WWTPs aiming to meet increasingly stringent discharge standards.},
}
@article {pmid41390369,
year = {2025},
author = {Yuan, X and Fang, M and Lan, W and Zhou, X and Yang, S and Wang, T},
title = {From urinary tract infection to deafness: community-acquired meningitis in an adult caused by hypervirulent Klebsiella pneumoniae-a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12340-0},
pmid = {41390369},
issn = {1471-2334},
abstract = {BACKGROUND: Hypervirulent Klebsiella pneumoniae (hvKP) is an emerging pathogen capable of causing lethal metastatic infections in healthy individuals. While liver abscesses are well-described, the urinary tract is increasingly recognized as a primary portal for hematogenous dissemination.<br><br>CASE PRESENTATION: A 46-year-old man with previously undiagnosed diabetes mellitus presented with community-acquired urinary tract infection (CA-UTI) that rapidly progressed to bilateral sensorineural deafness and meningitis. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified K. pneumoniae harboring hypervirulence genes rmpA and iucA. Blood, urine, and CSF cultures yielded an ESBL-negative, pansensitive hvKP strain. Brain MRI revealed septic emboli, consistent with hematogenous dissemination.<br><br>CONCLUSIONS: This case highlights the urinary tract as an underrecognized but lethal source of hvKP dissemination, particularly in diabetic patients. The rapid neurologic decline and permanent deafness highlight the need for early recognition and aggressive management. Virulence gene profiling should complement routine susceptibility testing. mNGS enabled rapid pathogen identification and guided targeted therapy. Clinicians must remain vigilant for CNS complications in diabetic patients with CA-UTI.},
}
@article {pmid41389890,
year = {2025},
author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW},
title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121035},
doi = {10.1016/j.jep.2025.121035},
pmid = {41389890},
issn = {1872-7573},
abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.<br><br>PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.<br><br>METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.<br><br>RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2, MAPK14, BCL2, TLR4, TNF, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.<br><br>CONCLUSION: SQFNXNP regulated the TNF/NOD&#x2012;like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.},
}
@article {pmid41389554,
year = {2025},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}
@article {pmid41389146,
year = {2025},
author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E},
title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy &amp; rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70082},
pmid = {41389146},
issn = {2042-6984},
support = {R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; },
}
@article {pmid41389008,
year = {2025},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics Alter Duodenal Immune Populations Upon Gluten Exposure in Mice: Implications for Non-Coeliac Gluten Sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {A growing proportion of the non-celiac population experience adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesised that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5mg/kg) or PBS-vehicle daily for 5-days. Mice were then treated with a 3mg wheat-gluten suspension, or vehicle, on days 4 and 5 before sacrifice on day 7. Duodenal immune cells were analysed by histology and flow cytometry, while the duodenal MAM and faecal microbiome were characterised via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in faeces, and resulted in altered microbial carbohydrate and lipid metabolism, compared to vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared to vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.},
}
@article {pmid41388903,
year = {2025},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo: and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf127},
pmid = {41388903},
issn = {1574-6941},
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterise the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulphur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognised species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}
@article {pmid41388659,
year = {2025},
author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G},
title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70214},
doi = {10.1111/1462-2920.70214},
pmid = {41388659},
issn = {1462-2920},
support = {C03X1802//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Biofilms/drug effects/growth &amp; development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; },
abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.},
}
@article {pmid41388485,
year = {2025},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical &amp; experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.<br><br>METHODS: B6 mice were given ethanol (EtOH; 5&#x2009;g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24&#x2009;h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96&#x2009;h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12&#x2009;h, 24&#x2009;h, and 192&#x2009;h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-&#x3b1;, IL-1&#x3b2;, P2Y12, ITG&#x3b2;2, and &#x3b1;7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.<br><br>RESULTS: Data revealed increased TNF-&#x3b1; expression in the Amg, Hyp, and NAc and increased IL-1&#x3b2; expression in the Amg and NAc, 12&#x2009;h after the first EtOH injection. &#x3b1;7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24&#x2009;h after the third EtOH dose, compared to the control group. &#x3b1;7nAChR expression in the Hyp was observed at 2&#x2009;min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24&#x2009;h after the third EtOH dose. ITG&#x3b2;2 showed an increasing trend in the Amg at 12&#x2009;h after the first dose, followed by a significant reduction at 24&#x2009;h, and 192&#x2009;h after the third dose. 16S rRNA sequencing revealed a significant difference in &#x3b2;-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.<br><br>CONCLUSION: This study showed that brain inflammation, indicated by &#x3b1;7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}
@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02272-x},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-33245S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.<br><br>RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the&#xa0;genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.<br><br>CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}
@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67388-y},
pmid = {41388019},
issn = {2041-1723},
support = {K08 AI123494/AI/NIAID NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}
@article {pmid41387926,
year = {2025},
author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H},
title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02200-z},
pmid = {41387926},
issn = {2049-2618},
support = {32192463//The Major Program of National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.<br><br>RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.<br><br>CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.},
}
@article {pmid41387788,
year = {2025},
author = {Zhu, H and Wu, W and Ran, Y and Cai, J and Wu, W and Zhao, Y and Zeng, Y and Hou, C and Tian, Y and Shen, H and Zhang, Y and Peng, B and Zheng, K and Gao, Y and Li, X},
title = {Central nervous system infection by Angiostrongylus cantonensis in children: experience from Guangdong, China.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1713},
pmid = {41387788},
issn = {1471-2334},
mesh = {Humans ; *Angiostrongylus cantonensis/genetics/isolation &amp; purification ; Male ; Female ; China/epidemiology ; *Strongylida Infections/diagnosis/parasitology/epidemiology/cerebrospinal fluid ; Infant ; Retrospective Studies ; Child, Preschool ; Animals ; Child ; High-Throughput Nucleotide Sequencing ; Adolescent ; *Central Nervous System Infections/parasitology/epidemiology/diagnosis/cerebrospinal fluid ; Metagenomics ; },
abstract = {BACKGROUND: Angiostrongylus cantonensis (A. cantonensis)-induced central nervous system (CNS) infection is a rare parasitic disease. Although global incidence is rising, pediatric cases remain underrecognized. This study aimed to characterize clinical features and evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) in children.<br><br>METHODS: We retrospectively analyzed pediatric CNS angiostrongyliasis cases admitted to a national neurology center in Guangdong, China, between 2017 and 2024.<br><br>RESULTS: A total of 22 pediatric patients were enrolled (median age 1.8 years; male: female&#x2009;=&#x2009;14:8). Most cases (68.2%) began between June and October; 45.5% had confirmed or probable exposure. Fever was the most common symptom (77.2%), followed by somnolence or lethargy (63.6%) and vomiting (59.1%). No patients reported neck stiffness or hyperesthesia. All patients showed peripheral eosinophilia (median peak 24.0%, IQR 16.0%-36.0%) and cerebrospinal fluid (CSF) pleocytosis. The initial CSF eosinophil percentage exceeded 10% in 10/22 patients (45.5%), and this increased in 7/22 patients (31.8%) during follow-up. Median peak CSF eosinophil percentage was 17.2% at day 18. Among 10 patients tested for CSF cytokines, 90.0% had elevations, with IL-6 being the most common and associated with higher CSF eosinophil percentages. Serum and CSF IgG against A. cantonensis were positive in 44.4% and 46.7%, respectively. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid was performed in 18 of the 22 patients, and A. cantonensis was identified in all tested cases (18/18, 100%), including four who were seronegative. The median mNGS read counts of A. cantonensis were 2,453 (IQR 353.5-28,641.75), which were not significantly correlated with CSF eosinophil percentages, white blood count, or protein levels. Brain magnetic resonance imaging abnormalities (81.8%) included leptomeningeal enhancement (45.5%), ventricular enlargement (40.9%), and cortical lesions (31.8%). Electroencephalogram was abnormal in 54.5%, mainly showing slowing (50.0%) or epileptiform activity 9.1%. Albendazole was used alone in 13.6% of patients, while 86.4% received combined therapy with corticosteroids. Of the 20 patients with follow-up (median 2.5 months), all recovered clinically and radiologically without relapse or sequelae.<br><br>CONCLUSION: Pediatric CNS angiostrongyliasis in Guangdong primarily affects rural children during summer-autumn. Clinical signs may be nonspecific. mNGS outperformed serology, especially in early or seronegative cases. Most patients had favorable short-term outcomes.},
}
@article {pmid41387706,
year = {2025},
author = {Bonnet, N and Capeding, MR and Siegwald, L and Garcia-Garcera, M and Desgeorges, T and Tytgat, HLP and Krattinger, LF and Lebumfacil, J and Phee, LC and Moll, JM and Gudjonsson, A and Rodriguez-Garcia, P and Baruchet, M and Feige, JN and Jankovic, I and Chen, Y and Egli, D and Horcajada, MN},
title = {A young child formula with Limosilactobacillus reuteri and GOS modulates gut microbiome and enhances bone and muscle development: a randomized trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66930-2},
pmid = {41387706},
issn = {2041-1723},
abstract = {In this randomized, double-blind controlled trial, 182 Filipino children aged 2-3 years received either an experimental young child formula (EYCF) containing a combination of Limosilactobacillus reuteri DSM 17938 and galacto-oligosaccharides (GOS; n = 91) or a minimally fortified milk (CM; n = 91) for 6 months. Primary outcome was tibia speed of sound and secondary outcomes were muscle strength, blood vitamin D levels, bone turnover markers, gut microbiota, fecal calcium fatty acid soaps and gastro-intestinal tolerance. Compared to CM, those in the EYCF group showed increased tibia speed of sound after 3 and 6 months. The intervention remodeled the stool microbiome composition, assessed by shotgun metagenomics, with enrichment of L. reuteri and higher bifidobacteria presence in the EYCF group. Increased L. reuteri abundance after 6 months of EYCF consumption associates with higher bone quality and muscle strength. Stool metabolomics show 45 metabolites modulated by EYCF consumption and associated to microbiome compositional changes, leading to enrichment of tryptophane and indole metabolism. In summary, consumption of EYCF containing a L. reuteri + GOS synbiotic improves musculoskeletal development in toddlers via modulation of microbiota composition and function. These results provide insights on gut-musculoskeletal crosstalk during early life. Clinicaltrial.gov NCT04799028.},
}
@article {pmid41387678,
year = {2025},
author = {Xin, G and Wang, D and Zhang, X and Cen, Q and Peng, M and Liao, Y and Wang, J and Le, S and Cheng, J and Wu, WC and Hou, X and Luo, G and Gou, Q and Kong, J and Pan, Z and Li, D and Gan, S and Chen, A and Zhao, H and Shi, P and Ren, Z and Zhao, W and Liu, J and Jia, P and Sun, C and Lin, W and Wu, J and Kuang, G and Chen, J and Li, J and Holmes, EC and Deng, Z and Shi, M},
title = {Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66462-9},
pmid = {41387678},
issn = {2041-1723},
support = {2022A1515011854//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 82341118 and 32270160//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Small mammals harbor a diverse array of potentially zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viruses, with limited attention directed to bacterial and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome-defined as the set of microorganisms infecting the host-across 2408 individual samples, representing lung, spleen, and gut from 858 animals in Guangdong province, China, considering the impact of host species, tissue, season, and geographic location on pathogen diversity. We identified 76 potential pathogen species, comprising 29 RNA viruses, 12 DNA viruses, five bacteria, and 30 eukaryotic pathogens, including 33 that are newly discovered. Distinct tissue tropisms were identified, suggesting varied transmission routes. Individual animals carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Total pathogen richness was largely influenced by geographic region, followed by host species and season, while zoonotic pathogen richness was primarily driven by host species. Collectively, these data provide insights into the structure of the pathogen infectome and the drivers of pathogen diversity and transmission in these key mammalian disease reservoirs.},
}
@article {pmid41387551,
year = {2025},
author = {Kelsey, C and Moulder, R and Yancey, H and Prescott, S and McCulloch, JA and Trinchieri, G and Dreisbach, C and Alhusen, J and Grossmann, T},
title = {Bidirectional relations between the maternal and infant gut microbiome and behavior.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41387551},
issn = {1530-0447},
abstract = {BACKGROUND: An infant's mother is one of the first sources of neonatal microbial colonization, and infant-maternal dyad microbial variations have been linked to childhood behavioral traits and mental health outcomes. However, how the gut microbiome influences mental health, including potential bidirectional relations between mother and child, remains poorly understood.<br><br>METHOD: Using metagenomic sequencing and behavioral questionnaires, we examined within-person and between-person (mother-infant dyad) associations between the gut microbiota and behavior across the first year of postnatal life (N&#x2009;=&#x2009;121 dyads; N&#x2009;=&#x2009;514 stool samples).<br><br>RESULTS: There were rapid changes in taxa diversity and gut microbiota composition for infants, whereas the maternal microbiome remains relatively constant. Gut microbes and functional terms (e.g., antibiotic resistance genes and virulence factors)&#xa0;were associated with infant temperament but not maternal depression symptoms. Whereas maternal depression was not associated with any maternal taxa or functional terms.<br><br>CONCLUSIONS: Our findings provide evidence for complex within- and between-person relations between maternal and infant gut microbiomes and behavioral traits.<br><br>IMPACT: How the gut microbiome influences maternal mental health and infant behavior remains poorly understood. We measured mothers' and infants' gut microbiota composition and behavior across the first year of the infant's life. Individual taxa from the infant, but not the maternal, gut were associated with infant behavioral temperament. Our findings provide evidence for complex bidirectional gut-behavior associations between mothers and infants.},
}
@article {pmid41387397,
year = {2025},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11003},
pmid = {41387397},
issn = {2041-1723},
support = {2020-03545//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2024-04942//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-06250//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; ALTF 740-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Phylogeny ; *Caulobacter crescentus/genetics/classification ; *Phototrophic Processes/genetics ; Biological Evolution ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here, we establish an evolutionary and ecological context for the model organism Caulobacter crescentus-an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the phylogenetic relatedness and genetic potential of hundreds of Caulobacterales species, we reveal substantial diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light on the evolution of fundamental prokaryotic features.},
}
@article {pmid41386833,
year = {2025},
author = {Sarkar, A and Patra, RK and Muthaiyan, M and Mallik, A},
title = {A metagenomic exploration of microbial distribution among the pond sediment, shrimp (Penaeus monodon) tissue and pond water: A special focus on nutrient cycling and shrimp viral pathogens.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {23},
number = {4},
pages = {100568},
doi = {10.1016/j.jgeb.2025.100568},
pmid = {41386833},
issn = {2090-5920},
abstract = {Penaeus monodon, a major shrimp species cultivated in Eastern Asia, has faced setbacks in aquaculture due to disease outbreaks. Metagenomic studies offer insights into the pond microbiome, revealing its critical roles in nutrient cycling, water quality, and disease control. This study investigated microbial communities in sediment, water, and shrimp samples from an aquaculture pond in Chaital, West Bengal, India. Shotgun metagenomic sequencing and bioinformatics analyses were used to assess taxonomic and functional profiles, focusing on nutrient cycling genes and viral populations. Sediments showed the highest microbial diversity, contributing to organic matter decomposition and ecological stability. Water microbes played roles in oxygenation and pathogen suppression, while shrimp tissues hosted microbes aiding digestion and immunity. Pathogenic viruses, especially Whispovirus (White Spot Syndrome Virus), dominated shrimp tissues. Functional gene analysis identified key pathways in carbon, nitrogen, and sulfur cycling. Integrating water quality data with microbiome profiles could help identify bioindicators and predict pathogen risks.},
}
@article {pmid41386129,
year = {2025},
author = {Bai, H and He, LY and Yadav, S and Gao, FZ and Liu, YS and Smidt, H and Ying, GG},
title = {Phages and plasmids mediate antibiotic resistance gene transfer in urban airborne bacteria.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140779},
doi = {10.1016/j.jhazmat.2025.140779},
pmid = {41386129},
issn = {1873-3336},
abstract = {Airborne antibiotic resistance genes (ARGs) pose emerging public health risks, particularly in urban settings, yet their dissemination mechanisms remain unclear. Here we cultured airborne bacteria from diverse urban environments and performed metagenomic sequencing to reconstruct 931 non-redundant metagenome-assembled genomes (MAGs), integrating horizontal gene transfer (HGT) detection, machine learning, and causal inference analyses. We identified hospitals, pharmaceutical factories, and railway stations as major sources of mobile ARGs. Both plasmids and phages actively mediate ARG transfer, promoting gene dissemination across broad phylogenetic distances. Machine learning revealed key phage functional modules related to structure, host attachment, lysis, DNA entry, and regulation that facilitate virus-mediated HGT, with synergistic interactions observed between plasmids and phages. These findings elucidate the dynamic resistome and mobility potential of metabolically active airborne bacteria, informing environmental surveillance and mitigation strategies to address airborne antimicrobial resistance within the One Health framework.},
}
@article {pmid41387308,
year = {2025},
author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R},
title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17747},
doi = {10.1002/advs.202517747},
pmid = {41387308},
issn = {2198-3844},
support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; },
abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.},
}
@article {pmid41387121,
year = {2025},
author = {Ji, Y and Liu, X and Zhao, S and Zhou, S and Yang, Y and Zhang, P and Shi, Y and Qin, W and Zhu, G and Zhu, Y and Gao, Y and Jiang, J and Wang, B},
title = {Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e09416},
doi = {10.1002/advs.202509416},
pmid = {41387121},
issn = {2198-3844},
support = {U22A20590//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; 42477318//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; 2025YFE0103900//National Key R&amp;D Program of China/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; BX20240168//China National Postdoctoral Program for Innovative Talents/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
abstract = {Patescibacteriota, also known as Candidate Phyla Radiation (CPR), is a diverse clade of ultra-small bacteria with an epibiotic lifestyle. Despite their ubiquity across diverse ecosystems and ecological importance in microbial networks, the global distribution of Patescibacteriota and functional interactions with their host organisms remain largely unknown. Here, by leveraging comprehensive Patescibacteriota genomic resources and global multi-habitat metagenomic datasets, it is demonstrated that ribosomal protein S3 (rpS3) as a reliable phylogenetic marker, enabling accurate recovery of Patescibacteriota diversity from short-read metagenomes. Using this framework, extensive taxonomic diversity and pronounced community heterogeneity are uncovered across eight ecosystems. Through network analysis and genome-wide functional screening, habitat-specific co-occurrence patterns are also revealed between Patescibacteriota and host-associated bacteria, especially potential functional synergies mediated by metabolic pathway cascades. Notably, Patescibacteriota-encoded NirK may assist sulfate-reducing bacteria in resisting nitrite stress, while NorB can mitigate nitric oxide toxicity for complete ammonia-oxidizing bacteria. Taken together, this study highlights the underappreciated diversity of Patescibacteriota and elucidates its important role in supporting host metabolism through complementary biochemical functions, offering new insights into its ecological significance and evolutionary adaptations in the global ecosystem.},
}
@article {pmid41386031,
year = {2025},
author = {Shu, M and Xue, H and Yang, Y and Zhang, X and Li, S and Bian, T and Yuan, K and Xu, C},
title = {Microbial-enzyme co-fermentation of low-grade tobacco: Metagenomics and metabolomic insights into flavor formation.},
journal = {Enzyme and microbial technology},
volume = {194},
number = {},
pages = {110803},
doi = {10.1016/j.enzmictec.2025.110803},
pmid = {41386031},
issn = {1879-0909},
abstract = {Microbial-enzyme co-fermentation effectively enhances the quality of low-grade tobacco leaves quality, but the underlying mechanisms of flavor formation remain unclear. This study investigated the dynamics and relationships of microbial communities and volatile aroma metabolites during low-grade tobacco leaves fermentation through metagenomics and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that during microbial-enzyme co-fermentation, the tobacco leaves fermented for four days (D4) exhibited the highest levels of total sugars and reducing sugars, the peak total content of aroma metabolites, and the best sensory quality. Pseudomonadota, Bacillota, and Ascomycota were dominant microorganisms during fermentation. During the initial stage (D1-D4), Saccharomyces was the dominant genus, which was subsequently displaced by Pantoea at D5. This microbial succession coincided with a decline in sensory quality, indicating its crucial role in shaping flavor evolution during co-fermentation. During microbial-enzyme co-fermentation process, a total of 46 volatile metabolites were detected in low-grade tobacco leaves. Among them, seven esters with high variable important in projection values and strong microbial correlations were identified as characteristic aroma metabolites, including ethyl phenylacetate, benzyl acetate, phenylethyl acetate, ethyl myristate, ethyl palmitate, ethyl oleate, and methyl linolenate. Gene function annotation revealed carbohydrate metabolism was the most abundant, followed by amino acid metabolism. Spearman correlation analysis elucidated the formation mechanism of characteristic ester metabolites. Specifically, short-chain esters correlated with glycerolipid and amino acid metabolism, while long-chain esters linked to glycolysis and fatty-acid biosynthetic pathways.},
}
@article {pmid41385957,
year = {2025},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
doi = {10.1016/j.psj.2025.106177},
pmid = {41385957},
issn = {1525-3171},
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}
@article {pmid41385764,
year = {2025},
author = {Yang, H and Yu, Y and Cui, R and Zhang, Q and Chen, B and Zhang, Z and Xu, N and Sun, L and Lu, T and Qian, H},
title = {Environmental and Microbial Drivers of Global Rhizosphere Resistome Assembly.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11060},
pmid = {41385764},
issn = {1520-5118},
abstract = {Soil serves as a critical reservoir for antibiotic resistance genes (ARGs); however, the ecological mechanisms driving ARG assembly at the plant-soil interface remain poorly understood. In this study, we analyzed 383 metagenomic samples and identified 4803 predicted ARGs, which were classified into two distinct clusters. The ARG-abundant cluster exhibited higher rhizospheric ARG abundance and diversity but posed a relatively lower health risk compared to the ARG-scarce cluster. Warm and nutrient-rich soils promote diverse resistomes shaped by complex microbial interactions, whereas humid environments promote more homogeneously predicted ARG compositions. Environmental variables such as the temperature and nitrogen were found to indirectly influence resistome composition by modulating microbial diversity. Notably, relatively high proportions of high-risk predicted ARGs were detected in grains and raw-eat vegetables, highlighting a potential threat to public health. Our findings underscore the importance of incorporating both environmental and microbial perspectives into agricultural practices to mitigate ARG dissemination in soil.},
}
@article {pmid41385625,
year = {2025},
author = {Kohtz, AJ and Nupp, S and Hatzenpichler, R},
title = {Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota.},
journal = {Science advances},
volume = {11},
number = {50},
pages = {eaea0936},
doi = {10.1126/sciadv.aea0936},
pmid = {41385625},
issn = {2375-2548},
mesh = {*Methane/metabolism ; *Archaea/metabolism/genetics/growth &amp; development/classification ; Phylogeny ; Metagenomics ; Genome, Archaeal ; },
abstract = {Methane is a potent greenhouse gas, largely produced by methanogenic archaea, contributing to Earth's dynamic climate and biogeochemical cycles. In the past decade, metagenomics revealed that lineages outside of the Euryarchaeota superphylum encode genes for methanogenesis. This was recently confirmed through the cultivation of two classes of methanogenic Thermoproteota. Thus far, all methanogens within the Thermoproteota are predicted or were shown to be methylotrophic. The only exception to this are the Nezhaarchaea, for which metagenomic predictions suggest they are CO2-reducing methanogens. Here, we demonstrate methanogenic activity in a third class of Thermoproteota, the Methanonezhaarchaeia. Contrary to genomic predictions for this class, we cultivated a methylotrophic species, Candidatus Methanonezhaarchaeum fastidiosum YNP3N, highlighting the importance of testing metagenomic hypotheses through experimentation. We investigate the metabolic diversity of Methanonezhaarchaeia, including metabolic modifications accompanying frequent loss of methanogenesis in this class. This highlights gaps in our understanding of the biochemistry, diversity, and evolution of thermoproteotal methanogens and their contributions to carbon cycling.},
}
@article {pmid41385173,
year = {2025},
author = {Othman, AA and Mohamed Zain, NI and Eshak, Z and Adman, MA and Abd Latif, Z and Aboshanab, KM and Ahmad, A},
title = {Diversity of necrophagous flies and microbiome profiling of Phumosia promittens as a rainforest health indicator.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01994-3},
pmid = {41385173},
issn = {2191-0855},
abstract = {Necrophagous flies play a critical role in decomposition and serve as bioindicators of environmental health and pollution. Malaysia's tropical rainforest ecosystems may host many necrophagous fly species, including unique blowflies and their associated bacteria. However, in many forest reserve areas, the diversity of these flies remains poorly studied. This study examines the diversity of necrophagous flies and their associated surface bacteria community, with a particular focus on Phumosia promittens (Walker in J Proc Linn Soc Lond Zool 4:90-96, 1859) in the Bangi Forest Reserve, Universiti Kebangsaan Malaysia. Sampling was conducted across three plots using baited traps, and collected flies were morphologically identified and processed under sterile conditions. Surface bacteria from P. promittens were isolated and analysed through metagenomic analysis targeting the 16S rRNA (V3-V4) amplicon sequencing gene to characterise their microbial communities comprehensively. Among 2,528 individuals collected, Chrysomya megacephala (Fabricius) was the most dominant species overall, while P. promittens was the most abundant among native forest species, suggesting their ecological adaptability and potential as a bioindicator of healthy rainforest. Shannon-Wiener and Simpson's diversity of flies in the study location were 0.67 ± 0.11 and 0.29 ± 0.06, respectively. Meanwhile, the Shannon-Wiener and Simpson's diversity of bacteria from P. promittens were 5.64 ± 0.70 and 0.96 ± 0.02, respectively. Bacterial microbiome analysis revealed the presence of core genera, including Wohlfahrtiimonas, Dysgonomonas, Vagococcus, and Ignatzschineria, which are implicated in both ecological symbiosis and public health concerns. These bacteria may contribute to nutrient cycling, such as heavy metals and antibiotics. Notably, several of these genera are emerging zoonotic pathogens with antimicrobial resistance, highlighting the dual role of necrophagous flies as ecosystem contributors and disease vectors. The findings underscore the importance of monitoring native fly species and their microbiota to assess the integrity of forest ecosystems and potential public health risks.},
}
@article {pmid41385155,
year = {2025},
author = {Nazaktabar, A and Khosravi, M},
title = {First detection and characterization of Bovine parvovirus 2 and Bopivirus A in a neonatal calf with diarrhea in Iran through metagenomic RNA-seq.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41385155},
issn = {1572-994X},
abstract = {Bovine parvovirus 2 (BoPV-2), officially classified as Ungulate copiparvovirus 1 by the ICTV, and Bopivirus A, a recently recognized picornavirus, are poorly characterized viruses sporadically reported in cattle worldwide. Here, we describe the first detection of BoPV-2 and Bopivirus A in Iran-and potentially the Middle East-through RNA-seq analysis of a diarrheic neonatal calf. Four BoPV-2 contigs (82-85% nucleotide identity; 91-100% amino acid identity) were identified, clustering within the Ungulate copiparvovirus 1 clade, while the Bopivirus sequence grouped with Chinese strains BoP8 and BoP9, supporting its classification within lineage A2. Both viruses were confirmed by phylogenetic analyses based on partial RdRp (3Dpol) and ORF regions. The concurrent detection of these viruses in a single calf suggests possible co-circulation in early-life gastrointestinal infections, highlighting the complexity of the calf virome. Notably, RNA detection of the DNA virus BoPV-2 in fecal material indicates potential intestinal replication and shedding, raising questions about its transmission dynamics. These findings expand the geographic range of BoPV-2 and Bopivirus A and underscore the value of metagenomic surveillance for uncovering under-characterized viral agents contributing to neonatal calf diarrhea.},
}
@article {pmid41384994,
year = {2025},
author = {Zhang, J and Liu, J and Bayani, A},
title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.},
journal = {Journal of cancer research and clinical oncology},
volume = {152},
number = {1},
pages = {8},
pmid = {41384994},
issn = {1432-1335},
mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.},
}
@article {pmid41384986,
year = {2025},
author = {Le, TT and Nguyen, HD and Dao, TK and Nguyen, HT and Nguyen, TQ and Do, TH and Truong, NH},
title = {Identification of endoglucanase-encoding genes from goat rumen bacterial metagenomes using homology- and motif-based approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {70},
pmid = {41384986},
issn = {1432-072X},
support = {CSCL08.04/25-26//Institute of Biology/ ; },
mesh = {*Goats/microbiology ; *Rumen/microbiology ; *Cellulase/genetics/metabolism/chemistry ; Animals ; *Metagenome ; *Bacteria/genetics/enzymology/classification/isolation &amp; purification ; *Bacterial Proteins/genetics/metabolism/chemistry ; Phylogeny ; Open Reading Frames ; Cellulose/metabolism ; Escherichia coli/genetics ; },
abstract = {The goat rumen harbors a dense and diverse microbial community that produces enzymes for degrading plant cell wall polysaccharides, representing a potential source of valuable enzymes for applications. In this study, we explored the diversity of endoglucanases from goat rumen bacterial metagenomes using homology- and motif-based approaches. HMM profiling identified 5,182 endoglucanase-encoding ORFs, whereas KEGG annotation (EC 3.2.1.4) detected 7,368 ORFs, with 2,902 shared between the two methods. Taxonomic assignment revealed Firmicutes and Bacteroidetes as the dominant phyla, followed by Fibrobacteres, Spirochaetes, and Lentisphaerae. At the genus level, Ruminococcus (Firmicutes) and Prevotella (Bacteroidetes) were dominant, followed by Butyrivibrio, Fibrobacter, and Treponema. Pfam domain analysis further revealed that the common endoglucanase domains, GH5 and GH9, exhibited a high degree of overlap (> 80%) between the two approaches. Notably, GH26 and GH8 were more frequently identified by HMM profiling, whereas KEGG-based mining revealed greater domain diversity. A candidate endoglucanase-encoding ORF was subsequently expressed in E. coli, and the recombinant protein was characterized. The enzyme displayed bifunctional activity on both cellulose (CMC, filter paper) and hemicellulose (xylan), with the highest activity toward CMC, and showed optimal activity at 50 °C and pH 4.0. Its activity was differentially affected by metal ions and chemical agents, and kinetic analysis revealed strong substrate affinity and high catalytic efficiency (Km = 0.8 mg/mL, Vmax = 186.12 U/mg). Overall, this study demonstrates complementary strategies for mining functional proteins from metagenomes and highlights the potential of goat rumen-derived endoglucanase for lignocellulose degradation in sustainable industrial applications.},
}
@article {pmid41384736,
year = {2025},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0136425},
doi = {10.1128/msystems.01364-25},
pmid = {41384736},
issn = {2379-5077},
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.<br><br>IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}
@article {pmid41384462,
year = {2025},
author = {Arfken, A and Mercante, J and Mattioli, M},
title = {Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70194},
doi = {10.1002/mbo3.70194},
pmid = {41384462},
issn = {2045-8827},
mesh = {*Salmonella/genetics/isolation &amp; purification/classification ; *High-Throughput Nucleotide Sequencing/methods ; Genome, Bacterial ; *Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; *Environmental Microbiology ; *Nucleic Acid Amplification Techniques/methods ; DNA, Bacterial/genetics ; },
abstract = {Detecting pathogens in environmental samples using molecular-based technologies can be challenging, particularly in low biomass environments or where pathogens represent a low percentage of the community. Multiple displacement amplification (MDA) is a whole genome amplification (WGA) method that has been developed for low biomass samples. However, there is a lack of information on how MDA could improve PCR and sequence-based detection and genomic characterization of pathogens in challenging environmental samples. In this study, MDA was evaluated on low template samples of the Salmonella LT2 isolate, a foodborne and waterborne environmental pathogen. MDA was also evaluated on a variety of low template mixed-microbial mock, environmental communities containing a range of Salmonella genome percentages to simulate different levels of Salmonella in the environment. Using MDA starting inputs of 1.8 × 10[4]-1.8 × 10[1] Salmonella LT2 genome copies, > 99% of the Salmonella genome was recovered following MDA at > 16X depth of coverage from as few as 500,000 merged, 250 bp paired-end reads. For the mock microbial communities, moderately high levels of genome abundance distortion were evident following MDA across all communities when compared to the expected compositions, which could not be attributed to either genome size or GC content alone. Overall, MDA may provide a useful method for increasing Salmonella detection sensitivity in low target environmental samples where downstream selective targeted applications such as real-time PCR or targeted amplicon sequencing are used, but MDA may not be appropriate for identification and detection of Salmonella when using untargeted, metagenomic sequencing.},
}
@article {pmid41384120,
year = {2025},
author = {Li, X and Guo, G and Shi, Q and Chen, Q and Li, L},
title = {Association study between intestinal microbiota dysbiosis in inflammatory bowel disease and the global disease burden growth trend.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1635242},
pmid = {41384120},
issn = {2296-858X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is a group of chronic intestinal inflammatory diseases. Its incidence and prevalence have been on the rise globally, imposing a heavy burden on patients' health and social medical resources. Intestinal microbiota dysbiosis is believed to play a crucial role in the occurrence and development of IBD, but the association between them and the global disease burden growth trend remains unclear.<br><br>METHODS: By searching the Global Burden of Disease (GBD) study database, we collected IBD disease burden data from 180 countries and regions between 1990 and 2023, including key indicators such as incidence, prevalence, mortality, and disability-adjusted life years (DALYs). Intestinal microbiota data were sourced from two parts: (1) Independent collection: A total of 20,000 healthy individuals and IBD patients were selected as research subjects from 180 countries and regions using a stratified random sampling method. Fecal samples (2-5 grams per person) were collected and immediately stored in a -80 &#xb0;C ultra-low temperature refrigerator to avoid changes in the microbial community structure; (2) Supplementary data from public databases: Published intestinal microbiota sequencing data of corresponding regions from 1990 to 2023 were extracted from the MGnify (https://www.ebi.ac.uk/metagenomics/), Human Microbiome Project (HMP), and GMrepo (https://gmrepo.humangut.info/) databases. The sample size for each country and region was no less than 500 to cover populations of different ages (18-70&#x202f;years), genders (male/female ratio approximately 1:1), and dietary habits (high-fiber diet, high-sugar and high-fat diet). Technologies like metagenomic sequencing and 16S rRNA gene sequencing were used to obtain data on the composition, abundance, and diversity of the intestinal microbiota of the corresponding regional populations. For metagenomic sequencing, the Illumina HiSeq or NovaSeq platform was used. Linear regression models, time-series analysis, and causal inference methods were applied to evaluate the correlation between intestinal microbiota dysbiosis and the growth trends of various disease burden indicators, and to explore the potential impact mechanisms.<br><br>RESULTS: The global incidence of IBD increased from 12.3 per 100,000 in 1990 to 25.6 per 100,000 in 2023, the prevalence rose from 396 per 100,000 to 523 per 100,000, and the DALY value also increased significantly (from 230 per 100,000 in 1990 to 380 per 100,000 in 2023). The average annual growth rates of the above indicators were 2.8% (95% CI: 2.5-3.1%, p <&#x202f;0.001), 1.0% (95% CI: 0.8-1.2%, p <&#x202f;0.001), and 1.5% (95% CI: 1.3-1.7%, p <&#x202f;0.001), respectively. Further analysis showed that intestinal microbiota dysbiosis was closely related to the growth of the disease burden. In regions with severe microbiota dysbiosis, the annual growth rate of the IBD incidence was 3.2 times higher than that in balanced regions (&#x3b2; =&#x202f;3.2, 95% CI: 2.8-3.6, p <&#x202f;0.001); when the average abundance of beneficial bacteria such as Bifidobacterium and Lactobacillus in the intestine decreased by 40% (relative to the average abundance of healthy populations) and the abundance of harmful bacteria such as Escherichia coli increased by 60%, the annual growth rate of IBD incidence in this region was as high as 8.5% (95% CI: 7.9-9.1%, p <&#x202f;0.001); in regions where the Shannon index decreased by 10%, the incidence of IBD increased by an average of 15% (&#x3b2; =&#x202f;0.15, 95% CI: 0.12-0.18, p <&#x202f;0.001). A positive correlation was observed between the degree of intestinal microbiota dysbiosis and disease severity (measured by DALYs): in regions where the intestinal F/B ratio deviated from the normal range by more than 30%, DALYs were 40% higher than those in regions with a normal ratio (&#x3b2; =&#x202f;0.40, 95% CI: 0.35-0.45, p <&#x202f;0.001); in regions where the content of short-chain fatty acids (SCFAs) decreased by 20%, DALYs increased by approximately 25% (&#x3b2; =&#x202f;0.25, 95% CI: 0.21-0.29, p <&#x202f;0.001). Among IBD patients with different severity levels in the Asian region, the abundance of specific bacterial genera related to inflammation regulation (e.g., Faecalibacterium) in the intestines of severe patients decreased by more than 50% compared with healthy populations, and their DALY values were 60% higher than those of mild patients (95% CI: 55-65%, p <&#x202f;0.001). Additionally, the SCFA levels of severe patients were significantly lower than those of mild patients and healthy populations (median SCFA level: 2.1&#x202f;mmol/L in severe patients; 4.5&#x202f;mmol/L in mild patients; 6.8&#x202f;mmol/L in healthy populations, p <&#x202f;0.001).<br><br>CONCLUSION: This study confirms a close association between intestinal microbiota dysbiosis in inflammatory bowel disease and the global disease burden growth trend. Intestinal microbiota dysbiosis can be used as a key indicator to predict the growth of the IBD disease burden, providing an important theoretical basis for formulating targeted prevention, control strategies, and treatment methods.},
}
@article {pmid41384118,
year = {2025},
author = {Bautista, J and Cardona-Maya, WD and Gancino-Guevara, K and López-Cortés, A},
title = {Reprogramming prostate cancer through the microbiome.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1690498},
pmid = {41384118},
issn = {2296-858X},
abstract = {Prostate cancer (PCa) is a major global public health challenge, driven by a multifactorial interplay of genetic, epigenetic, hormonal and environmental determinants. In recent years, the human microbiome has emerged as a critical and previously underappreciated contributor to PCa initiation, progression, and therapeutic response. Emerging high-resolution multi-omics studies have demonstrated that microbial communities across the gut, urinary tract and prostate form a functional axis that shapes immune surveillance, hormonal metabolism, inflammatory tone and epigenetic regulation. Dysbiosis in these compartments promotes chronic inflammation, modulates androgen receptor signaling, and produces bioactive metabolites, including short-chain fatty acids, that activate oncogenic IGF-1/MAPK/PI3K and NF-κB/JAK/STAT pathways. Cross-compartmental trafficking of bacterial taxa and metabolites reinforces tumor-promoting circuits, while specific commensals such as Akkermansia muciniphila enhance antitumor immunity and improve responses to androgen deprivation therapy. Importantly, microbiota-derived factors also modulate microRNA (miRNAs) expression and epigenetic signatures, thereby affecting tumor plasticity and resistance to therapy. These mechanistic insights have catalyzed interest in microbiome-based therapeutic approaches, including probiotics, prebiotics, fecal microbiota transplantation, dietary modulation and bacteriophage therapy, which hold promise for restoring eubiosis and enhancing treatment efficacy. Nevertheless, clinical translation remains limited by inter-individual variability and the need for well-designed, longitudinal studies integrating shotgun metagenomics, metabolomics and host-microbe interactomics. Overall, the prostate, urinary and gut microbiomes represent interconnected targets that may inform precision diagnostics and novel therapeutic strategies in PCa.},
}
@article {pmid41383742,
year = {2025},
author = {Bian, X and Xu, H and Li, J and Kuang, J and Shi, F and Li, X and Li, J},
title = {Integrated multi-omics reveals distinct maternal and neonatal gut microbial and metabolic signatures associated with small for gestational age status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668148},
pmid = {41383742},
issn = {1664-302X},
abstract = {INTRODUCTION: Children born small for gestational age (SGA) have an elevated risk of developing metabolic disorders in later life. However, the underlying gut microbiota and metabolomic alterations in SGA mother-infant dyads remain poorly understood.<br><br>METHODS: We performed an integrated analysis of fecal metagenomics, metabolomics, and short-chain fatty acids (SCFAs) profiling in 10 SGA and 10 appropriate for gestational age (AGA) mother-infant dyads at term. Taxonomic composition, microbial functional pathways, carbohydrate-active enzyme (CAZyme) profiles, differential metabolites, and metabolite pathway enrichment were systematically evaluated.<br><br>RESULTS AND DISCUSSION: SGA neonates exhibited reduced microbial richness (Chao1 index), distinct beta-diversity, and differential abundance of key bacterial species including increased Enterococcus faecalis and Escherichia coli. Functionally, SGA maternal subjects showed divergent profiles in CAZyme genes, with lower abundance of glycoside hydrolase family 13 subfamily 16, glycosyl transferase family 66, and carbohydrate-binding module family 6, and altered structural polysaccharide degradation capacity. Metabolomic profiling revealed significant perturbations in tryptophan metabolism pathways, notably enriched in kynurenine and taurine derivatives in SGA mother and neonates. Notably, SCFA profiles were disrupted, with increased butyrate in SGA mother and reduced propionate and isobutyrate in SGA neonates. Microbe-metabolite correlation networks revealed strong associations between SGA-specific bacterial taxa and fecal metabolites. In conclusion, our analysis identifies distinct features of the early fecal microbiome and metabolome within 48 h of birth in SGA neonates compared with AGA peers, reflecting differences in initial colonization and metabolism that warrant longitudinal follow-up.},
}
@article {pmid41383739,
year = {2025},
author = {Ni, B and Gong, Y and Li, B and Qiu, L and He, K and Guo, J and Fang, H and Gao, M and Chen, M and Wei, C and Sun, W and Liu, B and Li, M and Wang, S and Xu, L},
title = {Mesenchymal stem cells alleviate pulmonary fibrosis and gut microbiota dysbiosis in systemic sclerosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1635809},
pmid = {41383739},
issn = {1664-302X},
abstract = {INTRODUCTION: Mesenchymal stem cells (MSCs) have shown the potential to alleviate systemic sclerosis (SSc) tissue fibrosis. However, our knowledge of the effects of MSCs on gut microbiota remains limited.<br><br>METHODS: In this study, we employed a bleomycin induced SSc model to investigate the effects of MSCs on pulmonary fibrosis and gut microbiota in SSc using transcriptomic, microbial metagenomic, and metabolomic analyses.<br><br>RESULTS: Our results indicated that MSCs treatment alleviated lung injury in SSc mice. Transcriptomic analysis suggested that the therapeutic effects of MSCs were primarily associated with fatty acid metabolism, PPAR signaling pathway, and AMPK signaling pathway. Furthermore, MSCs restored the relative abundance of microbial taxa, including Bacteroidota, Actinomycetota, and Akkermansia muciniphila, and improved the gut microbiota dysbiosis induced by SSc. Metabolomic data showed that MSCs modulated the dysregulation of trimethyllysine, cholesteryl sulfate expression, and nicotinate and disturbances in nicotinamide metabolism caused by SSc. Correlation analysis demonstrated significant associations among transcriptomic, microbiomic, and metabolomic datasets.<br><br>DISCUSSION: Collectively, our findings indicate that MSCs may alleviate SSc pulmonary fibrosis by reshaping the gut microbiota, thereby offering novel scientific insights for the investigation of clinical treatment targets for SSc.},
}
@article {pmid41383738,
year = {2025},
author = {Chen, G and Wiegand, C and Willett, A and Herr, C and Müller, R and Bals, R and Kalinina, OV},
title = {Comparative metagenomic analysis on COPD and health control samples reveals taxonomic and functional motifs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1636322},
pmid = {41383738},
issn = {1664-302X},
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive lung condition marked by persistent respiratory symptoms and airflow limitation and significantly affects global health. The intricate relationship between COPD and the lung microbiome has garnered attention, with metagenomic analyses revealing critical insights into microbial community dynamics and their functional roles. In this study, we conducted a comprehensive metagenomic analysis comparing throat samples from COPD patients (n = 26) and healthy controls (n = 32) derived from a large cohort analyzed at the Saarland University Hospital. Taxonomic profiling and differential abundance analysis indicated a significant reduction of the microbial diversity in COPD patients, with notable overrepresentation of pathogenic bacteria, such as Veillonella parvula (NCBI:txid29466), Streptococcus gordonii (NCBI:txid1302), Scardovia wiggsiae (NCBI:txid230143), as well as a less stable microbiome composition than in healthy individuals. Functional profiling identified alterations in metabolic pathways implicating microbial dysbiosis in disease progression. The study also highlighted enrichment of inflammation-related pathways in COPD samples, emphasizing the microbiome's role in inflammatory processes. Comparative analysis of bronchoalveolar lavage (BAL) and throat samples collected from the same 11 individuals further underscored distinct microbial compositions across respiratory tract regions, suggesting spatial variability in microbial communities. Metagenomic approaches including analysis of metabolic pathways showed significant alteration of the microbiome of the lung in COPD.},
}
@article {pmid41383638,
year = {2025},
author = {Zhao, Z and Li, J and Peng, Z and Luo, X and Duan, L and Lin, Z and Wang, P and Li, W and Jiang, H},
title = {Light-driven diel oscillations in microbial metabolism underpin estuarine biogeochemical resilience.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf216},
pmid = {41383638},
issn = {2730-6151},
abstract = {Diel light cycles profoundly influence estuarine biogeochemical processes, yet the mechanistic responses of planktonic prokaryotic communities to these rhythmic cues remain incompletely understood. This study employed an integrative multi-omics approach-combining high-frequency sampling, 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-to elucidate diel dynamics in microbial diversity, interaction networks, and metabolic functions in the Pearl River Estuary. The results revealed significant temporal partitioning in microbial organization: nocturnal communities exhibited higher α-diversity and formed more densely connected co-occurrence networks, indicative of enhanced heterotrophic processes, whereas daytime assemblages were dominated by Cyanobacteria (particularly Synechococcales) with enriched pathways for photoautotrophic carbon fixation and nitrogen assimilation. Metabolic profiling further demonstrated distinct diel oscillations in key biogeochemical processes, including daytime enhancement of Calvin cycle-mediated CO2 fixation and nocturnal upregulation of dissimilatory sulfate reduction. Network topology analysis showed that nighttime communities displayed increased clustering coefficients and reduced path lengths, suggesting more efficient resource utilization under dark conditions. Through reconstruction of 786 metagenome-assembled genomes, we identified Cyanobiaceae as key mediators of diel carbon and nitrogen transformations, while diverse heterotrophic taxa facilitated nighttime nutrient remineralization. This study provides mechanistic insights into how light-driven diel oscillations shape microbial metabolic partitioning and ecological interactions, advancing our understanding of the temporal dynamics that underpin biogeochemical resilience in estuarine ecosystems.},
}
@article {pmid41383636,
year = {2025},
author = {Laperriere, SM and Minch, B and Weissman, JL and Hou, S and Yeh, YC and Ignacio-Espinoza, JC and Ahlgren, NA and Moniruzzaman, M and Fuhrman, JA},
title = {Phylogenetic proximity is a key driver of temporal succession of marine giant viruses in a five-year metagenomic time-series.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf217},
pmid = {41383636},
issn = {2730-6151},
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs), also called giant viruses, are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding "rules" underpinning their community dynamics over time. We leveraged a five-year monthly coupled metagenomic-viromic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize their temporal population dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and nonseasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic, showing strong seasonal signals. The Imitervirales group had the highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is an important driver of the temporal niche partition of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. We also identified distinct functional content and possible interactions of two major NCLDV orders with diverse eukaryotes in the study environment- revealing their putative hosts that include both primary producers and heterotrophic grazers. Together, our multiannual time-series study captures diverse temporal patterns among marine giant viruses and demonstrates that evolutionary history plays a key role in shaping their temporal niche partitioning.},
}
@article {pmid41383301,
year = {2025},
author = {Gauthier, J and Mohammadi, S and Kukavica-Ibrulj, I and Boyle, B and Landgraff, C and Goodridge, L and White, K and Chapman, B and Levesque, RC},
title = {Leveraging artificial intelligence community analytics and nanopore metagenomic surveillance to monitor early enteropathogen outbreaks.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1675080},
pmid = {41383301},
issn = {2296-2565},
mesh = {Humans ; Quebec/epidemiology ; *Metagenomics/methods ; *Disease Outbreaks ; *Artificial Intelligence ; Wastewater/microbiology ; *Nanopores ; *Salmonella Infections/epidemiology ; *Foodborne Diseases/epidemiology ; },
abstract = {Foodborne enteric infections are a major public health and economical burden, yet their surveillance often relies on latent indicators that delay containment efforts by several days and weeks. Conversely, whole metagenome shotgun sequencing of communal wastewater allows continuous monitoring of enteric pathogens. Spikes in abundance can be observed several weeks before the first case reports emerge. In addition, AI-driven social media mining, already in use for public opinion analytics, could be repurposed for predicting outbreaks at the community level by predicting the number of people experiencing symptoms in the population given their social media activity. Here we report how AI-driven community analytics and high-throughput long-read metagenomic surveillance of communal wastewater microbiota were combined to monitor non-typhoidal salmonellosis in Quebec City, Canada, from August 2023 to February 2024. Both approaches indicated similar fluctuations over time for: (i) people experiencing salmonellosis symptoms, and (ii) Salmonella enterica relative abundance in wastewater, with predicted cases leading metagenomic peaks by a week. Moreover, both approaches detected a maximum around September 13th, 2023, 5 weeks before a Salmonella food recall for the Quebec and Ontario provinces was made by the Public Health Agency of Canada. We therefore suggest that continuous AI-driven analytics and wastewater metagenomics monitoring could become part of a nationwide surveillance pipeline from the community scale to the molecular level.},
}
@article {pmid41382244,
year = {2025},
author = {Bae, IH and Kim, H and Kim, SM and Lee, YH},
title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02292-7},
pmid = {41382244},
issn = {2049-2618},
support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.<br><br>RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.<br><br>CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.},
}
@article {pmid41382192,
year = {2025},
author = {Xue, R and Li, Z and Qin, W and Wang, Y and Zhao, K and Liu, L and Bai, Y},
title = {Prolonged grazing reduces the diversity and weakens virus-host links of metagenome-assembled viral community in acidic karst soil.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-025-02489-0},
pmid = {41382192},
issn = {1741-7007},
support = {41907025//National Natural Science Foundation of China/ ; 32160337//National Natural Science Foundation of China/ ; 2025ZNSFSC0202//Natural Science Foundation of Sichuan Province/ ; },
abstract = {BACKGROUND: Soil viruses are fundamental yet often overlooked components of terrestrial ecosystems, where they profoundly influence microbial diversity, community assembly, and biogeochemical cycling through predator-prey dynamics and the carriage of auxiliary metabolic genes (AMGs). However, the impact of human-driven land use change on viral communities and their functional potential remains poorly understood.<br><br>RESULTS: In this study, we analyzed viral diversity, virus-host linkage, and functional profiles of AMGs across different land management regimes in acidic karst soil after reclamation. The results showed that both bacterial and viral communities significantly differ across the four land management regimes, which are unused land, grazing pastureland, abandoned pastureland, and fertilized grazing pastureland. Grazing led to a lower viral diversity, a decrease in lysogenic viral abundance, and fewer virus-host linkages. The diversity and function of AMGs were also significantly affected by land management regimes, with grazing leading to a reduction in both AMGs diversity and relative abundance. Furthermore, both the bacterial community and soil physiochemical properties were essential factors that shaped viral diversity and lifestyle.<br><br>CONCLUSIONS: Overall, our findings indicate that inappropriate land use (long-term grazing) disrupts the virus-host balance, thereby altering the functional profiles of the soil viral community.},
}
@article {pmid41381916,
year = {2025},
author = {Li, R},
title = {Metagenomic editing integrates large DNA sequences into gut bacteria in vivo.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-025-02966-5},
pmid = {41381916},
issn = {1546-1696},
}
@article {pmid41381751,
year = {2025},
author = {Tabe, C and Motooka, D and Fujita, T and Makiguchi, T and Taima, K and Tanaka, H and Itoga, M and Ishioka, Y and Akita, T and Ishidoya, M and Chubachi, K and Fukushima, T and Tanaka, Y and Odagiri, H and Kameyama, Y and Kobori, Y and Tasaka, S and Fujii, H},
title = {The gut microbiota as a potential biomarker in patients with EGFR-mutant lung cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31225-5},
pmid = {41381751},
issn = {2045-2322},
abstract = {Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are highly effective against EGFR-mutant non-small cell lung cancer (NSCLC); however, identifying biomarkers that predict prognosis and adverse events is necessary. Although the gut microbiota is considered to be a biomarker for NSCLC without mutations, no studies have examined its potential as a biomarker for EGFR-mutant NSCLC. Here, we investigated the association between gut microbiota composition and diarrhea, a common side effect caused by EGFR-TKIs. In addition, we examined the association between the efficacy of EGFR-TKIs and the gut microbiota. A total of 21 NSCLC patients with EGFR mutations were enrolled. Fecal samples were collected prior to EGFR-TKI treatment and 16S rRNA metagenome sequencing was performed to evaluate the microbiota profile. In addition, α-diversity, β-diversity, and Linear discriminant analysis Effect Size (LEfSe) analyses were performed. The α-diversity of the gut microbiota was higher in patients with grade 0-1 diarrhea than in those with grade 2-3 diarrhea (Shannon, p = 0.0367). In terms of β-diversity, there was a significant difference in the best overall response between patients with a partial response (PR) to EGFR-TKIs and those with stable disease (SD)/progressive disease (PD) (weighted p = 0.041). Analysis of microbial composition revealed an increased abundance of Ruminococcus in the PR group. In patients taking EGFR-TKIs, a higher α-diversity may be associated with less severe diarrhea. In addition, a high abundance of Ruminococcus may be a potential biomarker for predicting favorable efficacy of EGFR-TKIs.},
}
@article {pmid41381546,
year = {2025},
author = {Trubl, G and Roux, S and Borton, MA and Varsani, A and Li, YF and Sun, CL and Jang, HB and Woodcroft, BJ and Tyson, GW and Wrighton, KC and Saleska, SR and Eloe-Fadrosh, EA and Sullivan, MB and Rich, VI},
title = {Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67057-0},
pmid = {41381546},
issn = {2041-1723},
support = {DE-SC0010580, DE-SC0016440, DE-SC0248445, DE-SC0023307//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1632//DOE | SC | Biological and Environmental Research (BER)/ ; 3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; SCGSR//DOE | Office of Science (SC)/ ; 21-LW-060//DOE | LDRD | Lawrence Livermore National Laboratory (LLNL)/ ; },
abstract = {Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.},
}
@article {pmid41381437,
year = {2025},
author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J},
title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11067},
pmid = {41381437},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth &amp; development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; },
abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.},
}
@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
doi = {10.1111/1758-2229.70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}
@article {pmid41380982,
year = {2025},
author = {Wei, B and Zhang, L and Zhang, H and Gui, B and Deng, Q and Chang, X and Yu, P and Dong, X and Zou, B and Zhang, X and Zhao, Y and Zhao, Z and Chen, J},
title = {An integrated ultrasonic and cellulase pretreatment strategy: simultaneously enhancing medium-chain fatty acid production and reducing antibiotic resistance genes in anaerobic digestion of animal manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133780},
doi = {10.1016/j.biortech.2025.133780},
pmid = {41380982},
issn = {1873-2976},
abstract = {Rapid expansion of animal husbandry poses significant environmental challenges, including waste management and pollution. While medium-chain fatty acid (MCFA) production from livestock manure via chain elongation (CE) process in anaerobic digestion (AD) offers a promising and economically valuable waste management strategy, the associated risks of antibiotic resistance genes (ARGs) propagation through AD products are often overlooked. Additionally, the impact of substrate pretreatments on MCFA production and ARGs abundances in livestock manure during CE process remains unclear. This study assessed synergistic effects of cellulase and ultrasonic pretreatments on MCFA yield, microbial community, and ARGs during CE process of co-digesting lignocellulosic goat manure and corn straw. The results demonstrated that cellulase pretreatment increased caproate yield by 46.72 % (from 6.93 to 10.17 g of chemical oxygen demand (COD)/L). Combined cellulase and ultrasonic pretreatments decreased ARGs relative abundance by 25.28 %. The underlying mechanism was further explored through metagenome, revealing the roles of microbial community shifts and gene regulation in the beneficial outcomes. Specifically, we found that cellulase pretreatment enriched Clostridia and modulated genes related to reverse β-oxidation and ethanol oxidation, contributing to enhanced MCFA production. The reduction in ARGs abundance, particularly with combined pretreatments, was linked to a decrease in Massilibacterium abundance. Additionally, co-occurrence analysis indicated Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota as primary ARG hosts. This study demonstrates the viability of lignocellulosic goat manure for MCFA production via CE. Pretreatments effectively boost MCFA yield and mitigate ARGs, providing a basis for comprehensive biorefinery systems integrating resource valorization and ARGs control in lignocellulosic animal waste management.},
}
@article {pmid41380668,
year = {2025},
author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {12},
pages = {2148-2166.e8},
doi = {10.1016/j.chom.2025.11.011},
pmid = {41380668},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; },
abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.},
}
@article {pmid41380611,
year = {2025},
author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X},
title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119550},
doi = {10.1016/j.ecoenv.2025.119550},
pmid = {41380611},
issn = {1090-2414},
abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.},
}
@article {pmid41380516,
year = {2025},
author = {Geng, Y and Lian, CA and Yang, L and Pavlostathis, SG and Qiao, X and Qiu, Z and Wang, Y and Dong, N and Li, A and Luo, X and Yu, K},
title = {Unlocking microbial synergy in mcroalgae-bcteria gnules: RSM -driven optimization and lifecycle microbial metagenomics for high-ammonia wastewater treatment.},
journal = {Water research},
volume = {290},
number = {},
pages = {125098},
doi = {10.1016/j.watres.2025.125098},
pmid = {41380516},
issn = {1879-2448},
abstract = {Landfill leachate is challenging to treat biologically due to high ammonia toxicity and low C/N ratio, while suspended co-cultures, despite easing carbon limitations, show poor settleability and instability under high-strength conditions. This work focuses on investigating microbial synergy in microalgae-bacteria granules through RSM-driven optimization and lifecycle microbial metagenomics for high-ammonia leachate treatment. Initially, granules removed Total inorganic nitrogen (TIN) at 167.5 mg/L/d, outperforming algae-only systems. 16S rRNA analysis showed 25 % more Halomonas sp. and enriched Proteobacteria, linked to improved pollutant removal. Subsequent RSM optimization elevated TIN removal to 193.3 mg/L/d, with synchronous improvement in chemical oxygen demand (COD) removal, flocculation, Extracellular Polymeric Substances (EPS) production, and granule stability. In addition, reactor operation over 8 cycles sustained TIN removal above 193.4 mg/L/d until Cycle IV and then dropped by 5.0 %, displaying a typica granule life cycle from growth to decline. Metagenomic analysis of 326 metagenome-assembled genomes (MAGs) revealed dynamic microbial synergy that shifted from nutrient assimilation to stress adaptation, explaining the system's resilience. During assimilation-dominated stages, synergy focused on coordinated nutrient utilization, supporting energy-intensive nitrogen assimilation. As metabolism shifted to dissimilation, synergy reoriented toward stress adaptation: assimilation genes decreased to 44.3 % of their peak levels, while stress genes hcp and cah increased by 11.2-fold. This dynamic synergy provides a blueprint for lifecycle management. These findings highlight the great potential of microalgae-bacteria granules as a resilient, low-footprint approach for nitrogen removal and circular wastewater treatment.},
}
@article {pmid41380282,
year = {2025},
author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W},
title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104795},
doi = {10.1016/j.jconhyd.2025.104795},
pmid = {41380282},
issn = {1873-6009},
abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.},
}
@article {pmid41380256,
year = {2025},
author = {Yu, W and Zhang, J and Shi, Z and Wang, S and Lai, S and Huang, X and Zhang, J and Cai, Z and Zhao, J},
title = {Reductive soil disinfestation mitigates antibiotic resistance gene risk in the soil-lettuce continuum by restructuring dominant bacterial taxa and improving soil properties.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140745},
doi = {10.1016/j.jhazmat.2025.140745},
pmid = {41380256},
issn = {1873-3336},
abstract = {Reductive soil disinfestation (RSD) and chemical fumigation serve as effective methods for controlling soil-borne pathogens, yet their effects on soil antibiotic resistome remain poorly understood. This study combined high-throughput qPCR (HT-qPCR) and metagenomic sequencing to evaluate the impacts of dazomet fumigation (DZ) and RSD amended with alfalfa (AL) and molasses (MO) on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in an ARG-contaminated soil. Results demonstrated that both DZ and RSD treatments significantly altered the soil resistome and bacterial community. HT-qPCR revealed that DZ significantly increased the relative abundance of total ARGs, MGEs and high-risk ARGs (Rank I and Rank II) by 86.59 %, 43.12 %, 36.81 %, and 40.88 %, respectively, while RSD treatments effectively reduced MGEs by 53.96-63.30 % and significantly suppressed Rank II high-risk ARGs. Metagenomic sequencing further indicated that RSD, particularly AL, outperformed DZ in reducing most ARGs classes, with pronounced effects on predominant ARGs such as macB (16.32 %), tetA(58) (24.14 %), and TxR (29.31 %). Correlation analyses suggested that RSD mitigates ARGs contamination by modulating the dominant bacterial community, especially suppressing ARG hosts while enriching antagonists, and improving soil physicochemical properties. Variance partitioning analysis attributed greater explanatory power to bacterial community than to physicochemical properties in shaping high-risk (18.44 % vs. 3.72 %) and high-abundance (11.90 % vs. 2.79 %) ARG profiles. Moreover, RSD considerably reduced the ARGs transmission risk from soil to lettuce. These findings establish RSD as an effective strategy to curb ARGs dissemination in soil-plant system and support its adoption for safer agricultural production.},
}
@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
doi = {10.1371/journal.pone.0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation &amp; purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.<br><br>METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n&#x2009;=&#x2009;37; 66.1%), IBD-Unclassified (n&#x2009;=&#x2009;9; 16.1%), ulcerative proctitis (n&#x2009;=&#x2009;7; 12.5%), and Crohn's disease (n&#x2009;=&#x2009;3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.<br><br>RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).<br><br>CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.},
}
@article {pmid41379644,
year = {2025},
author = {Capoferri, G and Battegay, R and Hamelin, B and Keller, PM and Mertz, KD and Weisser, M},
title = {Borrelia afzelii Hepatitis in Patient Treated with Venetoclax and Obinutuzumab, Switzerland.},
journal = {Emerging infectious diseases},
volume = {31},
number = {11},
pages = {2167-2171},
doi = {10.3201/eid3111.250584},
pmid = {41379644},
issn = {1080-6059},
mesh = {Humans ; *Sulfonamides/adverse effects/therapeutic use ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; Switzerland ; *Borrelia burgdorferi Group/genetics ; *Bridged Bicyclo Compounds, Heterocyclic/adverse effects/therapeutic use ; *Lyme Disease/diagnosis/microbiology/drug therapy ; Male ; *Hepatitis/diagnosis/etiology/microbiology ; Immunocompromised Host ; *Antineoplastic Agents/adverse effects/therapeutic use ; Aged ; Female ; },
abstract = {We report Borrelia afzelii hepatitis in an immunosuppressed patient in Switzerland receiving anti-CD20 therapy and venetoclax. Diagnosis was made by metagenomic sequencing and PCR. This case underscores the need to consider Lyme borreliosis in unexplained hepatitis cases and highlights the value of molecular diagnostics in immunosuppressed patients when serologic test results are negative.},
}
@article {pmid41379519,
year = {2025},
author = {Aaby, M and Lalitha, P and Prajna, NV and Gunasekaran, R and Seitzman, GD and Doan, T and Redd, TK},
title = {Comparing Microbiologic Tests for Pathogen Detection in Infectious Keratitis Using Latent Class Analysis.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000004075},
pmid = {41379519},
issn = {1536-4798},
support = {K23EY032639/EY/NEI NIH HHS/United States ; P30EY010572/EY/NEI NIH HHS/United States ; Tom Wertheimer Career Development Award in Data Science//Research to Prevent Blindness/ ; unrestricted departmental funding//Research to Prevent Blindness/ ; },
abstract = {PURPOSE: To compare the diagnostic performance of traditional microbiologic tests and next-generation sequencing methods for infectious keratitis pathogen detection.<br><br>METHODS: Participants included 86 subjects diagnosed with acute infectious keratitis at Aravind Eye Hospital in Madurai, India. Corneal scrapings from all subjects were evaluated using Gram stain, potassium hydroxide (KOH) smear, culture, and metagenomic deep sequencing (MDS). The sensitivity and specificity of each test were estimated using latent class analysis.<br><br>RESULTS: Among 86 participants, clinical diagnostic tests demonstrated varying sensitivity and specificity for bacterial and fungal keratitis. Gram stain exhibited high sensitivity (89%) and specificity (94%) for bacterial detection, whereas KOH smears showed only moderate sensitivity (75%) and specificity (69%) for fungal detection. Culture testing had lower sensitivity for bacterial (68%) and fungal (56%) identification, but high specificity (92% and 88%, respectively). MDS demonstrated the best balance of sensitivity and specificity across pathogen classes, with 100% sensitivity and 90% specificity for bacterial keratitis and 82% sensitivity with 94% specificity for fungal keratitis. MDS detected critical pathogens missed by culture in 29% of cases, including those whose identification is essential for guiding clinical management and preventing vision-threatening complications.<br><br>CONCLUSIONS: MDS demonstrated a favorable balance between sensitivity and specificity for both bacterial and fungal keratitis, whereas smears performed well for bacterial but not fungal keratitis and cultures demonstrated high specificity but low sensitivity. Repeated evaluation of diagnostic performance across diverse populations and geographic settings is necessary to validate the reliability and optimize the clinical utility of microbiologic testing for infectious keratitis.},
}
@article {pmid41379255,
year = {2025},
author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D},
title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {65},
pmid = {41379255},
issn = {1432-072X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; },
abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.},
}
@article {pmid41379245,
year = {2025},
author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S},
title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {504},
pmid = {41379245},
issn = {1573-0972},
support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; },
mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation &amp; purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.},
}
@article {pmid41379027,
year = {2025},
author = {Esvap, E and Ulgen, KO},
title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.},
journal = {Biotechnology journal},
volume = {20},
number = {12},
pages = {e70164},
doi = {10.1002/biot.70164},
pmid = {41379027},
issn = {1860-7314},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; },
abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.},
}
@article {pmid41378921,
year = {2025},
author = {Montini, A and Pellegrini, C and Loddo, G and Ravaioli, F and Baldelli, L and Mainieri, G and Pirazzini, C and Mazzotta, E and Carano, F and Sala, C and De Fanti, S and Bacalini, MG and Provini, F},
title = {Analysis of gut microbiota in Restless Legs Syndrome: searching for a metagenomic signature.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsaf383},
pmid = {41378921},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: We aim to analyse the microbiota composition in RLS patients and its relationship with the different RLS phenotypes.<br><br>METHODS: We recruited idiopathic RLS (RLS) and insomnia (INS) patients and healthy subjects (CTRL). Validated questionnaires (PSQI, IRLS, ISI, BDI-II) were administered in the RLS and INS. Fecal microbiota was analysed by 16S rRNA gene sequencing according to Illumina metagenomics standard procedure on MiSeq Platform. Dada2 pipeline was used to process sequencing data, while DESeq2 and Aldex2 tools were used to calculate differential abundance taxa, correcting for age, sex, Body Mass Index, sequencing run and presence of mood disorders.<br><br>RESULTS: The sample included 37 RLS (28 females, mean age 64.78&#xa0;years), 31 INS (22 females, mean age 60.64&#xa0;years) and 33 CTRL (24 females, mean age 62.54&#xa0;years). Differential abundance analysis revealed a statistically significant decrease in the abundance of Lachnoclostridium and Flavonifractor genera in RLS compared to CTRL and INS, but not in the INS compared to CTRL. Lachnoclostridium abundance tended to decrease with long disease duration and a predominant motor phenotype. In the RLS group, several genera were identified as significantly associated with IRLS and PSQI scores.<br><br>CONCLUSIONS: Although only a few previous studies have reported the presence of small intestinal bacterial overgrowth (SIBO) in RLS, to the best of our knowledge this is the first study to highlight significant differences in the gut microbiota composition of RLS compared to both CTRL and INS, identifying a specific RLS metagenomic signature.},
}
@article {pmid41378915,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf275},
pmid = {41378915},
issn = {1751-7370},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.},
}
@article {pmid41378891,
year = {2025},
author = {Khanal Pokharel, S and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing conserved biosynthetic gene clusters of the phylum Myxococcota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0215125},
doi = {10.1128/aem.02151-25},
pmid = {41378891},
issn = {1098-5336},
abstract = {UNLABELLED: A surge in sequenced myxobacteria catalyzed by advancements in long-read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze 11 genera and 195 sequenced genomes, including 10 newly reported myxobacterial isolates, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to the diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.<br><br>IMPORTANCE: Critical contributions to soil nutrient cycles by predatory bacteria, including the Myxococcota, and utility as a resource for the discovery of novel enzymology and metabolism motive continued isolation and characterization of myxobacteria from the environment. Each of these motivating factors involves specialized metabolites produced by myxobacteria and the biosynthetic gene clusters (BGCs) responsible for their assembly. Primarily associated with the predatory lifestyles of myxobacteria, myxobacterial specialized metabolites have been pursued as therapeutic leads for novel antibacterials, antifungals, anthelmintics, and cancer therapies. Despite these efforts and the observation that nearly all genera within the Myxococcota have an extraordinary number of BGCs, there is no consensus view of the conserved BGCs in the phylum. Our study revealed the core BGCs consistently present throughout the phylum. By reporting these core specialized metabolites and their ecological roles, we hope to streamline the discovery and investigation of specialized metabolism in myxobacteria.},
}
@article {pmid41378809,
year = {2025},
author = {Huang, X and Wu, X and Huang, H},
title = {A Case of Tinea Nigra in Southern China.},
journal = {The American Journal of dermatopathology},
volume = {47},
number = {8},
pages = {640-641},
doi = {10.1097/DAD.0000000000002997},
pmid = {41378809},
issn = {1533-0311},
support = {SZSM202311029//Sanming Project of Medicine in Shenzen Municipality/ ; },
mesh = {Humans ; Female ; Adult ; China ; Antifungal Agents/administration &amp; dosage/therapeutic use ; Dermoscopy ; *Tinea/microbiology/drug therapy/pathology/diagnosis ; *Hand Dermatoses/microbiology/drug therapy/pathology/diagnosis ; Treatment Outcome ; },
abstract = {Tinea nigra, a rare superficial fungal infection caused by Hortaea werneckii, is often mistaken for a melanocytic lesion. We report a case in Shenzhen, a city in southern China, involving a 31-year-old woman with slowly enlarging brown patches on her left palm over 15 years. The patches were smooth, asymptomatic, and without scaling or travel history to tropical regions. Dermatological examination revealed a 30 mm × 25-mm brown macule with distinct borders. Dermoscopic analysis showed brownish-gray pigmented strands parallel to skin ridges, differing from the pattern in melanoma. Histopathological examination confirmed fungal hyphae in the upper stratum corneum. The fungus was identified as H. werneckii using metagenomic next-generation sequencing. The lesion resolved completely after an 8-week course of 1% butenafine cream. Accurate diagnosis is crucial to prevent misdiagnosis as malignant melanoma. Dermoscopy and fungal microscopy are key diagnostic tools. Treatment with topical antifungal agents is effective, with symptoms resolving within weeks.},
}
@article {pmid41378778,
year = {2025},
author = {Zhou, Y and Ren, X and Li, B and Tang, H and Guo, Y and Yang, L and Han, J and Zhou, B},
title = {Bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate Triggers IBD-like Pathology through the Gut Microbiota-Arachidonic Acid Axis: Protective Role of Akkermansia muciniphila.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12302},
pmid = {41378778},
issn = {1520-5851},
abstract = {Environmental pollutants are increasingly recognized as modulators of gut microbiota and metabolic pathways, contributing to the rising global incidence of inflammatory bowel disease (IBD). The novel brominated flame retardant bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH) is increasingly detected in ecosystems and human tissues, yet its impact on intestinal health remains unclear. Here, we combined shotgun metagenomics, untargeted metabolomics, and targeted biochemical assays in a murine model to reveal how TBPH drives IBD-like pathology. TBPH exposure resulted in shortened colons, disrupted epithelial barriers, and elevated systemic pro-inflammatory cytokines, accompanied by gut microbiota dysbiosis marked by depletion of Akkermansia muciniphila (AKK). Decreased abundance of AKK correlated with arachidonic acid (AA) accumulation and hyperactivation of the phospholipase A2 (PLA2)-cyclooxygenase 2 (COX2)-prostaglandin E2 (PGE2) inflammatory cascade, leading to NF-κB activation and mucosal injury. Supplementation with viable AKK restored AA homeostasis, suppressed inflammatory signaling, and preserved the barrier integrity. These results demonstrate a microbiota-dependent mechanism linking TBPH exposure to AA-driven intestinal inflammation and identify AKK as a critical protective species, which highlights the gut microbiota-AA metabolic axis as a potential mechanism for pollutant-induced intestinal disorders.},
}
@article {pmid41378133,
year = {2025},
author = {Langwig, MV and Sneed, SL and Rasmussen, A and Seitz, KW and Lee, JA and Anantharaman, K and De Anda, V and Francis, CA and Baker, BJ},
title = {Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf182},
pmid = {41378133},
issn = {2730-6151},
abstract = {Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With intensifying anthropogenic pressures, it is critical to understand the capacity of these communities to maintain essential functions under environmental change. Here, we examined the metabolic functions and redundancy in the microbial community of San Francisco Bay (SFB) sediments, providing the first large-scale, genome-resolved, and spatiotemporally resolved characterization of the estuary. Salinity, iron, phosphorus, sulfur, and total sediment nitrogen were significantly correlated with microbial community composition, suggesting these factors play a key role in structuring SFB communities. In support of this, we identified broad capabilities for iron cycling and key uncultured players that contribute to denitrification, nitrification, and complete nitrification (comammox). We also identified widespread capabilities for sulfur cycling, including understudied lineages capable of rDsr-mediated sulfur oxidation. SFB MAGs exhibited partitioning of multistep metabolisms, or metabolic handoffs, and the rare biosphere broadly encoded key nitrogen and sulfur cycling genes. Despite shifts in community composition across sites and fluctuations in environmental parameters, key nitrogen and sulfur metabolisms were maintained throughout the estuary, especially in nitrate reduction, nitrite reduction, and the Dsr/Sox pathway. The presence of multiple microbial taxa with similar functional roles (functional redundancy) may provide an ecosystem buffer, suggesting these functions could better recover from disturbances and ultimately contribute to the long-term health and sustainability of these vital coastal habitats.},
}
@article {pmid41377518,
year = {2025},
author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S},
title = {Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.26.689816},
pmid = {41377518},
issn = {2692-8205},
abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective curation. We performed comprehensive manual curation and harmonization of clinical metadata from 212,027 samples across 468 studies in two major repositories: curatedMetagenomicData (93 studies, 22,588 samples) and cBioPortal (375 studies, 189,438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into much fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions encountered during large-scale metadata harmonization across two distinct omics domains. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.},
}
@article {pmid41377425,
year = {2025},
author = {Nawaz, S and Nadeem, IA and Talha, M and Irshad, NUN and Imran, SB},
title = {Engineered microbes over immunosuppression: MAGIC as a transformative strategy for vasculitides.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {12},
pages = {9131-9132},
pmid = {41377425},
issn = {2049-0801},
}
@article {pmid41377246,
year = {2025},
author = {Singh, PK and Rathi, D and Shweliya, MA and Farooq, A and Anfaal, Z and Saleem, NUA and Hamza, M and Qadri, M and Rath, S and Hemida, MF and Rani, H and Mahgoub, AMA and Wazir, HU},
title = {The interplay of the microbiome and breast cancer: beyond the gut: a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {12},
pages = {8496-8507},
pmid = {41377246},
issn = {2049-0801},
abstract = {Breast cancer remains a leading cause of morbidity and mortality among women worldwide, with emerging evidence underscoring the microbiota's pivotal role in its etiology, progression, and therapeutic response. This narrative review synthesizes the intricate interplay between the breast tissue, skin, and lung microbiomes in breast cancer pathogenesis, with particular emphasis on inflammatory breast cancer (IBC) and metastatic dissemination. The healthy breast microbiome, dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes, maintains tissue homeostasis through pH regulation, metabolite production, and immune modulation. Dysbiosis disrupts this equilibrium, fostering carcinogenesis via chronic inflammation, estrogen deconjugation, and DNA damage-induced genomic instability, with subtype-specific microbial signatures influencing tumor growth and therapy resistance. In IBC, skin microbiome alterations characterized by overgrowth of pathogens like Pseudomonas aeruginosa and Staphylococcus aureus exacerbate inflammation, epithelial-mesenchymal transition (EMT), and lymphatic invasion, while promoting a pro-tumorigenic microenvironment enriched in regulatory T cells and M2 macrophages. Concurrently, lung microbiota dysbiosis impairs immune surveillance, remodels the extracellular matrix, and facilitates metastatic seeding through neutrophil extracellular traps and cytokine storms. Cross-talk among these microbiomes amplifies systemic effects, highlighting their synergistic contributions to disease aggressiveness. Advanced analytical techniques, including 16S rRNA sequencing, metagenomics, and metabolomics, offer promising microbial biomarkers for early detection and risk stratification. By elucidating these host-microbe dynamics, this review advocates for microbiome-centric interventionssuch as probiotics, fecal microbiota transplantation, and targeted antimicrobials to enhance precision diagnostics and therapies, ultimately improving outcomes in breast cancer management.},
}
@article {pmid41377184,
year = {2025},
author = {Ayilaran, E and McHugh, O and Jung, Y},
title = {Metagenomic sequencing dataset of microbial communities in onion and cabbage microgreens across substrates, Salmonella inoculation, and bacteriophage application.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112297},
pmid = {41377184},
issn = {2352-3409},
abstract = {This dataset comprises shotgun metagenomic sequencing results from edible portion of onion (Allium cepa) and cabbage (Brassica oleracea) microgreens cultivated on soil, biostrate, and jute fiber substrates, with and without Salmonella inoculation and bacteriophage application. Table 1 contains detailed sequencing quality metrics and National Center for Biotechnology Information Sequence Read Archive accession numbers (BioProject: PRJNA1327464) for all 24 samples. Figure 1 provides a species-level (≥5% relative abundance) heatmap highlighting microbial community clustering by seed type. These data can be reused for comparative microbiome analyses, evaluation of pathogen-phage-substrate interactions, and benchmarking of metagenomic workflows.},
}
@article {pmid41377047,
year = {2025},
author = {Lee, SH and Yun, YB and Kim, DS and Park, M and Um, Y and Kang, JW},
title = {Isolation of plant growth-promoting rhizobacteria from wild-simulated ginseng and evaluation of soil health following its application in the field.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682016},
pmid = {41377047},
issn = {1664-302X},
abstract = {Wild-simulated ginseng must be cultivated at natural forest sites without artificial structures, chemical fertilizers, or pesticides to qualify for certification. However, its extended cultivation period makes stable production challenging, necessitating effective strategies to enhance early growth and yield. In this study, we evaluated the ability of five bacterial strains isolated from the rhizosphere of wild-simulated ginseng to promote initial growth and development. The strains exhibited diverse functional traits, including indole-3-acetic acid (IAA) production, phosphate solubilization, siderophore production, and enzymatic activities such as protease and cellulase. Antifungal activity, however, was primarily observed in strains 79 and 81. We inoculated field-grown ginseng plants with each strain at biweekly intervals for a total of seven applications. Inoculation with strain 75 (Pseudomonas frederiksbergensis) significantly increased shoot dry weight by 48.9% and root biomass by 37.0% relative to uninoculated controls (p < 0.05). Strain 81 (Paenibacillus terrae) promoted stem elongation, whereas strain 89 (Paraburkholderia madseniana) reduced leaf size. Soil analysis showed that strain 75 and 77 plots maintained higher organic matter, phosphorus, calcium, and cation exchange capacity, whereas strains 79, 81, and 89 had lower values. Metagenomic analysis revealed a marked enrichment of the order Pseudomonadales and the maintenance or enhancement of bacterial alpha diversity (Chao1 and PD indices), suggesting a stable and resilient microbial ecosystem. Functional profiling revealed enhancements in nitrogen fixation and nutrient cycling pathways. We determined statistical significance using a t-test and one-way ANOVA with Duncan's multiple range test (p < 0.05). In contrast, strains 79 (Paraburkholderia terricola), 81 (Paenibacillus terrae), and 89 (Paraburkholderia madseniana) did not elicit significant growth responses. Our findings indicate that P. frederiksbergensis (strain 75) is a promising plant growth-promoting rhizobacterium for wild-simulated ginseng, offering a biologically based approach for improving early-stage development under forest cultivation conditions.},
}
@article {pmid41377041,
year = {2025},
author = {Zhou, Y and Qi, D and Chen, C and Bi, W and Yu, X and Liu, J and Lan, G and Hou, R and Li, Z and Ma, R},
title = {Divergent gut microbial metabolism supports niche partitioning in giant and red pandas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698108},
pmid = {41377041},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota plays a pivotal role in regulating the host's physiological functions and behavior. The coevolutionary relationship between the host and its gut microbiota facilitates adaptation to specific ecological niches. As obligate bamboo feeders, giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus styani) exhibit distinct feeding preferences: the former primarily consumes bamboo stems and leaves, while the latter feeds mainly on bamboo leaves. This study aims to elucidate how these species adapt metabolically to different parts of bamboo via gut microbial activity.<br><br>METHODS: We employed 16S rRNA gene sequencing to analyze the structure and function of fecal microbial communities in giant pandas (GP) and red pandas (RP).<br><br>RESULTS: Significant differences in gut microbiota composition were observed between the GP and RP groups. Eight core bacterial taxa constituted over 99.97% of the total microbial composition, with the RP group exhibiting higher species richness but lower overall diversity. At the phylum level, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, and Flavobacteria were significantly enriched in the GP group, whereas Firmicutes dominated in the RP group. At the genus level, Sphingomonas, Methylobacterium, Cryomonas, and Terriglobus were more abundant in the GP group, while Streptococcus and Rhizobium were enriched in the RP group. Functional metabolic analysis indicated that lipid and amino acid metabolism pathways were significantly enriched in the GP group, whereas nucleotide and carbohydrate metabolism pathways were prominent in the RP group. Further analysis revealed that Sphingomonas and Methylobacterium in the GP group positively regulated amino acid and lipid metabolism, while Streptococcus in the RP group enhanced nucleotide and carbohydrate metabolism.<br><br>DISCUSSION: These findings suggest that the distinct metabolic pathways of the gut microbiota in giant and red pandas have evolved in concert with their dietary strategies, energy acquisition modes, and ecological niche differentiation, forming a highly coordinated adaptive system.},
}
@article {pmid41376967,
year = {2025},
author = {Liu, H and Ji, S and Xing, F and Wang, C and Sun, W and Shao, H and Hu, C},
title = {Performance of metagenomic next-generation sequencing, Xpert MTB/RIF and acid-fast staining for diagnosing tuberculous pleurisy and empyema.},
journal = {Journal of thoracic disease},
volume = {17},
number = {11},
pages = {10298-10307},
pmid = {41376967},
issn = {2072-1439},
abstract = {BACKGROUND: The detection of Mycobacterium tuberculosis (MTB) is an important basis for the diagnosis of tuberculosis. Detecting fresh tissue, pus, and other samples is challenging. Both metagenomic next-generation sequencing (mNGS) and Xpert MTB/RIF have demonstrated excellent performance in the diagnosis of tuberculosis; however, their research base is still lacking in tissue or pus samples. We hope to explore the detection performance of mNGS and Xpert MTB/RIF in these sample types through this study.<br><br>METHODS: This study enrolled 154 patients suspected of having tuberculosis. Fresh tissues, pleural fluid or pus were collected from these patients and performed mNGS, Xpert, and acid-fast staining (AFS) tests. Their detection performance was statistically analyzed and compared.<br><br>RESULTS: Overall, the positivity rate of mNGS was 48.05% (74/154), Xpert was 44.44% (44/99), and AFS was 57.34% (82/143). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 55.22%, 100%, 100% and 25%, respectively. The sensitivity, specificity, PPV and NPV of Xpert were 48.35%, 100%, 100%, 18.97%, respectively. The sensitivity, specificity, PPV and NPV of acid-fast stain were 58.59%, 53.33%, 91.46%, 13.11%, respectively. A total of 93 samples underwent all three types of testing, and 45.16% (42/93) were completely consistent in the results of the three tests. The analysis results of these samples showed that the sensitivity, specificity, PPV and NPV of mNGS were 65.88%, 100%, 100%, 21.62%, respectively. The sensitivity, specificity, PPV and NPV of Xpert were 49.41%, 100%, 100%, 15.69%, respectively. The sensitivity, specificity, PPV and NPV of acid-fast stain were 57.65%, 62.50%, 94.23%, 12.20%, respectively. The sensitivity of mNGS was significantly higher than that of Xpert (P=0.01).<br><br>CONCLUSIONS: Our research results indicate that mNGS and AFS have higher sensitivity compared to Xpert, while mNGS and Xpert have higher specificity.},
}
@article {pmid41376957,
year = {2025},
author = {Liu, Y and Deng, N and Lu, Y and Peng, J and Yuan, S},
title = {Comparison of metagenomic next-generation sequencing (mNGS) technology with routine laboratory culture for bacterial and fungal detection in bronchoalveolar lavage fluid.},
journal = {Journal of thoracic disease},
volume = {17},
number = {11},
pages = {10036-10044},
pmid = {41376957},
issn = {2072-1439},
abstract = {BACKGROUND: Pulmonary infections continue to threaten human health. Metagenomic next-generation sequencing (mNGS) technology provides a rapid detection method for identifying the pathogens responsible for pulmonary infections, with many advantages compared to traditional culture method. Our objective is to collect and analyze testing data from patients with pulmonary infections at the Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, in order to compare the detection rates of mNGS and traditional culture method.<br><br>METHODS: This study conducted a retrospective analysis of bronchoalveolar lavage fluid (BALF) samples from 50 patients with pulmonary infections at the Department of respiratory medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, comparing the differences between mNGS and the traditional "gold standard" culture method.<br><br>RESULTS: The detection rate of mNGS for fungi or bacteria was 72.0% (36/50), while that of culture method was 12.0% (6/50). According to the McNemar &#x3c7;[2] test, there was a statistical significance between the detection results of mNGS and culture method (P<0.0001). In addition, mNGS can detect viruses that cannot be detected by culture method. Only 12.0% (6/50) tested positive for both mNGS and culture, while 60% (30/50) tested positive for mNGS but negative for culture. mNGS results led to treatment modifications for 18 patients. 8 cases added antifungal treatment, 7 cases adjusted antibiotic treatment, 2 cases adjusted both antifungal and antibiotic treatment, and 1 case adjusted antifungal treatment.<br><br>CONCLUSIONS: mNGS, as a new diagnostic testing technology, has significant advantages in identifying bacteria, fungi, and virus. The combination of mNGS analysis of BALF and traditional pathogen culture method can improve the efficiency of pathogen detection and facilitate the diagnosis of patients with pulmonary infections, allowing patients to receive targeted treatment as soon as possible.},
}
@article {pmid41376878,
year = {2026},
author = {Sengupta, S and Basak, P and Pramanik, A and Ghosh, P and Mukhopadhyay, M and Sen, A and Bhattacharyya, M},
title = {Altitude-driven variations in soil microbial communities of Himalayan subalpine forests.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {7},
pmid = {41376878},
issn = {2190-572X},
abstract = {UNLABELLED: The Himalayas offer a unique environment for the study of microbial diversity and their response to biotic and abiotic factors, enhancing knowledge on ecological processes under altitudinal control in subalpine forests. This study investigates the impact of altitude on bacterial diversity and soil physico-chemical properties of Himalayan subalpine coniferous forests at four different regions-Sillery Gaon (S1; 1829 m), Gangotri (S2; 3415 m), Kausani (S3; 1890 m) and Gwal Dam (S4; 1940 m). Using 16S rDNA amplicon sequencing, soil microbial diversity of the said subalpine ecosystems were explored. Physico-chemical studies of the soil samples showed that S1 had the highest moisture content (25.66 ± 0.26%) and C:N ratio (136.26 ± 5.4) while S4 had the highest TOC (22.78 ± 1.2%), TKN (0.7373 ± 0.043%) and available phosphate content. Results indicated presence of diverse microflora from various phyla, including Actinomycetota (7.52% in S2, 7.98% in S3), Planctomycetota (53.36% in S1, 51.09% in S3), Proteobacteria (14.3% in S1, 18.28% in S3, 14.96% in S4), and Verrucomicrobiota (18.75% in S2 and 21.88% in S4). Proteobacteria was the dominant phyla in mid (S4) and lower (S1, S3) subalpine forest soils, suggesting enhanced abundance due to human intervention at these altitudes. Multivariate analysis revealed a positive correlation between altitude, precipitation, moisture content, soil pH, organic carbon, nitrogen and phosphate contents with the presence of Proteobacteria and Actinomycetota phyla. The study highlights the connection between microbial communities and soil physicochemical properties, and the intricate interplay of biotic and abiotic factors affecting the microbial community composition in a unique region at different elevations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04608-8.},
}
@article {pmid41376791,
year = {2025},
author = {Liu, Y and Tan, Y and Xia, F and Wu, S and Zou, S and Chen, Q and Liu, J and Song, S and Du, Q and Guo, W and Liang, K},
title = {Diagnostic utility of metagenomic next-generation sequencing for tissue in patients with suspected infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634406},
pmid = {41376791},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Adult ; Retrospective Studies ; *Communicable Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; Aged ; HIV Infections ; Bacteria/genetics/isolation &amp; purification/classification ; Young Adult ; },
abstract = {Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methods because of its comprehensiveness. However, the diagnostic utility of mNGS for tissue hasn't been fully explored, especially for patient with HIV infection. HIV-positive and negative patients with suspected infectious diseases who performed tissue mNGS and conventional microbiological tests (CMTs) were retrospectively enrolled between October, 2020 and May 2024. The microbial spectrum of tissue mNGS and CMTs was analyzed, and the diagnostic accuracy and consistency of mNGS and CMTs for tissue were compared. The related factors of positive rate of mNGS was analyzed. Of 70 patients with suspected infectious diseases, 44 cases were confirmed with the infectious diseases. Among 44 patients with infectious diseases, aerobic bacteria (36.4%) was the most common detected pathogen, followed by mycobacterium tuberculosis (MTB, 18.2%), non-tuberculous mycobacteria (NTM, 13.6%) and fungus (11.4%). The sensitivity of tissue mNGS (72.7%, 95%CI 56.9%-84.5%) was significantly higher than that that in tissue CMTs (29.5%, 95%CI 17.2%-45.4%) (p<0.001), but the specificity was not statistically significant(P = 0.656). mNGS demonstrated higher detection rates than CMTs in the case with single microbial infections (70.0% vs. 30.0%; p<0.01). For the case with multiple microbial infections, the detection rates of mNGS and CMTs was 100.0% and 25.5% (p=1.000), respectively. Both positive mNGS and CMTs were observed in 22.7% patients with infectious diseases, and sole positive mNGS and sole positive CMTs were observed in 50.0% and 6.8% patients, respectively. There were no statistically differences in age, gender, HIV infection, PCT levels, neutrophil counts, CD4[+] lymphocyte count and antibiotic exposure between mNGS positive and mNGS negative groups (P > 0.05). Tissue mNGS could provide a higher sensitivity, more robust and broader method for pathogen identification by comparison with CMTs. However, CMTs shouldn't be ignored since the low consistency between CMTs and mNGS.},
}
@article {pmid41376097,
year = {2025},
author = {Jiang, W and Zhang, S and Feng, Z and Dong, Y and Ao, Z and Jia, J and Li, H and Chen, Z and Liu, R and Wen, X},
title = {Microenvironmental Gradients Drive Spatial Stratification of Saccharifying Microbial Communities and Enzyme Activity in Strong-Flavor Daqu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/foods14234160},
pmid = {41376097},
issn = {2304-8158},
abstract = {Daqu, a representative solid-state fermentation product, produces saccharifying enzymes to degrade sorghum starch into fermentable sugars for ethanol synthesis. Spatial heterogeneity in Daqu drives community assembly. However, its regulatory role in enzyme-driven saccharification remains unclear. By integrating metagenomics and PacBio full-length sequencing, this study investigated how microenvironmental gradients across distinct Daqu layers (QP (surface layer), HQ (middle layer), QX (center layer)) shape saccharifying microbiota and activity. Saccharifying activity exhibited a declining surface-to-center gradient (e.g., QP: 870.9 ± 21.2 U/mL > HQ: 631.2 ± 16.4 U/mL > QX: 296.5 ± 16.1 U/mL on day 30, p < 0.05), paralleled by divergence in microenvironments. Metagenomics identified α-amylase and α-glucosidase as key saccharifying enzymes, primarily encoded by fungi; their abundance was inhibited by heat and humidity, yet promoted by acidity. Enzymatic validation confirmed higher saccharifying activity in QP and HQ core microbes (e.g., Lichtheimia ramosa: 43.16 ± 1.97 U/mL) than in QX (e.g., Paecilomyces variotii: 14.27 ± 1.25 U/mL). Network analysis revealed Lactobacillaceae are closely linked with saccharifying communities. This study establishes microenvironmental gradients as critical regulators of spatial saccharification in Daqu, informing strategies to optimize microbial consortia for baijiu production.},
}
@article {pmid41375521,
year = {2025},
author = {Xiao, L and Liang, Y and Hao, S and Wu, K},
title = {Integrative High-Throughput Screening and Microscopic Evidence Implicates Microsporidia as a Potential Pathogen of "Pus Crab" in the Mud Crab (Scylla paramamosain).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233463},
pmid = {41375521},
issn = {2076-2615},
abstract = {The mud crab (Scylla paramamosain), an economically important crustacean aquaculture species in southern China, is susceptible to infections due to its immune system lacking acquired immunity. An emergent disease locally termed "pus crab" has caused severe muscle lesions in pond-farmed crabs, but its etiology remained unclear. Here, we applied an integrated approach, histopathology, electron microscopy, metagenomic sequencing, and experimental infection to identify the pathogen of "pus crab". Histological staining (H&amp;E, Wright-Giemsa, and Masson) revealed muscle fiber dissolution, disordered fiber arrangement, and abundant interstitial spore-like bodies. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) confirmed intracellular spore morphology consistent with microsporidia. Metagenomic profiling showed a pronounced shift in the muscle microbiome, with a marked increase in microsporidian taxa at the genus level and a concurrent decline in bacterial relative abundance. Functional annotation indicated enrichment of pathways related to protein processing, ribosome biogenesis, glycosylation, and the ubiquitin-proteasome system. Isolation of spores from diseased muscle and subsequent injection into healthy crabs reproduced wild-like clinical signs and histopathology, confirming infectivity and implicating microsporidia as the likely etiological agents of "pus crab". These findings establish a multidisciplinary framework for pathogen identification in aquaculture and provide candidate molecular and biochemical markers for early diagnosis and management.},
}
@article {pmid41375452,
year = {2025},
author = {Wang, Z and Yang, C and Li, Y and Dong, B and Song, Q and Bai, H and Jiang, Y and Chang, G and Chen, G},
title = {Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233393},
pmid = {41375452},
issn = {2076-2615},
support = {2023YFD1300301//National Key Research and Development Project of China/ ; 32472890//National Natural Science Foundation/ ; CARS-42-3//China Agriculture Research System of MOF and MARA/ ; },
abstract = {Abdominal fat deposition is an important economic trait in poultry, as excessive accumulation reduces feed efficiency and carcass yield. The gut microbiota is known to influence host energy metabolism and fat storage, suggesting its potential involvement in fat deposition. This study examined the relationship between intestinal microbiota and abdominal fat deposition in an F2 population derived from Cherry Valley Ducks (♂) × Runzhou Crested White Ducks (♀) at 42 days of age. Based on abdominal fat rate, ducks with values of 0-0.75% and 1.5-2.25% were defined as the low (LF) and high (HF) abdominal fat groups, respectively. A combined multi-omics approach was used, including 16S rRNA gene sequencing, metagenomics, and whole transcriptomics, to compare high and low abdominal fat rate groups. 16S rRNA gene sequencing results showed that the cecum had the highest microbial diversity among all intestinal segments (duodenum, jejunum, ileum, and rectum) and was significantly enriched in carbohydrate metabolism pathways, highlighting its key role in nutrient utilization and growth. Therefore, the cecum was selected for further analysis. Metagenomic analysis of the cecum contents revealed significantly different intestinal microbial β diversity between the high and low abdominal fat rate groups (p < 0.05). The low abdominal fat rate group was enriched in beneficial microorganisms such as Paenibacillus, Butyrivibrio, Coprococcus, Ruminococcaceae, Veillonellaceae (Clostridiales), and Firmicutes. Conversely, the high abdominal fat rate group was characterized by an increased abundance of Bacteroidetes, including both beneficial and potentially pathogenic taxa such as Alistipes and Eggerthellales. The integrated analysis of metagenomic and whole transcriptome sequencing showed that Firmicutes and Bacteroidetes were not only related to energy metabolism, lipid metabolism, and amino acid metabolism, but also to the expression of FGF2, FKBP5, PNPLA2, PLIN3, FGFR2, DGAT2, and ACER2. In addition, Firmicutes and Bacteroidetes were also associated with 7 lncRNAs: XR_003493494.1, XR_003492471.1, XR_001190174.3, TCONS_00005095, XR_001190238.3, TCONS_00005095, and XR_003492841.1. In conclusion, this study highlights that the cecal microbiota is closely associated with abdominal fat deposition in ducks, elucidating its potential influence on host metabolism and gene expression. These findings enhance our understanding of the gut microbiota's relationship with obesity and offer new strategies to modulate gut-microbe interactions to reduce abdominal fat accumulation in poultry.},
}
@article {pmid41375438,
year = {2025},
author = {Pacini, MI and Forzan, M and Mazzei, M},
title = {Fecal Sample Surveillance of the Wildlife Virome in Central Italy: Insights from the Foreste Casentinesi National Park.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233378},
pmid = {41375438},
issn = {2076-2615},
support = {Fondi Ateneo//University of Pisa/ ; },
abstract = {Wildlife can act as both a reservoir and a sentinel for emerging pathogens, but surveillance is often constrained by difficulties in obtaining samples without disturbing animals. This study explored the viral diversity of wild mammals inhabiting the Foreste Casentinesi National Park (Central Italy) using non-invasive fecal sampling. From 2021 to 2022, 99 fecal samples from several species were collected and analyzed by PCR and metagenomic next-generation sequencing. Of 26 pools examined, 10 (38.5%) tested positive for at least one viral target. Astroviruses were the most frequently detected, found in deer, foxes, wolves, small mustelids, and porcupines. Several sequences showed low similarity to known strains, suggesting divergent or novel viral lineages. Metagenomic analysis also identified members of Circoviridae, Anelloviridae, and Picobirnaviridae. While none of these virus families are currently recognized as major zoonotic agents, their widespread occurrence in wildlife and domestic animals underscores the importance of continued surveillance to better assess their ecological roles, host range, and potential implications for both animal and human health. These results provide new insights into the virome of European wildlife, including the first reports of some viruses in certain species. Overall, our study demonstrates that non-invasive surveillance is a valuable tool for monitoring ecosystem health and supports a One Health approach to early detection of viral threats.},
}
@article {pmid41375370,
year = {2025},
author = {Wang, Y and Hang, X and Shao, C and Zhang, Z and Guo, S and Li, R and Shen, Q},
title = {Organic Amendments and Trichoderma Change the Rhizosphere Microbiome and Improve Cucumber Yield and Fusarium Suppression.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/plants14233660},
pmid = {41375370},
issn = {2223-7747},
support = {ZZFH2024-2026QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; 42307171//the National Natural Science Foundation of China/ ; 2023M731724//the Postdoctoral Science Foundation of China/ ; },
abstract = {Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance.},
}
@article {pmid41375040,
year = {2025},
author = {Rogges, E and Bertolazzi, G and Vacca, D and Borro, M and Lopez, G and Simmaco, M and Scattone, A and Firmani, G and Sorotos, M and Santanelli di Pompeo, F and Noccioli, N and Savino, E and Vecchione, A and Di Napoli, A},
title = {High-Throughput Molecular Characterization of the Microbiome in Breast Implant-Associated Anaplastic Large Cell Lymphoma and Peri-Implant Benign Seromas.},
journal = {Cancers},
volume = {17},
number = {23},
pages = {},
doi = {10.3390/cancers17233839},
pmid = {41375040},
issn = {2072-6694},
abstract = {Background: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a mature T-cell lymphoma linked to textured breast implants. A leading hypothesis suggests that chronic inflammation, combined with immunological and genetic factors, drives its pathogenesis. Two previous studies investigating bacterial biofilms on breast implant capsules have produced conflicting results, particularly regarding the enrichment of Ralstonia spp. Methods: We analyzed the microbiota profiles in seroma samples from 10 BIA-ALCL patients and 12 patients with non-neoplastic effusion, subclassified into acute-, mixed-, and chronic-type based on cellular composition. We used two metagenomic approaches: 16S rRNA gene sequencing and Nanopore sequencing with the "What's in My Pot?" (WIMP) taxonomic classifier. Our analyses included alpha and beta diversity metrics, as well as comparisons of Gram status and oxygen requirements. Results: Both sequencing methods identified Staphylococcaceae, Propionibacteriaceae, and Bradyrhizobiaceae as the most prevalent bacterial families in both BIA-ALCL and benign seroma samples. Notably, the Burkholderiaceae family was more abundant in some of the benign seromas according to the 16S rRNA sequencing, but Ralstonia spp. were not detected. BIA-ALCL showed higher richness (based on Nanopore data) and higher evenness (based on 16S rRNA data) compared to acute-type seromas, indicating a more homogenous representation of the different taxa identified. BIA-ALCL seromas did not cluster together based on Nanopore data, but they did form a distinct cluster with 16S rRNA data. This cluster was differentiated from the other two clusters by a relatively balanced presence of multiple families without overt dominance. We observed no significant differences in Gram staining between BIA-ALCL and benign samples using either method. However, non-aerobic bacterial families were enriched in BIA-ALCL cases only when analyzed with the Nanopore pipeline. Conclusions: Overall, our findings did not identify a distinctive microbial signature specifically associated with BIA-ALCL.},
}
@article {pmid41374325,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Edrees, HM and Abdelsalam, MH and Aljizani, F and Alqarni, S and Khateeb, E and Alzaben, F and Ibrahem, M and Mousa, AM and Huraysh, N and Abu-Okail, A},
title = {Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/diagnostics15232944},
pmid = {41374325},
issn = {2075-4418},
abstract = {Bloodstream infections and sepsis necessitate rapid, sensitive, and clinically relevant diagnostics to minimize treatment delays and improve clinical outcomes. Next-generation sequencing enables culture-independent pathogen detection, antimicrobial resistance profiling, and genome-informed epidemiology. This narrative review integrates clinical evidence with practical workflows across three complementary approaches. We describe the use of plasma microbial cell-free DNA for broad organism detection and burden monitoring, as well as metagenomic next-generation sequencing of blood or plasma for unbiased pathogen discovery, including culture-negative and polymicrobial infections. Same-day Oxford Nanopore Technologies sequencing of positive blood culture broth is also discussed as a way to accelerate species identification, targeted resistance reporting, and infection-prevention decisions. We outline the sample-to-result steps, typical turnaround time (TAT), and stewardship-aligned decision points. Analytical reliability depends on effective reduction in human DNA background, stringent control of background and reagent-derived nucleic acids in low-biomass samples, and documented and validated bioinformatics workflows that are supported by curated taxonomic and resistance databases. Quantitative reports should adhere to validated thresholds and should be interpreted in the context of internal controls and clinical pretest probability. Ongoing challenges include variable correlation between genotype and phenotype for specific pathogen and antibiotic pairs, interpretation of low-level signals, and inconsistent regulatory and reimbursement environments. Advances in portable sequencing, faster laboratory and analytical workflows, and scaled liquid biopsy strategies may further reduce the TAT and expand access. Integrating these tools within One Health frameworks and global genomic surveillance programs could support early resistance detection and coordinated public health action, which could help to advance sepsis care toward more precise treatment and real-time infection control insights.},
}
@article {pmid41374080,
year = {2025},
author = {Kimble, R and Shannon, OM},
title = {Can Beetroot (Beta vulgaris) Support Brain Health? A Perspective Review on Alzheimer's Disease.},
journal = {Nutrients},
volume = {17},
number = {23},
pages = {},
doi = {10.3390/nu17233790},
pmid = {41374080},
issn = {2072-6643},
mesh = {Humans ; *Alzheimer Disease/prevention &amp; control ; *Beta vulgaris/chemistry ; *Brain/drug effects ; Antioxidants/pharmacology ; Nitrates/pharmacology ; Oxidative Stress/drug effects ; Neuroprotective Agents/pharmacology ; Animals ; Polyphenols/pharmacology ; Betalains/pharmacology ; },
abstract = {Alzheimer's disease (AD), the leading cause of dementia, has limited treatment options despite extensive pharmacological research. This has increased interest in dietary strategies that act across multiple pathological mechanisms. Beetroot (Beta vulgaris), known for its cardiovascular and metabolic benefits, contains a distinctive combination of bioactive compounds including inorganic nitrate, betalains, and polyphenols. Together these constituents influence vascular function, oxidative stress, mitochondrial efficiency, inflammation, and the microbiota. Previous reviews have typically focused on dietary nitrate in dementia prevention or have examined nitrate and betalains separately. In contrast, this review synthesises evidence on beetroot as a combined neuroprotective food. Preclinical data indicate that beetroot and its key constituents enhance antioxidant defences, support neuronal bioenergetics, and modulate cholinergic and inflammatory pathways. Human studies further suggest that nitrate-rich beetroot can improve cerebral blood flow and vascular responsiveness, and that higher intakes of plant-derived nitrate are associated with reduced cognitive decline. However, findings are inconsistent, most trials are small and short in duration, and research directly involving people with AD is scarce. By integrating vascular, antioxidant, and microbiome perspectives, this review identifies beetroot as a promising yet underexplored dietary candidate for AD management. Further mechanistic studies and multidomain approaches combining metagenomics, biomarkers, neuroimaging, and cognitive outcomes are needed.},
}
@article {pmid41373884,
year = {2025},
author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L},
title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311737},
pmid = {41373884},
issn = {1422-0067},
support = {LF-ST-21-500002//LEO Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.},
}
@article {pmid41373816,
year = {2025},
author = {Wang, F and Sun, X and Wang, K and Long, B and Li, F and Xie, D},
title = {Physiological and Multi-Omics Insights into Trichoderma harzianum Alleviating Aged Microplastic Stress in Nicotiana benthamiana.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311667},
pmid = {41373816},
issn = {1422-0067},
support = {2022GDASZH-2022010110//'GDAS' Project of Science and Technology Development/ ; 0525149001//Innovation Capacity Building Project for Provincial Scientific Research Institutions/ ; 2024A1515030175//Guangdong Basic and Applied Basic Research/ ; },
mesh = {*Nicotiana/microbiology/drug effects/metabolism/genetics/growth &amp; development ; *Stress, Physiological/drug effects ; *Microplastics/toxicity ; *Hypocreales/physiology ; Reactive Oxygen Species/metabolism ; Transcriptome ; Gene Expression Regulation, Plant/drug effects ; *Trichoderma ; Multiomics ; },
abstract = {Microplastics derived from biodegradable PBAT film, widely used in agriculture, pose ecological and biological hazards. This study explores how Trichoderma harzianum T4 mitigates this microplastic-induced stress in Nicotiana benthamiana. Using five experimental setup-control (CK), low/high-dose aged microplastics (MP80/MP320), and their co-treatments with T. harzianum T4 (MP80+T4/MP320+T4), multi-omics analyses reveal the microplastic stress-alleviating mechanisms of T. harzianum T4. Aged microplastics significantly inhibit plant growth, promote reactive oxygen species (ROS) and malondialdehyde (MDA) accumulation, and disrupt metabolic homeostasis. Conversely, T. harzianum T4 activates the plant antioxidant defense system, reducing ROS/MDA levels and upregulating superoxide dismutase (SOD)/peroxidase (POD) activities, and promotes biomass. Transcriptomic analysis shows T. harzianum T4 reverses gene expression patterns disrupted by microplastics, particularly in DNA replication and pentose-glucuronic acid pathways. Metagenomic sequencing indicates T. harzianum T4 restores soil microbial diversity, increases the abundance of Bacteroidota and Myxococcota, downregulates antibiotic resistance genes (e.g., tetA5, MDR), and upregulates carbohydrate-active enzymes (CAZys), thereby enhancing carbon metabolism. In conclusion, T. harzianum T4 alleviates microplastic stress through a tripartite mechanism: activating plant stress-response gene networks, reshaping soil microbial communities, and modulating functional gene expression, offering a promising bioremediation strategy.},
}
@article {pmid41373768,
year = {2025},
author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311616},
pmid = {41373768},
issn = {1422-0067},
support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation &amp; purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.},
}
@article {pmid41373093,
year = {2025},
author = {Ströher, JA and Flôres, SH and de Freitas, AS and Salazar, MM and da Silva, LFF and Bresciani, L and Sant'Anna, V and Malheiros, PDS},
title = {Consumer Perception, Sensory Acceptance, and Microbial Characterization of Artisanal Milk Kefir During Shelf Life.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70739},
doi = {10.1111/1750-3841.70739},
pmid = {41373093},
issn = {1750-3841},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico-CNPq/ ; 140557/2024-5//Secretaria de Inova&#xe7;&#xe3;o, Ci&#xea;ncia e Tecnologia do Rio Grande do Sul (SICT)/ ; },
mesh = {*Kefir/microbiology/analysis ; *Consumer Behavior ; Humans ; Food Storage ; Animals ; Taste ; Probiotics/analysis ; Adult ; Food Microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; Female ; Brazil ; Male ; *Milk/microbiology ; Middle Aged ; Young Adult ; Fungi/isolation &amp; purification/classification ; Fermentation ; },
abstract = {Milk kefir is a traditional fermented beverage with a complex microbiota of bacteria and yeasts that contributes to its distinctive sensory profile and functional properties. Artisanal kefir, in particular, preserves this natural microbial diversity but faces challenges related to sensory stability and limited shelf life. This study investigated the physicochemical, microbiological, metagenomic, and sensory characteristics, as well as gastrointestinal survival, of artisanal kefir samples stored for 0, 15, and 30 days. The physicochemical and microbiological parameters remained within the limits established by Brazilian legislation throughout storage. Metagenomic analysis revealed changes in microbial composition, with reductions in certain bacterial species and alterations in the relative abundance of fungal genera over time. Simulated gastrointestinal survival tests confirmed the stability of bacterial populations, indicating the maintenance of probiotic potential. Sensory analysis demonstrated general acceptance of the product, with significant differences detected mainly in texture. The analysis of social representations highlighted associations with health, naturalness, and positive consumer perceptions. Together, these findings show that artisanal kefir remains safe, microbiologically stable, and acceptable to consumers for at least 30 days, providing insights that can guide future standardization and commercial development strategies. PRACTICAL APPLICATIONS: Artisanal kefir showed physicochemical, microbiological, and sensory stability for up to 30 days, maintaining its probiotic potential and consumer acceptance. These findings contribute to strategies for standardization, increased shelf life, and strengthened commercial development of the product.},
}
@article {pmid41373036,
year = {2025},
author = {Fidler, DB and George, PBL and Le Brun, LJ and Griffiths, RI and Jones, DL and McDonald, JE},
title = {Soil microbial adaptation to carbon deprivation: shifts in lignocellulolytic gene profiles following long-term plant exclusion.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00810-6},
pmid = {41373036},
issn = {2524-6372},
support = {NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; },
abstract = {BACKGROUND: Lignocellulose represents a primary input of organic carbon (C) into soils, yet the identity of specific microorganisms and genes which drive lignocellulose turnover in soils remains poorly understood. To address this knowledge gap, we used a 10-year grassland plant-exclusion experiment to investigate how reduced plant C inputs affect microbial communities and their lignocellulolytic potential using a combination of metagenomic sequencing and untargeted metabolomics. We specifically tested the hypothesis that microbial community function in bare fallow plots would transition towards microbiota with genes for recalcitrant biomass degradation (i.e., lignocellulose), when compared to grassland plots with high labile C inputs.<br><br>RESULTS: Long-term plant exclusion lowered soil C and nitrogen (N) and reduced cellulose content, whilst hemicellulose and lignin were unchanged. Similarly soil microbiomes were highly distinct in long-term bare soils, along with soil extracellular enzyme profiles, though short-term plant-removal effects were less apparent. Plant exclusion resulted in a general enrichment of Firmicutes, Thaumarchaeota, Acidobacteria, Fusobacteria, and Ascomycota, with a general reduction in Actinobacteria. However, changes in bare soil lignocellulose degradation genes were more associated with discrete taxa from diverse lineages, particularly the Proteobacteria. Grouping of lignocellulose-degrading genes into broad substrate classes (cellulases, hemicellulases and lignases) revealed a possible increase in lignin degradation genes under plant exclusion confirming our hypothesis, although all other changes were at the level of the carbohydrate-active enzyme (CAZy) family. Intriguingly, untargeted metabolome profiles were highly responsive to plant exclusion, even after only one year. Bare soils were depleted in oligosaccharides and enriched in monosaccharides, fatty and carboxylic acids, supporting emerging evidence of long-term persistent C being within simple compounds.<br><br>CONCLUSIONS: Together our data show that extracellular lignin degrading enzymes increase under long-term plant exclusion. There is now a need for increased focus on the microbial metabolic mechanisms which regulate the processing and persistence of enzymatically released compounds, particularly in energy limited soils.},
}
@article {pmid41373015,
year = {2025},
author = {Duvivier, M and Moumen, B and Héchard, Y and Moulin, L and Delafont, V and Wurtzer, S},
title = {Implementation and comparison of two concentration methods to detect and characterize bacteriophages and bacterial hosts from large drinking water samples.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00818-y},
pmid = {41373015},
issn = {2524-6372},
abstract = {Drinking water distribution systems (DWDS) are low biomass biomes harboring a large variety of microorganisms. Much of the attention has been focused on bacteria, whose diversity and abundance in DWDS were repeatedly shown to be influenced by abiotic factors such as pH, temperature, growth inhibitors and water sources. However, little is known about biotic factors, such as bacteriophage presence, even though they are known to be present in DWDS and to influence bacterial dynamics. While bacteriophage impact has been assessed in natural environments such as oceans, little is known about the way they shape DWDS bacterial communities. To fill this knowledge gap and accessing bacteriophage diversity from such low biomass environment, the present study aimed to propose and compare two methods based on ultrafiltration and adsorption/elution methods, already used for the concentration of bacteria and virus from water. To this end, both methods were compared with a weekly sample collection, for one month, on the DWDS of Paris, France. Metagenomic sequencing was performed on concentrated samples to investigate the presence and diversity of bacteriophages, using a coupling of complementary bioinformatic prediction tools. Though viral fractions represented a minority of recovered contigs (1.5 to 2.5%), most were associated with Caudoviricetes class. The predicted bacterial hosts matched with the observed bacterial diversity, highlighting the robustness of host prediction tool. A total of 437 putative phages were present in all samples, constituting a core phage diversity. Among those, 380 viral contigs contained sequences showing significant non-viral matches. We leveraged this information to further refine the inference of bioinformatics pairs of bacterial hosts and their phages. In conclusion, we propose a method to simultaneously concentrate bacteriophages with bacteria from low-biomass environment. Through metagenomics, this study showed that an optimized bioinformatic pipeline could provide an overview of DWDS phage diversity. Moreover, this method allowed to detect sequence similarities between phages and bacteria, suggesting potential genetic exchanges and providing clues for host spectrum. Altogether, this study highlights the tight interactions between bacteria and bacteriophages in drinking water and the possibility to study both phages and potential hosts to better grasp their intricate interplay.},
}
@article {pmid41372802,
year = {2025},
author = {Almas, S and Carpenter, RE and Tamrakar, VK and Singh, A and Sharma, A and Sharma, R},
title = {Precision metagenomics reveals microbial landscape in acute upper respiratory infections: a comprehensive dataset.},
journal = {BMC research notes},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13104-025-07519-2},
pmid = {41372802},
issn = {1756-0500},
abstract = {OBJECTIVES: The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina[®]/IDbyDNA Respiratory Pathogen ID/AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance.<br><br>DATA DESCRIPTION: This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial resistance detection, and therapeutic interventions. Its potential for reuse and integration with other omics datasets enhances its significance. The comprehensive nature of the data facilitates research into relationships between the respiratory microbiota and host factors, including clinical outcomes, immune responses, or genetic predispositions. Moreover, the article underscores the interdisciplinary potential by advocating for the integration of this dataset with other relevant datasets such as transcriptomics or metabolomics, enabling a deeper understanding of the intricate interactions in acute upper respiratory infections. The presented dataset contributes to the expanding knowledge in precision metagenomics and holds the promise to propel research and clinical practices in the field of respiratory diseases.},
}
@article {pmid41372750,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04560-w},
pmid = {41372750},
issn = {1471-2180},
abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.<br><br>METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.<br><br>RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37&#xa0;&#xb5;g/L), chromium (1.89&#xa0;&#xb5;g/L), and nickel (4.93&#xa0;&#xb5;g/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P&#x2009;<&#x2009;0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P&#x2009;<&#x2009;0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P&#x2009;<&#x2009;0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.<br><br>CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.},
}
@article {pmid41310458,
year = {2025},
author = {Li, Q and Chen, T and Hu, B and Guo, L and Dou, Z and Feng, W and Ning, X and Xiao, H and Liu, G},
title = {Clinical characteristics and management of Listeria monocytogenes meningitis in children beyond the neonatal stage: a 10 years retrospective study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1708},
pmid = {41310458},
issn = {1471-2334},
abstract = {INTRODUCTION: The data of Listeria monocytogenes (LM) meningitis in children beyond the neonatal stage has been limited. We aimed to summarize the clinical characteristics, management, and risk factors of neurological complications in LM meningitis children beyond the neonatal stage.<br><br>METHODS: We retrospectively reviewed LM meningitis cases from January 2013 to December 2022 at Beijing Children&#x2019;s Hospital. Clinical characteristics, pathogen detection results and management were analyzed.<br><br>RESULTS: There were 41&#x2009;LM meningitis patients at our center, with a median age of 2.3&#x2009;years (ranging from 6&#x2009;months to 9&#x2009;years). Most patients (97.6%) were immunocompetent. Fourteen patients (34.1%) had a history of suspected food contamination. The most common symptom was fever (100%), and 29.2% of patients presented with diarrhea in the early stages of the disease. About 61% of patients showed monocyte predominance in their cerebrospinal fluid (CSF). Thirteen patients (31.7%) experienced neurological complications. Multivariate analysis indicated that a diagnosis delay of more than one week and a CRP level of 50&#x2009;mg/L or higher were significant risk factors for these neurological complications (p&#x2009;<&#x2009;0.05). CSF culture rates were much higher before hospital admission (85.7%) compared to after (31.7%, p&#x2009;<&#x2009;0.05). Metagenomic next-generation sequencing (mNGS) identified pathogens in 3 culture-negative cases. In total, 97.5% of patients received meropenem, either alone or with other antibiotics, and all children recorded a Glasgow Outcome Scale (GOS) score of 5.<br><br>CONCLUSION: LM meningitis can affect immunocompetent children. Strengthening food hygiene and safety education is crucial to prevent LM infection. Penicillin or ampicillin are the preferred treatments, while meropenem may be considered as an alternative treatment.},
}
@article {pmid41270835,
year = {2025},
author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L},
title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.},
journal = {Virus research},
volume = {362},
number = {},
pages = {199666},
pmid = {41270835},
issn = {1872-7492},
mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; },
abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.},
}
@article {pmid41372637,
year = {2025},
author = {Kosmopoulos, JC and Pallier, W and Malik, AA and Anantharaman, K},
title = {Ecosystem health shapes viral ecology in peatland soils.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41372637},
issn = {2058-5276},
support = {DBI2047598//National Science Foundation (NSF)/ ; 2137424//National Science Foundation (NSF)/ ; },
abstract = {Peatlands hold up to one-third of Earth's soil carbon but are increasingly turning from being carbon sinks to becoming carbon sources due to human impacts. Restoration efforts aim to reverse this trend, but viral influences on peatland recovery remain unclear, despite viruses being potent regulators of microbiomes and ecosystem function. Here we sequenced soil metagenomes to study viral communities across seven UK peatlands, each encompassing areas representing three peatland ecosystem health statuses: natural, damaged and restored. We found that viral diversity and community structure were shaped by both geography and ecosystem health. Viruses were geographically widespread, yet exhibited ecosystem health-specific endemism and functional adaptation, highlighting their sensitivity to restoration. Virus-host dynamics ranged from stable 'piggyback-the-winner' relationships to decoupled dynamics in those infecting keystone aerobes, sulfate reducers, carbohydrate degraders and fermenters. These findings position viruses as dynamic drivers of peatland ecosystem recovery and could unlock pathways to bolster carbon retention and accelerate climate mitigation.},
}
@article {pmid41372407,
year = {2025},
author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N},
title = {Gut micro-organisms associated with health, nutrition and dietary interventions.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41372407},
issn = {1476-4687},
abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.},
}
@article {pmid41371202,
year = {2025},
author = {Xu, B and Zhang, H and Li, M and Lin, H and Wang, C},
title = {Application of metagenomic next-generation sequencing in diagnose the pulmonary infections caused by Aureobasidium melanogenum: A case report and review of the literature.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117213},
doi = {10.1016/j.diagmicrobio.2025.117213},
pmid = {41371202},
issn = {1879-0070},
abstract = {Aureobasidium melanogenum (A. melanogenum) is a black-yeast-like fungus widely present in nature that rarely causes human infections. We report a case of pulmonary infection caused by A. melanogenum in a 60-year-old male farmer, who initially presented with severe paroxysmal coughing and right-sided chest pain and was initially misdiagnosed with tuberculosis or lung cancer. While sputum cultures were negative, metagenomic next-generation sequencing (mNGS) detected A. melanogenum in bronchoalveolar lavage fluid, which was confirmed by PCR-Sanger sequencing. Susceptibility thresholds for Aureobasidium have not been established, and the optimal treatment requires further investigation. This case highlights that A. melanogenum infection should be considered even when lung lesions cannot be diagnosed by conventional methods. mNGS demonstrates potential advantages in detecting this pathogen, underscoring its value in diagnosing such rare fungal pulmonary infections.},
}
@article {pmid41371154,
year = {2025},
author = {Tervo, S and Zalewski, A and Vauhkonen, H and Nieoczym, M and Kołodziej-Sobocińska, M and Lehikoinen, S and Aaltonen, K and Smura, T and Sironen, T and Pettersson, J},
title = {Virus circulation in native, introduced, and farmed mustelids in Poland.},
journal = {Virology},
volume = {615},
number = {},
pages = {110771},
doi = {10.1016/j.virol.2025.110771},
pmid = {41371154},
issn = {1096-0341},
abstract = {American mink (Neogale vison) are known carriers of various viruses, including many zoonoses. Their susceptibility to a wide range of pathogens and anatomical similarities to human lungs raise concerns about their potential role in facilitating interspecies transmission. Here we analysed viruses detected in tissue samples of native mustelids, and feral and farmed mink in Poland (2019-2022). The species included American mink, pine and stone marten (Martes martes, Martes foina), weasel (Mustela nivalis), European badger (Meles meles), European polecat (Mustela putorius), and Eurasian otter (Lutra lutra). Blood samples were tested for antibodies against SARS-CoV-2 (n = 270), and lung samples were subjected to genetic studies by PCR (n = 129) or metagenomics (n = 37). No evidence of SARS-CoV-2 was found in feral or wild populations, although two farmed mink tested positive for SARS-CoV-2 by PCR. Aleutian mink disease virus (AMDV) and mink Torque teno neovison virus (mTTV) were identified by metagenomics, and PCR analyses revealed frequent co-infection. AMDV was most prevalent in mink, while other mustelids showed serological evidence but were PCR-negative suggesting viral clearance. AMDV-DNA was found in 26.4 % and mTTV-DNA in 87.8 % of tissue samples. Two animals were co-infected with AMDV, mTTV, and SARS-CoV-2. Phylogenetic analysis revealed both local persistence and inter-farm transmission of AMDV, including transmission between feral and farmed mink. mTTV showed mixing of strains between Poland and China. The findings stress the need for improved surveillance and biosafety to monitor zoonotic threats and cross-species transmission.},
}
@article {pmid41371144,
year = {2025},
author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y},
title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140716},
doi = {10.1016/j.jhazmat.2025.140716},
pmid = {41371144},
issn = {1873-3336},
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.},
}
@article {pmid41371128,
year = {2025},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}
@article {pmid41370957,
year = {2025},
author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G},
title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.},
journal = {Environment international},
volume = {207},
number = {},
pages = {109971},
doi = {10.1016/j.envint.2025.109971},
pmid = {41370957},
issn = {1873-6750},
abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.},
}
@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97751},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}
@article {pmid41369685,
year = {2025},
author = {Mohammadi, R and Morovati, H and Safari, F},
title = {The human mycobiome: a critical yet understudied component of health and disease.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001631},
pmid = {41369685},
issn = {1465-2080},
mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; },
abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.},
}
@article {pmid41369293,
year = {2025},
author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L},
title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf273},
pmid = {41369293},
issn = {1751-7370},
abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.},
}
@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001632},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation &amp; purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}
@article {pmid41369016,
year = {2025},
author = {Southwood, LL and Long, A and Perez, J and Daniel, S and Bittinger, K and Aitken, M and Redding, L},
title = {Effect of surgical antimicrobial prophylaxis duration for colic surgery on complications and resistome.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/evj.70137},
pmid = {41369016},
issn = {2042-3306},
support = {//Raymond Firestone Research Foundation/ ; },
abstract = {BACKGROUND: Based on human studies, surgical antimicrobial (AMD) prophylaxis (SAP) beyond 24 h is unnecessary and potentially detrimental.<br><br>OBJECTIVE: To compare clinical and microbiological outcomes in patients receiving 24- or 72-h of SAP for colic surgery.<br><br>STUDY DESIGN: Prospective randomised clinical trial.<br><br>METHODS: Horses that recovered from colic surgery were considered. Exclusion criteria were (1) age <2&#x2009;years; (2) Miniature Horses, pony, and draught breeds; (3) azotaemia; (4) recent hospitalisation, colic surgery, or AMDs; (5) local AMD administration. Eligible horses were randomly assigned to receive SAP with potassium penicillin and gentamicin for 24- or 72-h. Clinical data and complications were compared between SAP groups. Admission and discharge faecal samples from a subset of horses (N&#x2009;=&#x2009;49) underwent shotgun metagenomic sequencing on an Illumina platform. Host reads were filtered by aligning to reference genomes using the Burrows-Wheeler Aligner, and taxonomic classification was performed with kraken2. Sequencing reads were aligned to the Comprehensive Antimicrobial Resistance Database (CARD)5 and characterised using the AMR++ pipeline. The microbiome/resistome was characterised and compared between SAP groups over time.<br><br>RESULTS: One hundred and forty horses completed the study (24-h N&#x2009;=&#x2009;71 and 72-h N&#x2009;=&#x2009;69). The only clinical variable that was different between SAP groups was age (24-h median age 16 [IQR 9, 20] and 72-h 12 [6, 18] years, p&#x2009;=&#x2009;0.03). There was no significant difference between groups for any complications including incisional infection (24-h 17 [95% CI 10-27]% and 72-h 16 [9-26]%, p&#x2009;=&#x2009;0.9). Time was the main driver of changes in the microbiome/resistome: alpha diversity decreased while AMD resistance genes associated with administered AMD increased between admission and discharge. Discharge beta-lactam resistance genes were significantly higher in the 72-h than the 24-h group.<br><br>MAIN LIMITATIONS: Single hospital, small numbers for complications, clinicians not blinded to SAP group.<br><br>CONCLUSIONS: SAP for 24-h is recommended for horses undergoing colic surgery.},
}
@article {pmid41368664,
year = {2025},
author = {Diaz, AJ and Centurioni, DA and Lasek-Nesselquist, E and Lapierre, P and Egan, CT and Perry, MJ},
title = {Whole genome sequencing of neurotoxin-producing Clostridium species in New York state to bolster epidemiological investigations and reveal patterns of diversity and distribution.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1651032},
pmid = {41368664},
issn = {2296-2565},
mesh = {New York/epidemiology ; *Whole Genome Sequencing ; Humans ; *Clostridium/genetics/isolation &amp; purification/classification ; Phylogeny ; Polymorphism, Single Nucleotide ; Botulism/epidemiology ; *Neurotoxins ; Retrospective Studies ; Botulinum Toxins/genetics ; },
abstract = {Clostridia that produce neurotoxins are highly relevant organisms to public health. While cases of botulism [caused by C. botulinum and other organisms that produce botulinum neurotoxin (BoNT)] are rare, the severity of this disease necessitates robust epidemiologic surveillance to promptly identify and mitigate outbreaks. Next generation sequencing (NGS) can provide additional support to these investigations through single nucleotide polymorphism (SNP)-based analysis, phylogenetic reconstruction, toxin subtyping, and structural analysis. Until recently, testing for this disease was restricted to traditional culture or molecular methods such as polymerase chain reaction (PCR) to detect bont genes, while mouse bioassay and endopeptidase-mass spectrometry (Endopep-MS) methods confirmed the presence of enzymatically active toxin. The New York State Department of Health (NYSDOH) Wadsworth Center Biodefense Laboratory performed a retrospective whole genome sequence (WGS) analysis of approximately 240 Clostridium spp. isolates from the past 40 years to supplement traditional test results and further characterize these organisms. Genomic analyses identified seven BoNT serotypes/serotype combinations, including A4(B5), A5(B2'), and B5F2 that were uncharacteristic of samples typically received. Additionally, SNP-based analysis and de novo genome assemblies retrospectively validated several epidemiology links or differentiated samples previously tested with only traditional methods. Our work highlights the clinical utility of supplementing conventional data with NGS to further characterize BoNT-producing organisms and underscores the importance of incorporating WGS into laboratory workflows to support epidemiologic investigations. However, several obstacles still exist which may prevent implementation. These include the expertise needed to execute bioinformatic analyses and interpret the resulting data, a lack of standardized bioinformatic workflows, and difficulty in determining SNP-based thresholds to identify linked samples without incorporation of additional data and analyses. Supplementing or replacing short-read sequencing with long-read sequencing (LRS) and the use of metagenomic or capture-based enrichment for analysis of primary specimens could increase the leverage obtained from WGS in epidemiological investigations.},
}
@article {pmid41368641,
year = {2025},
author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L},
title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1696701},
pmid = {41368641},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs &amp; derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; },
abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.<br><br>METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.<br><br>RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/I&#x3ba;B&#x3b1;/NF-&#x3ba;B pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.<br><br>CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-&#x3ba;B signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.},
}
@article {pmid41368505,
year = {2025},
author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D},
title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20328},
pmid = {41368505},
issn = {2167-8359},
mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; },
abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.},
}
@article {pmid41368072,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Geers, A and , and Busi, SB and Battin, TI},
title = {Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf076},
pmid = {41368072},
issn = {2730-6151},
abstract = {The factors and processes that shape microbial genomes and determine the success of microbes in different environments have long attracted scientific interest. Here, leveraging 2855 metagenome-assembled genomes sampled by the Vanishing Glacier Project from glacier-fed streams (GFSs), we shed light on the genomic architecture of the benthic microbiome in these harsh ecosystems-now vanishing because of climate change. Owing to glacial influence, the GFS benthic habitat is unstable, notoriously cold, and ultra-oligotrophic. Along gradients of glacial influence and concomitant variation in benthic algal biomass across 149 GFSs draining Earth's major mountain ranges, we show how genomes of GFS bacteria vary in terms of size, coding density, gene redundancy, and translational machinery. We develop a novel, phylogeny-rooted analytical framework that allows pinpointing the phylogenetic depth at which patterns in genomic trends occur. These analyses reveal both deep- and shallow-rooting phylogenetic patterns in genomic features associated with key GFS taxa and functional potential relevant to live in these ecosystems. Additionally, we highlight the role of several clades of Gammaproteobacteria in shaping community-level genomic architecture. Our work shows how genome architecture is shaped by selective environmental constraints in an extreme environment. These insights are important as they reveal putatively important adaptations to the GFS environment which is now changing at rapid pace due to climate change.},
}
@article {pmid41367710,
year = {2026},
author = {He, M and Chen, F and Xian, X and Guo, Z},
title = {Diagnosis and treatment of invasive fungal disease in children with hematological malignancies after chemotherapy: Challenges and strategies (Review).},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {1},
pages = {21},
pmid = {41367710},
issn = {1792-1015},
abstract = {Invasive fungal disease (IFD) has a high incidence rate in pediatric patients with hematological malignancies and hematopoietic stem cell transplantation, markedly elevating mortality rates. Major pathogens include Aspergillus, Candida and emerging non-Aspergillus molds. Clinical manifestations such as persistent fever and dyspnea are frequently non-specific, complicating early diagnosis. Invasive candidiasis typically manifests as candidemia or hepatosplenic infection, whereas invasive aspergillosis predominantly involves the lower respiratory tract. Prophylactic antifungal therapy reduces IFD risk but may lead to breakthrough IFD, particularly during prolonged neutropenia (>14 days). Treatment strategies require individualized selection between monotherapy and combination regimens, incorporating patient status, local epidemiology, prior antifungal exposure, drug metabolism and socioeconomic factors; however, treatment strategies can be hindered by diagnostic challenges including age-specific biomarker thresholds. Emerging techniques such as metagenomic next-generation sequencing show promise for rapid pathogen identification. Central nervous system involvement occurs in a certain proportion of pediatric cases and requires multimodal intervention. Early diagnosis through optimized imaging and timely initiation of targeted therapy are key to overcome clinical challenges and improving prognosis in this vulnerable population. The present review aimed to systematically review the epidemiological characteristics, diagnostic challenges and therapeutic strategies of IFD in pediatric hematological malignancies post-chemotherapy. By collating current clinical evidence, the present review provides an evidence-based framework for optimizing management in this high-risk population.},
}
@article {pmid41367425,
year = {2025},
author = {An, Y and Xu, M and Kang, Y and Fang, J and Zhang, X},
title = {Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588029},
pmid = {41367425},
issn = {1664-302X},
abstract = {BACKGROUND: The frequency of acute exacerbations (AECOPD) is a critical predictor of disease progression in chronic obstructive pulmonary disease (COPD). However, the dynamics of the lower respiratory microbiome across a spectrum of exacerbation frequency remain poorly characterized, limiting insights into microbial drivers of susceptibility.<br><br>METHODS: We conducted a cross-sectional study of 39 hospitalized AECOPD patients, stratified into non-frequent (NFE, &#x2264; 1 event/year, n = 11), moderate (ME, 2 events/year, n = 13), and frequent exacerbators (FE, &#x2265;3 events/year, n = 15). Metagenomic next-generation sequencing (mNGS) was performed on bronchoalveolar lavage fluid (BALF) to profile the airway microbiome.<br><br>RESULTS: Microbial alpha diversity exhibited a significant, graded decline from NFE to FE groups (e.g., Shannon index: NFE 3.68 &#xb1; 0.34, ME 3.02 &#xb1; 1.02, FE 0.84 &#xb1; 0.54; p < 0.05). Beta diversity analysis revealed distinct community clustering by exacerbation phenotype (PERMANOVA R[2] = 0.19, p = 0.001). The FE group was characterized by a striking dominance of Pseudomonadota (relative abundance: 72.25%), which correlated positively with exacerbation frequency (r = 0.536, p < 0.001). In contrast, commensal taxa including Streptococcus (r = -0.814, p < 0.0001) and others within the Bacillota and Bacteroidota phyla were depleted in FE and were negatively associated with exacerbation frequency. Twelve exacerbation-resilient taxa (83.3% belonging to Bacillota/Bacteroidota) were positively correlated with FEV1% predicted (r = 0.322-0.483, p < 0.05). Alpha diversity indices showed a strong inverse association with exacerbation frequency (r = -0.84 to -0.86, p < 0.001) but not spirometric measures.<br><br>CONCLUSION: Our findings delineate a gradient of airway microbial dysbiosis along the exacerbation frequency spectrum in COPD. The exacerbation-prone phenotype is defined by a loss of microbial diversity, expansion of Pseudomonadota, and depletion of potentially protective commensals. These microbiome features represent promising biomarkers for identifying high-risk patients and may inform future microbiome-targeted therapeutic strategies.},
}
@article {pmid41367410,
year = {2025},
author = {Tansirichaiya, S and Songsomboon, K and Wigand, J and Winje, E and Chaianant, N and Leartsiwawinyu, W and Al-Haroni, M},
title = {Geographic signatures in the oral resistome: a comparative metagenomic analysis of healthy individuals from Thailand and Norway.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589656},
pmid = {41367410},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is an important yet understudied reservoir of antimicrobial resistance genes (ARGs), potentially shaped by geographic variation in antibiotic usage.<br><br>OBJECTIVE: To compare the oral resistomes of healthy adults from Thailand and Norway, two countries with contrasting antimicrobial use practices, using shotgun metagenomic sequencing.<br><br>DESIGN: Stimulated saliva samples were collected from healthy adults in Thailand (n&#x2009;=&#x2009;43) and Norway (n&#x2009;=&#x2009;50). ARGs were identified with AMRPlusPlus against the MEGARes database, and microbial taxonomy was profiled with KrakenUniq. Diversity metrics, ordination, and clustering analyses assessed resistome and microbiome structures.<br><br>RESULTS: Thai samples exhibited significantly greater ARG richness, evenness, and diversity (p&#x2009;<&#x2009;0.001), driven by higher abundances of multi-biocide, nucleoside, and copper resistance genes. Norwegian samples were enriched in aminoglycoside, sulfonamide, and quaternary ammonium compound resistance genes. Both cohorts shared core oral genera, but Thai samples showed greater taxonomic richness without differences in overall microbiome diversity. Non-metric multidimensional scaling and PERMANOVA revealed stronger geographic separation for resistomes (R&#xb2;&#x2009;=&#x2009;0.639) than microbiomes (R&#xb2;&#x2009;=&#x2009;0.382). Co-occurrence networks highlighted structured associations between ARG groups and bacterial genera, suggesting ecological influences beyond taxonomic composition.<br><br>CONCLUSIONS: These results reveal distinct geographic signatures in the oral resistome that are not fully explained by microbiome structure, reflecting the influence of local ecological and societal factors, including antimicrobial exposure. The findings highlight the oral cavity as a dynamic ARG reservoir and support its inclusion in regional antimicrobial resistance surveillance to inform public health strategies.},
}
@article {pmid41367394,
year = {2025},
author = {Oke, OE and Fasasi, LO and Opowoye, IO and Akosile, OA},
title = {The role of gut microbiota-derived metabolites in modulating poultry immunometabolism.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1700406},
pmid = {41367394},
issn = {1664-042X},
abstract = {The poultry sector is crucial to global food security, but it faces increasing challenges from heat stress, viral diseases, and restrictions on antibiotic use. These stressors highlight immunometabolism, the junction of immune function and metabolic pathways, as a crucial factor in determining the productivity and health of poultry. There is growing evidence that the gut microbiota is a dynamic metabolic organ that produces a diverse range of bioactive metabolites in addition to its function in nutritional digestion. The immunometabolism of poultry is significantly influenced by these microbiota-derived metabolites, including short-chain fatty acids, bile acid derivatives, amino acid catabolites, vitamins, and polyamines. Disease resistance, vaccination responsiveness, and stress adaptability are shaped by their modulation of intestinal barrier integrity, energy balance, oxidative stress resilience, and immune cell activation. This review summarises what is currently known about the functional diversity and composition of the gut microbiota in poultry, describes the concept of immunometabolism in birds, and assesses the mechanisms by which microbial metabolites regulate metabolic and immunological crosstalk. Prebiotics, probiotics, synbiotics, postbiotics, phytochemicals, and other nutritional and managerial interventions that improve advantageous metabolite profiles are given particular consideration. Applications to enhance poultry health, alleviate heat stress, reduce reliance on antibiotics, and promote sustainable production are also discussed. For mapping metabolite-immune interactions, emerging methods such as germ-free models, metabolomics, metagenomics, and systems biology approaches are emphasised as revolutionary. Metabolites produced by the gut microbiota are crucial to poultry immunometabolism and offer promising opportunities for precision nutrition and healthcare. Bridging the existing research gaps using integrative, multidisciplinary methods to promote sustainable and resilient poultry production is needed. This review centres on the mechanistic axis linking gut microbiota-derived metabolites to host immunometabolic regulation, tracing the pathway from metabolite generation through receptor activation and immune-metabolic reprogramming to measurable phenotypic outcomes in poultry.},
}
@article {pmid41367385,
year = {2025},
author = {Cavenaghi, A and Mallah, NEZ and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A and Salas, A},
title = {Decoding the peripheral transcriptomic and meta-genomic response to music in autism spectrum disorder via saliva-based RNA sequencing.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1696704},
pmid = {41367385},
issn = {2296-889X},
abstract = {INTRODUCTION: Behavioral interventions for autism spectrum disorder show variable outcomes, highlighting the need for complementary therapies. Music-based interventions are promising, yet their molecular mechanisms remain unclear. Saliva-based RNA sequencing (RNA-seq) provides a non-invasive framework to monitor neuroimmune and metabolic dynamics, but its application in autism remains underexplored.<br><br>METHODS: We explored the buccal transcriptional effects of music exposure in five individuals with autism (8-37 years; 60% female). To overcome saliva-specific limitations, we combined Poly-A selection and Human-Enriched protocols preparation methods to enhance human transcript detection and reproducibility while capturing microbial signals.<br><br>RESULTS: Individually, each dataset revealed a few differentially expressed genes, but integrated analysis improved biological resolution. Consistently modulated genes included HERC6, TSPAN5, and REM2, involved in neurodevelopmental and immune functions. Enrichment analyses highlighted pathways associated with immune regulation, oxidative phosphorylation, and epithelial differentiation, hallmarks of autism, such as immune dysregulation and mitochondrial dysfunction. Co-expression network analysis identified modules correlated with music exposure. The AKNA module, previously linked to autism, was downregulated and enriched for Ras-related GTPase and immune pathways, suggesting modulation of intracellular signaling and inflammation. Conversely, upregulation of the UBE2D3 module indicated activation of endoplasmic reticulum stress responses, a contributor to autism. Exploratory metagenomics identified 15 microbial species responsive to music exposure, including Acidipropionibacterium acidipropionici and Propionibacterium freudenreichii, producers of propionic acid, a metabolite associated with autism-like behaviors and neuroinflammation.<br><br>CONCLUSION: Saliva-based RNA-seq can stably capture transcriptomic and microbial responses to behavioral stimuli. Music exposure modulates neuroimmune pathways relevant to autism, supporting the biological plausibility of music therapy and demonstrating saliva-based RNA-seq as a viable, non-invasive tool for monitoring intervention outcomes.},
}
@article {pmid41366867,
year = {2025},
author = {Khaengraeng, C and Mhuantong, W and Chaiprom, U and Bunkoed, W and Kuncharoen, N and Kasem, S and Chatnaparat, T and Suwannarat, S},
title = {Fungal and Bacterial Communities Associated with Northern Corn Leaf Blight in Resistant and Susceptible Sweet Corn.},
journal = {The plant pathology journal},
volume = {41},
number = {6},
pages = {736-754},
doi = {10.5423/PPJ.OA.05.2025.0060},
pmid = {41366867},
issn = {1598-2254},
support = {FF(KU)2.66//Kasetsart University Research and Development Institute/ ; },
abstract = {Northern corn leaf blight (NCLB), caused by Exserohilum turcicum (Setosphaeria turcica), is a major disease that negatively impacts the yield and quality of sweet corn. Plant-associated microbes hold great potential for enhancing crop productivity and sustainability. This study investigated the fungal and bacterial communities associated with NCLB in resistant and susceptible sweet corn cultivars using amplicon metagenomic sequencing. The structural composition and diversity of the fungal community in symptomatic NCLB-susceptible cultivars differed significantly from those in asymptomatic NCLB-resistant cultivars. In contrast, the bacterial communities showed no significant differences between resistant and susceptible cultivars in both the phyllosphere and rhizosphere. Exserohilum and Alternaria were significantly more abundant in the phyllosphere of symptomatic NCLB-susceptible plants, while fungal genera such as Sporobolomyces and Aureobasidium, along with the order Dothideales and the bacteria Bacillus, were significantly more abundant in the phyllosphere of asymptomatic NCLB-resistant cultivars. Microbial metabolic functions related to sugar metabolism-including sucrose biosynthesis and the degradation of glucose and xylose, compounds abundant in plant cell walls-were enriched in the phyllosphere of symptomatic NCLB-susceptible plants. In contrast, functions associated with detoxification and defense responses to plant phenolic compounds were enriched in microbes from asymptomatic NCLB-resistant cultivars. Additionally, Bacillus, identified ash part of the core microbiome, and the epiphytic yeast Sporobolomyces, identified as a hub in the microbial network, exhibited antimicrobial activity that may suppress E. turcicum. These findings offer valuable insights into the role of microbial communities in plant health and disease resistance, with promising implications for developing microbiome-based strategies to manage NCLB.},
}
@article {pmid41366832,
year = {2025},
author = {Wu, X and Yang, C and Qing, L and Yang, W and Zhou, K and Lu, G},
title = {Metagenomic Next-generation Sequencing Aids Diagnosis of Leishmania donovani-associated Hemophagocytic Lymphohistiocytosis in Infants: Case Report and Systematic Review.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005078},
pmid = {41366832},
issn = {1532-0987},
abstract = {Diagnosing hemophagocytic lymphohistiocytosis (HLH) triggers in infants is challenging. In a 9-month-old boy with unresponsive fever and pancytopenia, conventional tests were negative. Metagenomic next-generation sequencing detected Leishmania donovani, confirming Leishmania donovani-associated HLH. Targeted antiparasitic therapy replaced empiric immunosuppression, leading to rapid recovery. This case demonstrates that metagenomic next-generation sequencing is crucial for rapid pathogen identification in critically ill infants with HLH of unknown cause.},
}
@article {pmid41366711,
year = {2025},
author = {Rey Redondo, E and Xu, W and Xu, Y and Sun, R and Wan, SH and Leung, SKK and Yung, CCM},
title = {Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00803-5},
pmid = {41366711},
issn = {2524-6372},
support = {Hong Kong PhD Fellowship Scheme//Research Grants Council of Hong Kong/ ; 16102024//Research Grants Council of Hong Kong/ ; },
abstract = {BACKGROUND: Marine microbial communities drive global biogeochemical cycles and oceanic food webs, yet our understanding of their holistic temporal dynamics remains limited, particularly in the South China Sea. Most studies have focused on specific taxonomic groups or single temporal scales, leaving a gap in comprehensive, multi-domain, and multi-timescale analyses.<br><br>RESULTS: Using an integrated multi-omics approach that combined metagenomic, metatranscriptomic, and metaviromic analyses, we conducted time-series sampling over 48-h periods during winter and summer to investigate microbial community dynamics in the coastal South China Sea. Seasonal transitions were identified as the primary drivers of community shifts, with diel variations playing a secondary role across all taxonomic domains. Within seasons, diel changes followed a progressive trajectory rather than recurring cyclic patterns. Eukaryotic communities exhibited the most pronounced temporal fluctuations, while prokaryotic and viral communities displayed remarkable stability. Unlike previous coastal studies, viral communities maintained high similarity between seasons, suggesting the presence of a persistent viral reservoir in this region. Gene expression analysis revealed dynamic population shifts in photosynthetic microorganisms, with Mamiellophyceae green algae and their associated Prasinovirus displaying pronounced seasonal and diel rhythmicity.<br><br>CONCLUSIONS: This study provides novel insights into the temporal dynamics of microbial communities and host-virus interactions in the South China Sea. The stability of viral communities, coupled with synchronised host-virus activities, highlights potential mechanisms supporting ecosystem resilience in this coastal region. These findings enhance our understanding of marine ecosystem processes and establish a robust framework for exploring microbial responses to environmental changes on both diel and seasonal scales.},
}
@article {pmid41366428,
year = {2025},
author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW},
title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {285},
pmid = {41366428},
issn = {1742-2094},
support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; },
mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.<br><br>METHODS: C57BL6/J mice were randomized to CCI (6&#xa0;m/s, 2&#xa0;mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16&#xa0;S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.<br><br>RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.<br><br>CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.},
}
@article {pmid41366253,
year = {2025},
author = {Breselge, S and de Paula Dias Moreira, L and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Porcellato, D and Cotter, PD},
title = {Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {265},
pmid = {41366253},
issn = {2396-8370},
support = {818368//European Union's Horizon 2020/ ; 818368//European Union's Horizon 2020/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; USIRL-2019-1//HRB/SFI/ ; USIRL-2019-1//HRB/SFI/ ; SFI/16/RC/3835//Irish Department of Agriculture, Food and the Marine/ ; TC/2018/0025//Food for Health Ireland/ ; NA-AGFOODDEVELAUTH20201216//Institute for the Advancement of Food and Nutritional Sciences/ ; 101060218//European Union's Horizon Europe/ ; },
abstract = {Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specialized metabolic pathways and VOC profiles diverged. Metaproteomic analysis revealed a strong underappreciation of yeast contributions in metagenomic datasets, with yeasts representing a larger fraction of the proteome than predicted by DNA-based abundance. Lentilactobacillus hilgardii was enriched on WK grains, suggesting a specialized niche role. Our findings highlight the value of integrating multi-omics approaches to uncover microbial activity and community function in fermented foods and offer insights for the design of tailored WK starter cultures.},
}
@article {pmid41366061,
year = {2025},
author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY},
title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41366061},
issn = {1532-1827},
support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.<br><br>METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.<br><br>RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC&#x2009;=&#x2009;0.95, 95% CI&#x2009;=&#x2009;0.92-0.98).<br><br>CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.},
}
@article {pmid41365917,
year = {2025},
author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D},
title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {227},
pmid = {41365917},
issn = {2055-5008},
support = {314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; },
mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; },
abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.},
}
@article {pmid41279710,
year = {2025},
author = {Joshi, B and Zulk, JJ and Serchejian, C and Hameed, ZA and Larson, AB and Terwilliger, AL and Kumar, D and Mysorekar, IU and Britton, RA and Maresso, AW and Patras, KA},
title = {Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279710},
issn = {2692-8205},
abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, ΦHP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage significantly inhibited UPEC growth in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal ΦHP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed to uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable treatment option for UTI prevention.},
}
@article {pmid41055130,
year = {2025},
author = {Henson, LH and Christensen, KA and Sutherland, BJG and Johnson, HA and vonHoldt, B and Stronen, AV and Paquet, PC and Moody, J and Koop, BF and Darimont, CT},
title = {Grizzly bear population genomics across a coastal-interior ecotone in British Columbia, Canada.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {12},
pages = {},
doi = {10.1093/g3journal/jkaf237},
pmid = {41055130},
issn = {2160-1836},
support = {GEN013//Genome BC GeneSolve/ ; //LHH/ ; IT07676//MITACS Accelerate/ ; //Raincoast Chair of Applied Conservation Science/ ; },
mesh = {Animals ; British Columbia ; *Ursidae/genetics ; Polymorphism, Single Nucleotide ; *Genetics, Population ; *Metagenomics/methods ; Genotype ; *Ecosystem ; *Genomics/methods ; },
abstract = {Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning from central to northern latitudes in coastal and interior regions (to the west and east of the coastal mountain range [CMR], respectively). Clustering grizzly samples by genotypes identified 3 groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the 3 geographic groupings and were used to identify putative nonmigrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015 to 0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.},
}
@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
doi = {10.1111/1758-2229.70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}
@article {pmid41365463,
year = {2025},
author = {Xi, L and Chen, J and Chen, Y and Lai, K and Xu, S},
title = {Nonthyroidal illness syndrome and diagnostic utility of CSF mNGS: insights from a case series of neurological scrub typhus.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108291},
doi = {10.1016/j.ijid.2025.108291},
pmid = {41365463},
issn = {1878-3511},
abstract = {We describe five cases of neurological scrub typhus that highlight two critical, underrecognized aspects of this disease. First, cerebrospinal fluid metagenomic next-generation sequencing (CSF mNGS) accurately identified Orientia tsutsugamushi in all three patients tested, while the conventional Weil-Felix test was negative in every case, establishing mNGS as a pivotal diagnostic tool. Second, we uncovered a high prevalence of thyroid dysfunction, with nonthyroidal illness syndrome (NTIS) present in three of four patients tested, a novel systemic complication linked to severe inflammatory stress. Additional notable findings included frequent hypokalemia, at times severe enough to mimic periodic paralysis, and urban acquisition in two cases, suggesting an expanding epidemiological footprint. All patients improved on doxycycline-based regimens. This series underscores the diagnostic superiority of CSF mNGS and reveals NTIS as a key endocrine manifestation in neurological scrub typhus, urging greater clinical vigilance.},
}
@article {pmid41365368,
year = {2025},
author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X},
title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133782},
doi = {10.1016/j.biortech.2025.133782},
pmid = {41365368},
issn = {1873-2976},
abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.},
}
@article {pmid41365245,
year = {2025},
author = {De Koch, MD and Kraberger, S and Fielding, R and Smith, K and Schiavone, K and Hall, KR and Reid, VS and Boyea, D and Smith, EL and Schmidlin, K and Fontenele, RS and Martin, DP and Krupovic, M and Varsani, A},
title = {Novel circoviruses identified in short-finned pilot whale and orca from the North Atlantic Ocean.},
journal = {Virology},
volume = {615},
number = {},
pages = {110768},
doi = {10.1016/j.virol.2025.110768},
pmid = {41365245},
issn = {1096-0341},
abstract = {The family Circoviridae comprises viruses with small single-stranded DNA genomes that are known to infect various animals, resulting in considerable morbidity and mortality in some hosts. Circoviruses have been recently identified through metagenomic sequencing in diverse terrestrial vertebrate species, but their distribution and diversity in marine vertebrates remains underexplored. Here, we use high-throughput sequencing (HTS) to identify circoviruses from archived tissue samples of delphinids (order Artiodactyla, infraorder Cetacea, family Delphinidae). Based on the HTS data, we designed specific abutting primer pairs to recover seven complete circovirus genomes from individual delphinid hosts, namely, the short-finned pilot whale (Globicephala macrorhynchus, n = 5) and the orca (Orcinus orca, n = 2). The circoviruses from the two delphinid species share <65.4 % genome-wide pairwise nucleotide identity with all classified circovirus representative sequences and 66 % amongst themselves. Accordingly, these viruses, which we have named shofin circovirus and orcin circovirus, respectively, represent two novel species. This report also marks the first detection of cetacean circoviruses in the North Atlantic Ocean (near St. Vincent, Caribbean). Notably, analysis of the capsid protein sequences and structures of the delphinid circoviruses revealed notable elaborations within the surface exposed loops that have been previously shown to be a major antigenic epitope in porcine circovirus 2. Collectively, the delphinid circovirus genomes expand the known diversity of circoviruses of marine vertebrates and suggest similar evolutionary pressures exerted by the immune systems of cetacean and suina hosts, both members of the order Artiodactyla.},
}
@article {pmid41365225,
year = {2025},
author = {Jin, W and Zhang, Y and Li, Y and Li, R and Su, X and Jing, S and Wang, R and Qiu, Y and Xie, X and Guo, Z and Zhao, X},
title = {Polyethylene microplastics induce microbial functional reprogramming via rhizosphere network disruption, accelerating soil decline.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128236},
doi = {10.1016/j.jenvman.2025.128236},
pmid = {41365225},
issn = {1095-8630},
abstract = {Polyethylene microplastics (PE-MPs) are emerging soil pollutants with unclear mechanisms of impact on rhizosphere ecosystem functions. Using Angelica sinensis, a medicinal plant valued for its root use, as a model, this study integrated untargeted metabolomics, metagenomic sequencing, and PLS-PM modeling to investigate rhizosphere responses to different PE-MPs concentrations (250, 500, 1000 mg/kg). With increasing PE-MPs dosage, rhizosphere metabolic pathways shifted toward stress adaptation, featuring functional homeostasis and energy reprogramming. Exposure to PE-MPs significantly altered microbial community structure: bacterial and viral shannon, richness, and pielou evenness indices increased, fungal dominance and reduced evenness were observed, and archaeal diversity indices declined. Microbial network stability and functional redundancy weakened, increasing ecosystem sensitivity. Metabolite-microbe association analysis revealed synergistic enrichment patterns, suggesting that plants may recruit beneficial microbes through metabolite regulation. The PLS-PM modeling results indicated that metabolite changes regulate the expression of C/N/S/P cycling functional genes through shifts in bacterial and viral community compositions, where bacteria serve as the primary regulatory hubs and viruses play a key role in amplifying microbial signaling by influencing the microbial community. The expression of these functional genes was negatively correlated with the Soil Quality Index (SQI), indicating that PE-MPs-induced metabolic stress accelerates soil functional degradation. This study provides new insights into microplastic-driven rhizosphere disruption and offers a theoretical basis and biomarkers for microbial regulation and soil ecological restoration.},
}
@article {pmid41365051,
year = {2025},
author = {Wang, H and Congzhu, and Wang, J and Lin, X and Guo, Y and Kiani, FA and Zhou, X and Ding, Y},
title = {Clostridium perfringens can promote the formation of fatty liver in cows.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110826},
doi = {10.1016/j.vetmic.2025.110826},
pmid = {41365051},
issn = {1873-2542},
abstract = {During the periparturient period, reduced feed intake often causes negative energy balance in dairy cows, leading to fat mobilization, hepatic lipid accumulation, and fatty liver disease (FLD), ultimately compromising health and milk production. This study investigated the association between FLD and gut microbiota dysbiosis, with a particular focus on the role of Clostridium perfringens within the gut-liver axis. Metagenomic sequencing of ileal contents revealed a marked decrease in microbial diversity in cows with FLD, along with increased abundances of potential pathogens such as C. perfringens, Enterobacter cloacae, and Vibrio alginolyticus. Functional annotation indicated elevated expression of virulence factors (e.g., Hsp60, flagella, mu-toxin), antibiotic resistance genes (e.g., otrA, lsaC), and pathways related to lipopolysaccharide (LPS) biosynthesis and mitogen-activated protein kinase (MAPK) signaling pathways, suggesting enhanced pro-inflammatory potential. qPCR analysis of ileal tissue demonstrated reduced expression of tight junction proteins (zona occludens 1 (ZO-1), Claudin-1, and Occludin) and increased levels of pro-inflammatory cytokines (Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumour necrosis factor-alpha (TNF-α)), alongside a decrease in the anti-inflammatory cytokine interleukin-10 (IL-10), indicating compromised intestinal barrier function and local inflammation. Given the significant enrichment of C. perfringens in the ileum of FLD cows, we hypothesized its involvement in disease pathogenesis. To test this, C. perfringens was isolated and orally administered to antibiotic-pretreated mice fed a high-fat diet. These mice developed exacerbated hepatic steatosis, metabolic disturbances, and heightened inflammatory responses. Moreover, Western blot analysis revealed reduced expression of intestinal tight junction proteins (ZO-1, Claudin-1, Occludin), indicating increased intestinal permeability. Quantitative PCR confirmed upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and downregulation of IL-10 in both intestinal and hepatic tissues. These findings indicate that C. perfringens may promote FLD by impairing gut barrier integrity and enhancing inflammatory responses. In conclusion, our findings suggest that C. perfringens may contribute to the development of FLD in dairy cows by impairing intestinal barrier integrity and promoting systemic inflammation.},
}
@article {pmid41364992,
year = {2025},
author = {Alharbi, M and Nguyen-Dinh, T and Wong, WW and Leung, PM and Kessler, AJ and Greening, C and Cook, PLM},
title = {Dissimilatory nitrate reduction to ammonium driven by iron tolerant Lutibacter in coastal sediments.},
journal = {The Science of the total environment},
volume = {1010},
number = {},
pages = {181095},
doi = {10.1016/j.scitotenv.2025.181095},
pmid = {41364992},
issn = {1879-1026},
abstract = {The processes of denitrification and dissimilatory NO3[-] reduction to ammonium (DNRA) occupy a competing pivotal point in the nitrogen cycle. Denitrification leads to a loss of fixed nitrogen, while DNRA recycles NO3[-] as bioavailable ammonium. Iron (II) is known to enhance DNRA, by acting as an electron donor, however, the organisms responsible for iron driven DNRA remain poorly understood. Here we undertook incubations of sediment with NO3[-] and Fe[2+] additions followed by process measurements and metagenomic analysis to measure DNRA and microbial community structure. Addition of Fe[2+] stimulated DNRA, and greatly increased the relative abundance of flavobacteria (Lutibacter) in slurries over a period of 12-24 days compared to controls. We isolated a strain of Lutibacter from these slurries which mediated organotrophic and mixotrophic DNRA (while oxidising sulphide). No genes capable of Fe[2+] oxidation were detected in agreement with experiments that showed this strain had no ability to oxidise Fe[2+]. The addition of Fe[2+] to pure cultures had no significant effect on DNRA, suggesting these bacteria are not stimulated nor inhibited by the presence of Fe[2+]. As such, in contrast to previous studies, we find Fe[2+] addition to sediments enhances DNRA by favouring Fe tolerant Lutibacter and is uncoupled Fe[2+] oxidation in coastal sediments. This has implications for how pollutants such as higher Fe[2+] concentrations and disturbance can lead to bacterial community shifts that enhance nitrogen retention within ecosystems. Isolates of these robust bacteria have the potential to help recover NO3[-] as NH4[+] in novel water treatment systems.},
}
@article {pmid41364990,
year = {2025},
author = {Shen, S and Shimotori, K and Tsuchiya, K and Shigeta, S and Sueyoshi, M and Matsuda, T and Shimizu, Y},
title = {Carrier-resolved metagenomics suggests the dual "filter-hub" function of a large freshwater lake toward incoming antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {1010},
number = {},
pages = {181145},
doi = {10.1016/j.scitotenv.2025.181145},
pmid = {41364990},
issn = {1879-1026},
abstract = {Rivers and wastewater-treatment plants (WWTPs) convey antibiotic resistance genes (ARGs) to lakes. Studies simultaneously profiling ARGs and their carriers and tracking their persistence in lakes remain scarce. We collected cell- and virus-size fractions from Lake Biwa, Japan, 11 in-flowing rivers, and one WWTP for shotgun metagenomic sequencing. We reconstructed 326 bacterial metagenome-assembled genomes, 7917 plasmid contigs (472 harboring conjugation genes), and 32,375 viral contigs. The chromosomes contained 1502 ARGs (predominantly fluoroquinolone and glycopeptide resistance). The plasmids encoded efflux- and target-alteration determinants spanning 25 drug classes. Only 3.6 % of the viral genomes carried ARGs, chiefly qnr and dfr. ARG class composition differed among carriers, forming a spatial mosaic unrelated to land use or livestock density. Of the ARG-carrying cells and viruses, 85-97 % were undetectable in the lake, suggesting dilution and adaptation failure. Chromosome comparison identified 1809 putative horizontal gene transfer events, 2.1 % of which bridged lake-resident and external taxa. ARG profiles differed according to carrier type. Thus, Lake Biwa might function simultaneously as a filter, removing incoming ARG-carrying cells and viral particles, and as a "silent hub," potentially integrating external ARGs into lake-resident bacteria through horizontal gene transfer. These data provide a foundation for assessing and managing antimicrobial resistance in large freshwater ecosystems.},
}
@article {pmid41364878,
year = {2025},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B cell lymphoma.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016858},
pmid = {41364878},
issn = {2473-9537},
abstract = {CD19 CAR T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (RR-DLBCL), but challenges like post-treatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from RR-DLBCL patients were analyzed at apheresis (47 samples) and one month post-infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly diagnosed DLBCL, RR-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders to treatment had higher levels of Bacteroides fragilis, while non-responders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs, and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in RR-DLBCL.},
}
@article {pmid41364497,
year = {2025},
author = {Saroff, MJ and Haile, AA and Baniel, A and Kraberger, S and Regney, M and Harrach, B and Kaján, GL and Lu, A and Beehner, JC and Bergman, TJ and Snyder-Mackler, N and Varsani, A and Schneider-Crease, IA},
title = {Early-life infection dynamics and genomic diversity of adenoviruses in a wild primate (Theropithecus gelada).},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001595},
pmid = {41364497},
issn = {2057-5858},
mesh = {Animals ; Feces/virology ; *Theropithecus/virology ; Ethiopia ; *Adenoviridae Infections/virology/veterinary ; Phylogeny ; Genome, Viral ; *Adenoviruses, Simian/genetics/classification ; *Adenoviridae/genetics/classification ; Genetic Variation ; Female ; Male ; },
abstract = {In humans, adenoviruses (AdVs) are frequently associated with respiratory illnesses, posing risks to children with developing immune systems and immunocompromised individuals. Outbreaks and epidemics are generally centred in close-contact settings, such as childcare facilities, and transmission occurs through faecal-oral and airborne pathways. AdVs have coevolved across the primate lineage, but very little is known about whether the early-life dynamics in non-human primates mirror those in humans. Here, we leverage longitudinal data collected on a population of geladas (Theropithecus gelada) in the Simien Mountains National Park, Ethiopia, to evaluate AdV dynamics across the gelada lifespan. We identified ten coding-complete AdV genomes representing seven unique simian adenovirus (SAdV) types, four of which are adequately different from the known ones to establish new species. We assessed behavioural and seasonal drivers of SAdV presence and richness across repeated faecal samples from known individuals. Contrary to our expectation that the highest risk would occur after the initiation of play behaviour in infancy (~6 months of age), when peer-to-peer transmission risk is expected to increase, SAdV likelihood was highest in infants under 6 months of age. Risk and richness declined over the lifespan, with very few adults infected, and higher minimum temperatures were weakly but significantly negatively associated with richness. Our results suggest that, unlike in humans, SAdV exposure occurs prior to the initiation of close-contact play behaviours and likely results from the close spatial proximity of conspecifics throughout the dependent period. Like AdVs in humans, SAdVs in geladas maintain low levels in adulthood, with early infections potentially conferring life-long immunity.},
}
@article {pmid41364398,
year = {2025},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Strain-level dynamics of Akkermansia muciniphila in the human gut microbiota.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01982-7},
pmid = {41364398},
issn = {2191-0855},
support = {2018YFC1200100//National Key Research and Development Program of China/ ; },
abstract = {Akkermansia muciniphila (Akk), a mucin-degrading bacterium residing in the human gut, plays a pivotal role in intestinal health. This study investigated its temporal dynamics, strain-level diversity, and cross-regional transmission using longitudinal metagenomic data from the Chinese Microbiome Project (CMP). We observed significant fluctuations in Akk relative abundance across 52 time points in 7 healthy individuals, with detection rates of 56.9% (16S rRNA gene sequencing) and 33.3% (whole-genome sequencing, WGS). Notably, "short-term blooms"--rapid increases followed by declines in relative abundance--were identified in multiple subjects. Genomic analysis of 39 Akkermansia metagenome-assembled genomes (MAGs), combined with 89 publicly available strains with complete genome, revealed phylogenetically distinct clusters (average nucleotide identity, ANI < 98% between clusters). Strikingly, individuals harbored different clusters at varying time points (e.g., AmII replaced by AmIb and later AmIa in subject P4), suggesting strain replacement and recurrent colonization. Furthermore, high-similarity strains (ANI > 99%) were shared between individuals with close contact (e.g., cohabiting subjects P2 and P4) and across geographically distant regions (China, South Korea, and the United States), implicating human-mediated or environmental transmission pathways. These findings underscore the dynamic nature of Akk within the gut microbiota and highlight the need to explore factors driving its colonization, strain competition, and ecological dissemination.},
}
@article {pmid41363757,
year = {2025},
author = {Li, J and Pang, Y and Yu, H},
title = {Robot-Assisted Stereotactic Aspiration of a Parietal Brain Abscess With Metagenomic Identification of Fusobacterium nucleatum.},
journal = {The Journal of craniofacial surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SCS.0000000000012287},
pmid = {41363757},
issn = {1536-3732},
abstract = {Robot-assisted stereotactic aspiration offers a minimally invasive approach to brain abscesses near the eloquent cortex. We report a rare case of a left parietal abscess caused by Fusobacterium nucleatum in an immunocompetent adult, managed successfully with this approach. The patient, a 52-year-old man, presented with right-sided limb numbness. MRI and contrast-enhanced CT revealed a cystic, ring-enhancing lesion with diffusion restriction in the left parietal lobe. Despite empiric broad-spectrum antibiotics, neurological deterioration occurred due to progressive mass effect. Robot-assisted stereotactic aspiration enabled single-stage, precise drainage of the abscess. Metagenomic next-generation sequencing identified F. nucleatum, prompting adjustment of antibiotics to ceftriaxone plus metronidazole, followed by metronidazole monotherapy. The patient improved clinically, and a 6-month MRI confirmed complete resolution, underscoring the precision of robotic stereotaxy for eloquent-region abscesses and highlighting the diagnostic value of metagenomic sequencing in detecting anaerobic pathogens.},
}
@article {pmid41363534,
year = {2025},
author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y},
title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0053925},
doi = {10.1128/msphere.00539-25},
pmid = {41363534},
issn = {2379-5042},
abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.},
}
@article {pmid41362850,
year = {2025},
author = {Shu, H and Li, X and Chen, Y and Wang, W},
title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis in an HIV-negative patient: A case of misdiagnosis.},
journal = {Medical mycology case reports},
volume = {50},
number = {},
pages = {100752},
pmid = {41362850},
issn = {2211-7539},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to disseminated histoplasmosis (DH) is rare and often misdiagnosed, especially in non-endemic areas. We present a case of a 70-year-old Chinese man who was admitted with fever, nausea, and vomiting, initially misdiagnosed with pulmonary tuberculosis. The use of metagenomic next-generation sequencing (mNGS) played a crucial role in the early and accurate diagnosis, highlighting its potential as a valuable diagnostic tool for rare infections.},
}
@article {pmid41362398,
year = {2025},
author = {Xu, X and Li, J and Pan, L and Yu, H and Huang, J},
title = {Gastropleural Fistula Following Combined TACE, Immunotherapy, and Bevacizumab in HCC: A Case Report.},
journal = {Journal of hepatocellular carcinoma},
volume = {12},
number = {},
pages = {2671-2677},
pmid = {41362398},
issn = {2253-5969},
abstract = {Gastropleural fistula (GPF) is an extremely rare complication after treatment for liver cancer. We report a case of a 54-year-old man with hepatitis B virus (HBV)-related liver cancer who developed a GPF after multiple sessions of transarterial chemoembolization (TACE) combined with immunotherapy and targeted therapy. During the third treatment, because of arterial remodeling and changes in tumor vascular supply, the embolization route was changed to the left inferior phrenic artery. After the procedure, the patient presented with abdominal pain, chest pain, and fever. Metagenomic next-generation sequencing (mNGS) of the pleural effusion identified Porphyromonas endodontalis, and Pneumocystis jirovecii was also detected in the sputum. Upper gastrointestinal endoscopy and water-soluble contrast radiography confirmed a gastric fundus perforation with a fistulous communication to the pleural cavity. After multidisciplinary evaluation, the patient underwent laparoscopic fistula repair and had a favorable postoperative recovery. This case highlights that, while the combination of TACE, immunotherapy, and targeted agents may provide synergistic antitumor benefits, it also carries a potential risk of serious gastric complications.},
}
@article {pmid41362143,
year = {2025},
author = {Gao, WJ and Wan, YQ and Bian, WJ and Sun, KK and Gao, ZC},
title = {[A case of pulmonary alveolar proteinosis secondary to GATA2 deficiency combined with splenic M. kansasii infection and literature review].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {12},
pages = {1153-1161},
doi = {10.3760/cma.j.cn112147-20250527-00287},
pmid = {41362143},
issn = {1001-0939},
mesh = {Humans ; *Pulmonary Alveolar Proteinosis/etiology ; Male ; *Mycobacterium Infections, Nontuberculous/complications ; *GATA2 Deficiency/complications ; Young Adult ; *GATA2 Transcription Factor/genetics/deficiency ; Mycobacterium kansasii ; Spleen/microbiology ; },
abstract = {Objective: To enhance the understanding of the rare disease GATA2 deficiency syndrome leading to pulmonary alveolar proteinosis (PAP) and non-tuberculous mycobacterial (NTM) disease. Methods: The clinical data of a patient with GATA2 deficiency-associated PAP and splenic M. kansasii disease admitted to Peking University People's Hospital were summarized. Relevant literature from January 1, 2010 to March 31, 2025 was retrieved and reviewed through Wanfang Data, China National Knowledge Infrastructure, and the National Center for Biotechnology Information database. Results: The patient was a 19-year-old male. The clinical manifestations included recurrent fever for 7 years. The peripheral blood routine test showed peripheral blood pancytopenia accompanied by monocytopenia. The serum granulocyte-macrophage colony-stimulating factor (GM-CSF) antibody was negative. Chest CT revealed diffuse interstitial lung changes, while [18]F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG PET-CT) demonstrated splenomegaly with multiple focal FDG-avid lesions. Bone marrow biopsy indicated marrow failure. Histopathological examination of lung biopsy specimens was consistent with alveolar proteinosis, whereas histopathology of the spleen biopsy revealed granuloma and patellar necrosis. Metagenomic next-generation sequencing (mNGS) of the splenic specimen detected M. kansasii, and genetic testing identified a germline GATA2 mutation(c.1128del, p.Y377fs). Based on these findings, a diagnosis of GATA2 deficiency with secondary PAP and splenic M. kansasii infection was established. Following anti-NTM treatment, the patient's infection was controlled; however, hematopoietic stem cell transplantation was planned due to bone marrow failure. Literature search revealed 4 cases of GATA2 deficiency syndrome with bone marrow dysplasia. Three cases developed PAP. All 4 cases had NTM infection, including 1 case with disseminated NTM infection in the lungs, spleen, and bone marrow. GATA2 deficiency syndrome patients are prone to decreased numbers and functional defects of cells such as monocytes and NK cells, resulting in immune dysfunction and pulmonary alveolar macrophage dysfunction, reduced ability to resist NTM, leading to the patient being prone to NTM infection, namely MonoMAC syndrome, and can cause secondary PAP. Early identification and timely completion of genetic testing are beneficial for clear diagnosis and establishment of precise intervention strategies. Conclusion: GATA2 deficiency is a rare autosomal dominant genetic disorder caused by mutations in the GATA2 gene. Patients with cytopenia, GM-CSF antibody-negative PAP accompanied by NTM infection should be considered to have the possibility of this disease. Those patients should undergo GATA2 gene screening. Hematopoietic stem cell transplantation is currently the only possible method for curing GATA2 deficiency.},
}
@article {pmid41361579,
year = {2025},
author = {Anunobi, OO and Abiola, RB and Ogah, CF},
title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {6},
pmid = {41361579},
issn = {1572-9699},
mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation &amp; purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.},
}
@article {pmid41361265,
year = {2025},
author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J},
title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04586-0},
pmid = {41361265},
issn = {1471-2180},
support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; },
}
@article {pmid41361202,
year = {2025},
author = {Korzekwa, K and Lepionka, T and Bisak, A and Obuch-Woszczatyńska, O and Bylińska, K and Kauc, A and Skuza, K and Zaborski, B and Krzyżowska, M},
title = {Long-term biological surveillance of SARS-CoV-2 in critical points for municipal sewage catchment in light of wastewater-based epidemiology, public health and environmental hygiene.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43320},
pmid = {41361202},
issn = {2045-2322},
support = {National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; },
mesh = {*SARS-CoV-2/genetics/isolation &amp; purification ; *Sewage/virology ; *COVID-19/epidemiology/virology ; Humans ; *Wastewater/virology ; Public Health ; *Wastewater-Based Epidemiological Monitoring ; Poland/epidemiology ; Hygiene ; Environmental Monitoring ; },
abstract = {Routine monitoring and wastewater-based bio-surveillance represents a strong supporting tool for following and understanding SARS-CoV-2 endemicity or epidemic dynamics in society. The main objective of the research was a two-year qualitative and quantitative monitoring program of SARS-CoV-2 in sewage in a model urban agglomeration (the capital city), including the development of an algorithm for action in this area and a joint evaluation of procedures with a water and sewage company (public administration sector). To resolve problems, we continuously investigated inflows and outflows of four wastewater treatment plants and raw sewage of the whole catchment (including healthcare units, airport and military areas) within the Warsaw capital city for SARS-CoV-2, during two waves of COVID-19 in 2023 and 2024. The screening was performed by RT-qPCR (N1, N2, E probes) and NGS metagenomics analysis. The average cumulative load of the virus in sewage for the whole tested period was 3.5 × 10[5] genomic copies per litre. The highest load was found for wastewater inflows and the lowest one was found for housing estates and wastewater outflows. Higher viral concentrations in the wastewater than expected in medical records suggested a higher number of undiagnosed COVID-19 infections within the community. The obtained genotypes segregated within 11 clades (21I to 24 F), making '23 and '24 waves distinguishable. We consider our results and methodological approaches hold significant potential for public health, with particular emphasis on the needs of the Directive (EU) 2024/3019 of the European Parliament and of the Council.},
}
@article {pmid41360901,
year = {2025},
author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R},
title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30604-2},
pmid = {41360901},
issn = {2045-2322},
support = {BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10045515//Innovate UK/ ; },
abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.},
}
@article {pmid41360540,
year = {2026},
author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J},
title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117842},
doi = {10.1016/j.foodres.2025.117842},
pmid = {41360540},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; },
abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.},
}
@article {pmid41360290,
year = {2025},
author = {Obermeier, PE and Alchikh, M and Ma, X and Reiche, J and Schweiger, B and Rath, BA},
title = {Digital severity scoring and viral metagenomics: A feasibility study on integrated diagnosis of pediatric influenza-like illness.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105223},
doi = {10.1016/j.idnow.2025.105223},
pmid = {41360290},
issn = {2666-9919},
abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) holds promise for identifying diverse pathogens in complex cases of influenza-like illness (ILI). Interpreting results requires comprehensive clinical context. We aimed to explore the feasibility of an integrated diagnostic approach by linking shotgun viral mNGS with standardized clinical data for unbiased ascertainment and hypothesis generation in pediatric ILI patients.<br><br>PATIENTS AND METHODS: We studied a cohort of 6,073 pediatric ILI patients (mean age 3.1&#x202f;years, range 0-18.8&#x202f;years), assessed using the VIVI ScoreApp for immediate computation of Disease Severity and Risk Factor Scores. Nasopharyngeal samples were tested for nine respiratory viruses by PCR. In a nested pilot feasibility study, we linked the clinical dataset of 100 ILI patients with neurological complications (mean age 3.9&#x202f;years, range 0-17.8&#x202f;years) to additional viral mNGS. PCR and mNGS were compared by agreement rates and Cohen's &#x3ba; for inter-method reliability.<br><br>RESULTS: In the pilot feasibility study, the mean VIVI Disease Severity Score was above the cohort average (>67th percentile, p&#x202f;<&#x202f;0.0001), with 'age&#x202f;<&#x202f;2 years' as the most prevalent risk factor (n&#x202f;=&#x202f;44/100). mNGS identified 15 viruses, expanding the range of viral identifications by six viruses compared to PCR. Linking VIVI Scores with mNGS-discovered viruses suggested high disease severity. Sensitivity of mNGS was relatively low; overall agreement with PCR was 77-98&#x202f;% and overall reliability was 'moderate' (&#x3ba; scores of 0.1-0.85).<br><br>CONCLUSIONS: Digital surveillance tools can successfully integrate with mNGS to capture complex clinical patterns and generate data-driven hypotheses. Large-scale investigation and technical refinement are warranted.},
}
@article {pmid41359546,
year = {2025},
author = {Provatas, K and Mouratidis, I and Georgakopoulos-Soares, I},
title = {KmerCrypt: private k-mer search with homomorphic encryption.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf648},
pmid = {41359546},
issn = {1477-4054},
support = {//University of Texas at Austin/ ; },
mesh = {*Computer Security ; Humans ; Cloud Computing ; *Software ; Algorithms ; *Genomics/methods ; Databases, Genetic ; },
abstract = {Outsourcing the storage and analysis of genomic data to third-party servers is often necessary due to the scale of modern datasets, but it introduces significant privacy challenges that must be addressed to ensure secure handling. K-mer-based analyses offer broad applications across genomics research, clinical diagnostics, pathogen surveillance, and metagenomic classification, though implementation requires careful ethical and technical considerations, particularly when processing human genomic data in clinical settings. We present a novel protocol utilizing homomorphic encryption that enables a client to store a fully encrypted version of a genome on an untrusted server and perform private k-mer searches. The protocol ensures the server never gains access to the client's non-encrypted genome sequence, nor does it learn the content of any k-mer query. After a one-time client-side encryption of the genome, the server performs all computations on ciphertext, returning only encrypted results that can be decrypted solely by the data owner. This framework transforms an honest but curious cloud server into a secure storage and computation system, enabling practical and confidential querying of encrypted, client-owned genomic data. The system supports exact k-mer searches on genomic data, as well as position weight matrix searches. Finally, we provide KmerCrypt, a private k-mer search toolkit that implements this protocol, offering researchers an efficient and secure solution for querying encrypted genomic datasets without compromising privacy.},
}
@article {pmid41359366,
year = {2025},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41359366},
issn = {2767-9764},
abstract = {Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.},
}
@article {pmid41359148,
year = {2025},
author = {Rao, PM and Radha, P},
title = {Pioneering approaches to plastic biodegradation and upcycling for sustainability.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {1},
pages = {23},
pmid = {41359148},
issn = {1573-2959},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism/analysis ; Waste Management/methods ; },
abstract = {Plastic pollution has become one of the most significant threats to the environment and human health of the twenty-first century, with more than 300 million tons of waste generated annually, and conventional disposal methods are inadequate. To address this challenge, recent research has increasingly shifted toward biodegradation and upcycling as sustainable alternatives. Microbial degradation of synthetic plastics has shown advancement. This includes the introduction of novel strains like Aspergillus niger MG654699 for the 3.6% and 5% degradation of polyethylene terephthalate and polystyrene, respectively. Also, Streptomyces sp., Methylobacterium, Arthrobacter, and Sphingomonas have been studied to be responsible for mulch film degradation. Advances in metagenomics have further revealed the complexity of microbial consortia for driving these processes, whereas kinetic modeling has provided insights into degradation rates and conditions. Building on this foundation, artificial intelligence and machine learning are now expediting enzyme discovery, optimizing degradation pathways, and enabling intelligent waste management systems. Similarly, biosensors based on Vibrio fischeri and Escherichia coli improve monitoring by detecting plastic monomers. Beyond degradation, the integration of microbial and chemical processes has enabled the upcycling of plastic monomers into value-added products such as polyhydroxyalkanoates, vanillin, bacterial nanocellulose, fuels, and biochemicals, promoting a circular bioeconomy. These advances highlight a paradigm shift from waste accumulation to resource recovery, underscoring the potential of biotechnology and engineering innovations to transform plastic management. The review concludes by highlighting the challenges of scalability, environmental variability, and policy support while positioning biodegradation and upcycling as integrated strategies for a sustainable and resilient future.},
}
@article {pmid41358839,
year = {2025},
author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q},
title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0189025},
doi = {10.1128/aem.01890-25},
pmid = {41358839},
issn = {1098-5336},
abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.<br><br>IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (&#x2264;20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.},
}
@article {pmid41358761,
year = {2025},
author = {Xu, S and Ding, Y and Li, M and Lin, Y and Wang, X and Liu, N and Zhang, L and Xu, T},
title = {Metagenomic next-generation sequencing diagnoses Talaromyces marneffei infections: case report and review.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {11},
pages = {1727-1736},
doi = {10.3855/jidc.20367},
pmid = {41358761},
issn = {1972-2680},
mesh = {Humans ; *Talaromyces/genetics/isolation &amp; purification ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Mycoses/diagnosis/drug therapy/microbiology ; *Metagenomics/methods ; Antifungal Agents/therapeutic use ; Amphotericin B/therapeutic use ; Adult ; China ; },
abstract = {INTRODUCTION: Talaromyces marneffei is a pathogenic dimorphic fungus known for causing severe opportunistic infections that can be life-threatening. The fungus is most commonly found in Southeast Asia and southern China.<br><br>CASE REPORT: This case report describes the case of a young male patient infected with T. marneffei who was neither human immunodeficiency virus (HIV)-positive nor possessed anti-IFN-&#x3b3; antibodies, and who resided outside the typical endemic regions. The patient developed cough and sputum three months after the removal of the left arm fracture fixator, and was initially misdiagnosed with tuberculosis; however, the response to anti-tuberculosis treatment was not good. The diagnosis of subsequent recurrence was unknown. The condition recurred during the illness, and he was ultimately diagnosed with talaromycosis via metagenomic next-generation sequencing (mNGS). The patient's condition improved after appropriate treatment with liposomal amphotericin B.<br><br>CONCLUSIONS: Previous studies have found that T. marneffei infections are concentrated in patients with acquired immunodeficiency syndrome due to HIV infection, and in anti-IFN-&#x3b3; antibody-positive patients. However, infections are increasing in individuals who are not immunosuppressed and are often misdiagnosed and underdiagnosed during the initial course of the disease. Therefore, clinicians should be aware that mNGS is an effective technique for detecting T. marneffei infection in non-endemic areas where they encounter non-HIV infected patients. This case report aims to raise the awareness of physicians regarding this rare disease in non-endemic areas and non-HIV patients.},
}
@article {pmid41358744,
year = {2025},
author = {Li, Y and Lin, W and Li, Z and Tran, T and Metcalf, BJ and Velusamy, S and Gross, A and Snippes Vagnone, P and Lynfield, R and Beall, B and McGee, L and Chochua, S},
title = {Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/jcm.01126-25},
pmid = {41358744},
issn = {1098-660X},
abstract = {Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. Consequently, public health laboratories can benefit from assays that directly process blood culture samples without requiring submission of clinical isolates to determine additional pathogen features not identified by clinical tests, such as vaccine serotype and bacterial genomic relatedness, for surveillance and outbreak response purposes. In partnership with the Minnesota Active Bacterial Core surveillance (ABCs) site, we identified blood culture samples positive for ABCs streptococcal pathogens and characterized them by a direct whole-genome sequencing from blood culture (dWGS) assay. The dWGS results were compared with the results of a reference method (WGS of isolates from the same cultures) to evaluate concordance in pathogen features and genome assemblies. Of the 97 eligible blood culture samples, 83 (86%) passed dWGS quality control criteria and were subjected to a total of 655 dWGS-based tests, which yielded 651 (99.3%) evaluable results. The percent agreement with reference results was 100% (83/83) for M protein gene (emm)/capsular types and 100% (81/81) for multilocus sequencing types. For genotypic antimicrobial susceptibility testing prediction, the percent prediction agreement was 100% (487/487), false resistant prediction rate was 0% (0/417), and the false susceptible prediction rate was 0% (0/66). Assemblies of pathogen genomes from the same patient differed by 1.08 ± 1.68 (mean ± SD) sites per genome. The dWGS assay can extract high-quality, important streptococcal strain characteristics directly from positive blood culture samples to support evolving public health needs.IMPORTANCEWhole-genome sequencing (WGS) technologies have emerged as a transformative toolkit used by public health microbiology laboratories to detect and characterize pathogens. The surveillance of bacterial diseases often relies on clinical laboratories to submit pathogen isolates to regional or national public health laboratories, which have the capacity to routinely conduct WGS-based strain characterization. Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. The study evaluated a direct whole-genome sequencing from blood culture (dWGS) assay that directly processes blood culture samples. The dWGS assay recovered high quality, important streptococcal strain characteristics, including vaccine serotypes and whole-genome assemblies, without requiring submission of clinical isolates. Thus, the dWGS assay represents a promising tool for addressing the evolving needs of public health laboratories in the metagenomics era.},
}
@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
doi = {10.1080/19490976.2025.2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation &amp; purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Ascaris lumbricoides/isolation &amp; purification ; Strongyloides stercoralis/isolation &amp; purification ; Necator americanus/isolation &amp; purification ; Trichuris/isolation &amp; purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}
@article {pmid41358536,
year = {2025},
author = {Amornloetwattana, R and Eiamthong, B and Meesawat, P and Bunkum, P and Royer, B and Zeballos, N and Valenzuela-Ortega, M and Robinson, RC and Wallace, S and Uttamapinant, C},
title = {Cellular Upcycling of Polyethylene Terephthalate (PET) With an Engineered Human Saliva Metagenomic PET Hydrolase.},
journal = {ChemSusChem},
volume = {},
number = {},
pages = {e202502560},
doi = {10.1002/cssc.202502560},
pmid = {41358536},
issn = {1864-564X},
support = {B42G670039//National Science Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; MR/S033882/1//UK Research and Innovation/ ; BB/Y007972/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Recent advances in biocatalytic recycling of polyethylene terephthalate (PET) using PET hydrolase enzymes have sparked interest in integrating PET degradation capabilities into living systems. Although cell-based strategies are limited by the mesophilic temperature constraints of microbial hosts, they offer a unique opportunity to couple PET depolymerization with biological upcycling into value-added chemicals. Here, a comprehensive approach for the cellular degradation and valorization of PET is reported. The crystal structure of MG8, a PET hydrolase identified from the human saliva metagenome is solved, and molecular dynamics simulations are used to pinpoint loop regions for targeted mutagenesis aimed at enhancing activity under moderate temperatures. Over 1000 MG8 loop variants are evaluated with a high-throughput mass spectrometric screening platform. Two catalytically improved mutants-MG8[G127Y/F250A] and MG8[N125S/G127Y/F250A]-exhibit significantly enhanced PET hydrolysis at 37°C. To enable whole-cell PET valorization, a two-strain Escherichia coli system called PETCAT is constructed: one strain is engineered to secrete MG8[G127Y/F250A] for PET degradation, and the other harbors a synthetic pathway comprising seven heterologous genes for the conversion of terephthalic acid (TPA) into catechol, a versatile intermediate used in pharmaceuticals and fragrances. This study establishes a modular, one-pot microbial platform for PET recycling and upcycling under physiologically relevant conditions.},
}
@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}
@article {pmid41357797,
year = {2025},
author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J},
title = {Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1632123},
pmid = {41357797},
issn = {2296-2360},
abstract = {In the neonatal period, infectious diseases associated with high morbidity (e.g., neonatal sepsis and meningitis) are preliminarily assessed using indicators like C-reactive protein (CRP) and procalcitonin, but definitive diagnosis relies on pathogen detection through methods such as blood culture, which is time-consuming and has low sensitivity. To improve diagnostic efficiency, metagenomic next-generation sequencing (mNGS) is increasingly utilized, offering three testing modalities: DNA-only, RNA-only, and combined DNA+RNA channels. This retrospective study analyzed 894 clinical samples (peripheral blood, sputum, bronchoalveolar lavage fluid) to compare detection rates across channels. The overall mNGS positivity rate was 51.9% (464/894), with no significant differences among DNA-only (50.8%), RNA-only (55.7%), and combined channels (49.6%) (p > 0.05). Notably, bronchoalveolar lavage fluid samples exhibited the highest positivity rate (84.57%, 148/175), reaching 97.33% (73/75) with dual-channel testing. Sputum samples showed a 53.7% positivity rate (87/172), increasing to 82.35% (14/17) with dual-channel detection. Conversely, peripheral blood had an overall positivity rate of 43.14% (132/306), with the DNA-only channel outperforming RNA-only and dual channels (45.34% 5s. 43.00% and 34.21%). These findings underscore the importance of channel selection based on sample type to optimize diagnostic accuracy and cost-effectiveness.},
}
@article {pmid41357776,
year = {2025},
author = {Yoshino, N and Matsumoto, K and Ishikawa, M and Nishio, J and Matsuzawa, T},
title = {Identity of Carbohydrate-Responsive Genes in a Cultured Microbial Community Using Metagenomic and Metatranscriptomic Approaches.},
journal = {Journal of applied glycoscience},
volume = {72},
number = {4},
pages = {7204201},
pmid = {41357776},
issn = {1880-7291},
abstract = {Metagenomics can be used to obtain sequence information on putative genes in a microbial community. However, it is difficult to identify genes with specific functions among the numerous predicted genes. In this study, we attempted to identify genes induced in cultured microbes by the addition of saccharides using metagenomic and metatranscriptomic analyses. A mixture of arabinoxylan and its derived oligosaccharides was used as the inducer in this study. Some genes were highly induced in the presence of additive saccharides and formed gene clusters for the utilization of additive saccharides, suggesting that metatranscriptomic and metagenomic analyses are useful for analyzing carbohydrate-responsive genes in microbial communities and screening novel carbohydrate-active enzymes.},
}
@article {pmid41357502,
year = {2025},
author = {He, Y and Liang, L and Wei, S},
title = {Giant intracranial Brucella abscess after head trauma: a Case Report of neurobrucellosis in an urban elderly male without exposure history.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1676548},
pmid = {41357502},
issn = {2296-858X},
abstract = {Giant intracranial Brucella abscess is a severe and rare central nervous system infection whose pathogenesis remains incompletely understood. We detail the case of a 75-years-old urban male without Brucella exposure history who presented with fever and headache. Initial attribution of cephalgia to head trauma delayed diagnosis and treatment. Magnetic resonance imaging, metagenomic next-generation sequencing, and cerebrospinal fluid culture confirmed rapid development of a giant Brucella abscess (31 mm × 58 mm) within 2 weeks after head trauma. Head trauma may be potentially associated with the formation of Brucella brain abscess. Consequently, brucellosis patients with recent head trauma may warrant vigilant monitoring for this rare complication. It is imperative to avoid the premature attribution of headache to head trauma in such patients, as such an oversight risks delaying the diagnosis and management of a Brucella brain abscess.},
}
@article {pmid41357037,
year = {2025},
author = {Syromyatnikov, MY and Burakova, IY and Smirnova, YD and Morozova, PD and Pogorelova, SV and Chirkin, EA and Tolkacheva, AA},
title = {Study of Akkermansia muciniphila Effect on the Gut Microbiome of Mice Under LPS-Induced Systemic Inflammation.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {8695182},
pmid = {41357037},
issn = {2090-8040},
abstract = {Probiotics are strains of living bacteria and yeast that play an important role in regulating the gut microbiota and enhancing host immunity. In the last decade, the bacterial species Akkermansia muciniphila has attracted great interest due to its possible probiotic properties, which play an important role in human health. However, the mechanisms of action of A. muciniphila are still poorly understood. The effect of the A. muciniphila on the intestinal microbiome of model animals with systemic inflammation induced by lipopolysaccharide (LPS) is unexplored. This study aims to investigate the impact of A. muciniphila on the microbiological composition of the mouse gut under LPS-induced systemic inflammation using high-throughput sequencing. The study used a new generation sequencing method aimed at genome-wide sequencing of microorganisms, which makes it possible to study changes in the composition of the microbiome at the bacterial species level, as well as to identify the genes of the metabolic pathways of intestinal bacteria in the studied mice. Our analysis revealed statistically significant differences across all studied groups, with a notable predominance of members from the families Muribaculaceae, Rikenellaceae, and Oscillospiraceae. Consumption of A. muciniphila increased the alpha diversity of gut bacteria (Shannon index) in the context of induced inflammation. Evaluation of the effect of LPS and A. muciniphila on metabolic pathways showed statistically significant differences for the pathways of synthesis and degradation of amino acids, transforming folic acid, and synthesis of sugars. Genetic analysis showed that the probiotic bacterium A. muciniphila reduced the degree of negative effects of LPS on the mouse gut microbiome under systemic inflammation.},
}
@article {pmid41356787,
year = {2025},
author = {Chatterjee, T and Roy, M and Almoujahed, MO and Ahmad, S},
title = {Aspergillus calidoustus: An Emerging Cause of Invasive Aspergillosis and the Role of Metagenomic Next-Generation Sequencing Test in Its Diagnosis.},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {3221057},
pmid = {41356787},
issn = {2090-6625},
abstract = {Transplant recipients have a high risk of infection with opportunistic pathogens. The type, dose, and duration of immunosuppression and use of prior broad-spectrum antimicrobials contribute to overall risk of infections. Aspergillosis is a known opportunistic infection that can occur as mid or late infection after visceral transplant. Aspergillus fumigatus is the commonly isolated species, but with the use of prophylactic broad-spectrum antifungals, other species such as Aspergillus calidoustus are emerging. We report a case of invasive sinusitis and brain mass due to this species of Aspergillus that was identified using next-generation sequencing (NGS). Use of NGS early in clinical presentation may help in effective management of opportunistic infections in immunocompromised hosts.},
}
@article {pmid41356481,
year = {2025},
author = {Rao, AV and Ghare, SS and Gautam, V and Hoffman, KL and Petrosino, J and So-Armah, K and Samet, JH and Patts, GJ and Cheng, DM and Blokhina, E and Krupitsky, EM and Lioznov, D and Zvartau, E and McClain, CJ and Tindle, H and Freiberg, MS and Barve, SS},
title = {Sex differences in beneficial and pathogenic bacteria in People With HIV (PWH) with a history of heavy alcohol drinking.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632949},
pmid = {41356481},
issn = {1664-302X},
abstract = {BACKGROUND: HIV-1 infection and hazardous levels of alcohol consumption have been independently linked to gut dysbiosis affecting beneficial butyrate-producing bacteria. However, sex-based differences in the composition and function of gut microbiome of People With HIV (PWH) with a history of heavy alcohol drinking remain undetermined, which is the focus of this study.<br><br>METHODS: Cross-sectional study examining structural and functional features of the gut microbiome in PWH between men and women with a history of hazardous alcohol drinking recruited at St. Petersburg, Russia. 16S rDNA sequencing information was used for metataxonomic, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and Linear Discriminant Analysis Effect Size (LEfSe) analyses. Group-wise comparisons were done using Mann-Whitney U-test. Further, linear and logistic regression models were used to evaluate the association between sex and measures of gut microbial dysbiosis and Firmicutes/Bacteroidota (F/B) ratio, respectively. Data were adjusted for confounding covariates particularly, HIV-viral load, Anti-retroviral Therapy (ART) and alcohol usage.<br><br>RESULTS: Metataxonomic analysis demonstrated that women depicted significantly higher microbial diversity (Operational Taxonomic Units, OTUs and Shannon Index), higher percent relative abundance (%RA) of Firmicutes, lower %RA of Bacteroidota and higher F/B ratio. Importantly, logistic regression revealed that women had twice the odds of having F/B ratio > 1. Notably, women demonstrated significantly higher %RA of butyrate-producing bacterial families, i.e., Lachnospiraceae, Oscillospiraceae, Rikenellaceae and Marinifilaceae and genera. Correspondingly, significantly greater expression of bacterial genes involved in butyrate synthesis in women was demonstrated by PICRUSt2 analysis. Additionally, women depicted lower %RA of pathobiont, Prevotellaceae particularly, Prevotella_9 genus.<br><br>CONCLUSION: Overall, we observed significant sex-based differences in the relative abundances of beneficial bacterial communities such as butyrate producers and potential pathogenic Prevotella community in the gut microbiome of PWH with a history of heavy alcohol consumption. The observed sex-based differences are clinically relevant and could inform therapeutic strategies with evidence-based probiotics.},
}
@article {pmid41356476,
year = {2025},
author = {Chen, Q and Guan, J and Yang, L and Lv, J and Gui, G and Xu, J and Yang, Z and Wang, X and Sun, B},
title = {Exploring the characteristics of gut microbiota in the development and progression of early-stage colorectal cancer based on metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658160},
pmid = {41356476},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC), a leading cause of cancer-related morbidity and mortality worldwide, often presents asymptomatically, resulting in late diagnosis. Accumulating evidence links gut microbiota dysbiosis to CRC initiation and progression.<br><br>OBJECTIVE: This study aimed to investigate the differences in gut microbiota composition and diversity among healthy controls (HC) and patients with colorectal lesions-including common colorectal polyps, small colorectal adenomas (SCRA), large colorectal adenomas (LCRA), and intramucosal carcinoma (IMC)-to identify bacterial species associated with disease progression and provide novel insights into the diagnosis and treatment of CRC based on the "polyp-adenoma-carcinoma" sequence.<br><br>METHODS: A total of 250 participants were recruited from the First Affiliated Hospital of Anhui Medical University between July 2023 and June 2024. The cohort included 30 HC, 52 with common colorectal polyps, 58 with SCRA, 56 with LCRA, and 54 with IMC. Fecal samples were collected for bacterial DNA extraction, followed by metagenomic sequencing to analyze microbial diversity. Differential microbiota analysis was performed using the R package microbiomeMarker and LEfSe. Group classification and feature identification were conducted using a random forest model. Functional profiling was performed using DIAMOND against the KEGG and MetaCyc databases.<br><br>RESULTS: No significant differences in &#x3b1;-diversity were observed across the groups. &#x3b2;-diversity analysis revealed significant differences in Bray-Curtis and Jaccard distances among the groups. The composition and abundance of gut microbiota at the phylum, class, order, family, genus, and species levels were significantly altered. LEfSe analysis identified specific bacterial species with significant differences in IMC compared to other groups. Furthermore, the random forest model effectively distinguished patients with IMC from other groups based on distinct microbial signatures. Functional profiling revealed that the gut microbiota undergoes metabolic reprogramming from a homeostatic to a pro-tumorigenic phenotype during CRC progression as well as reduced protective pathway abundance and impaired energy/biosynthetic metabolism in CRC-associated microbiota.<br><br>CONCLUSION: Gut microbiota profiles varied significantly among HC, polyp, SCRA, LCRA, and IMC groups. Specific microbial signatures were able to effectively differentiate IMC from both HC and non-malignant colorectal lesions, highlighting their potential as diagnostic biomarkers.},
}
@article {pmid41356466,
year = {2025},
author = {Han, X and Sun, QG and Zang, D and Chen, J},
title = {Comprehensive fecal metagenomic and metabolomic analysis reveals the role of gut microbiota and metabolites in detecting brain metastasis of small cell lung cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673983},
pmid = {41356466},
issn = {1664-302X},
abstract = {BACKGROUND: Brain metastasis (BM) is a common and highly lethal complication in patients with small cell lung cancer (SCLC). People have paid great attention to exploring the relationship between gut microbiota and the occurrence and development of cancer. This study investigated the relationship between brain metastasis, gut microbiota, and their metabolites in SCLC, providing new insights for the prevention and diagnosis of brain metastasis in SCLC.<br><br>METHODS: Baseline fecal samples were collected from 45 participants, including 15 patients with BM and 30 patients with no distant metastasis who were newly diagnosed with SCLC. The gut microbiota and metabolite levels were analyzed using metagenomics and untargeted metabolomics, and machine learning models were utilized to identify differences and potential biomarkers.<br><br>RESULTS: Gut microbiota composition varied significantly between the two groups. Genus such as Alistipes and Streptococcus were more abundant in the brain metastasis group, while Bacteroides and Prevotella predominated in patients without distant spread. Metabolomic profiling identified several metabolites inversely associated with brain metastasis, including leukotriene F4, benzoic acid, velnacrine, piperidine, and an unidentified compound labeled C20916. KEGG pathway analysis linked multiple key physiological processes, such as aminobenzoate degradation, carbapenem biosynthesis, toluene degradation, dioxin degradation, and benzoate degradation, underscoring the complex role of gut microbial metabolites in cancer progression. Furthermore, machine learning models identified key biomarkers, including the genus Marvinbryantia and the metabolites benzoic acid, which showed strong discriminatory ability for brain metastasis. After robust validation, the model demonstrated good performance with excellent discriminative power (AUC&#x202f;=&#x202f;0.80).<br><br>CONCLUSION: Compared to patients without distant metastasis, SCLC patients with BM exhibit distinctive gut microbial and metabolite profiles. These findings suggest that specific gut microbes and their metabolic products may serve as valuable biomarkers for diagnosing and stratifying treatment in brain metastatic SCLC.},
}
@article {pmid41355980,
year = {2025},
author = {Wu, X and Wang, W and Xu, L and Zhou, W and Zhou, J and Zhou, H},
title = {Value of plasma metagenomic next-generation sequencing for the diagnosis of invasive aspergillosis: a multicenter-center retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1656233},
pmid = {41355980},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Aged ; *Metagenomics/methods ; *Aspergillus/genetics/isolation &amp; purification/classification ; Adult ; Risk Factors ; Aged, 80 and over ; Young Adult ; China ; *Aspergillosis/diagnosis/microbiology ; *Plasma/microbiology ; },
abstract = {INTRODUCTION: Invasive aspergillosis (IA) is a severe fungal infection. Metagenomic Next Generation Sequencing (mNGS) is abroad and highly sensitive pathogen detection method that can accurately differentiate fungi to the species, and even subspecies level.<br><br>METHODS: To explore the value of plasma mNGSs in the diagnosis of invasive aspergillosis, a retrospective analysis was conducted on the clinical data of 334 patients with findings of Aspergillus spp. From mNGS from plasma at 4 hospitals, Zhejiang, from February 2021 to December 2022. The study analyzed risk factors, clinical manifestations, imaging features, microbiological results, and treatment outcomes of patients with Aspergillus infection.<br><br>RESULTS AND DISCUSSION: According to the diagnostic criteria for IA, among the 334 patients, there were 4 confirmed cases, 62 probable cases, 134 possible cases, and 134 false-positive cases. All 196 probable and possible cases exhibited risk factors, clinical manifestations, imaging features, and treatment outcomes consistent with Aspergillus infection. In 18 out of the 62 probable cases, the same Aspergillus nucleic acid was found in 2-4 peripheral blood mNGS samples collected at intervals of 17 days. The remaining 134 patients had detectable Aspergillus in plasma mNGS but lacked high-risk factors and clinical characteristics of Aspergillus infection, and there was a lack of other microbiological evidence, determined as false positives. Among the cases included in this study, the positive predictive value of plasma mNGS for diagnosing invasive aspergillosis was 59.9%. Plasma mNGS detection has significant reference value for diagnosing IA. However, comprehensive judgment should still be made in conjunction with clinical features.},
}
@article {pmid41355608,
year = {2026},
author = {Chong, SY and Ilham, Z and Wan-Mohtar, WAAQI and Cheng, A},
title = {The Road to Sustainable Soy Sauce Production and Consumption.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70352},
doi = {10.1111/1541-4337.70352},
pmid = {41355608},
issn = {1541-4337},
support = {//Universiti Malaya/ ; },
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; Food Microbiology ; Humans ; },
abstract = {Soy sauce (SS), a fermented condiment integral to various global cuisines, has undergone considerable technological advancements while preserving its traditional microbiological processes. This systematic review, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, synthesized findings from 181 peer-reviewed articles to examine trends in SS production and consumption. Our descriptive statistics and thematic analysis revealed five key focus areas: process optimization, microbial fermentation, safety, waste management, and evolving analytical technologies. Advances, such as metagenomics, synthetic biology, and enzyme engineering, have refined fermentation dynamics, improving flavor and production efficiency. Concurrently, sustainability-orientated innovations, including by-product bioconversion, low-sodium formulations, and traceable packaging, support both environmental goals and health-conscious consumption. The integration of multi-omics approaches (e.g., metabolomics, genomics, and transcriptomics) and high-resolution analytical tools (e.g., spectroscopy and sensor-based systems) has further strengthened quality control by enhancing authenticity, safety, and traceability. However, integrating traditional methods with emerging technologies such as precision fermentation, which facilitates targeted microbial control to improve product consistency, remains challenging due to microbial strain incompatibility, scalability issues, and the necessity to maintain cultural authenticity and sensory attributes. It is essential to implement scalable and sustainable solutions that improve microbial function while minimizing hazardous by-products and environmental effects. This review presents an integrated framework connecting five key thematic areas with the core pillars of sustainability: environment, economy, society, technology, and nutrition, offering a foundation for directing future research, policymaking, and industrial practices. Key priorities include the development of salt-tolerant microbial consortia, the valorization of fermentation by-products via circular economy strategies, and the standardization of sustainability certification criteria to facilitate practical implementation.},
}
@article {pmid41355553,
year = {2025},
author = {Kim, MJ and Park, JH and Eom, YB},
title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70197},
doi = {10.1002/mbo3.70197},
pmid = {41355553},
issn = {2045-8827},
support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; },
mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; },
abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.},
}
@article {pmid41355481,
year = {2025},
author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD},
title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70121},
doi = {10.1002/mbo3.70121},
pmid = {41355481},
issn = {2045-8827},
support = {//This study was supported by Ministerio de Ciencia e Innovaci&#xf3;n, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; },
abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.},
}
@article {pmid41354995,
year = {2025},
author = {Li, J and Jiang, E and Zhang, M and Pan, C and Lei, C and Han, L and Lan, X},
title = {Phloretin inhibits ferroptosis by restoring the antioxidant capacity of bovine adipose and muscle cells via the AMPK-PPAR signaling pathway.},
journal = {Stress biology},
volume = {5},
number = {1},
pages = {74},
pmid = {41354995},
issn = {2731-0450},
support = {No.32372852//National Natural Science Foundation of China/ ; No.32402726//National Natural Science Foundation of China/ ; Innovative Exploration Category//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No.2025JC-QYCX-027//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No. 2024JC-JCQN-30//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; No.2023SR205//Shaanxi Provincal Innovation Leadership Program in Sciences and Technologies for Young and Middle-aged Scientists/ ; },
abstract = {Ferroptosis has been increasingly implicated in adipose and muscle dysfunction, systemic metabolic disturbances, and several diseases in livestock, which necessitates effective and side-effect-free inhibition strategies. Phloretin, a dihydrochalcone with excellent antioxidant and anti-inflammatory properties, may have the potential to restrain cell ferroptosis. Herein, phloretin was verified to significantly inhibit (1S,3R)-RSL3-induced ferroptosis by reducing intracellular MDA, Fe[2][+], and ROS levels and restoring cell total antioxidant capacity in bovine and mouse preadipocytes or myoblasts. It also alleviated oxidative stress (OS), a vital inducer of ferroptosis, by restoring antioxidant enzyme activity in the above cells and obese mice. In vivo, phloretin gavage significantly reversed the trend where high-fat diet (HFD)-induced OS promoted the expression of ferroptosis-promoting genes and proteins (e.g., ACSL4 and PTGS2) while inhibiting the expression of ferroptosis-negative regulators (e.g., Fth1 and Gpx4). Unlike most flavonoids that exert anti-inflammatory or antioxidant activities by altering the gut microbiota composition, metagenomic sequencing analysis of cecal contents from phloretin-gavaged and HFD mice revealed that phloretin exerts its antioxidative and ferroptosis-inhibitory effects independent of modulating gut microbiota diversity. Further transcriptomic analyses of mouse adipose tissues revealed that phloretin alleviated ferroptosis in adipocytes by modulating the transcription of genes enriched in AMPK and PPAR signaling pathways, such as Camkk2. Hence, based on multi-omics analysis combined with in vivo and in vitro verification, phloretin effectively alleviated the OS to further inhibit ferroptosis of adipose or muscle cells through the AMPK-PPAR pathway, which can provide new research ideas for ameliorating adipose or myocyte dysfunction induced by ferroptosis in animals.},
}
@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25645-6},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; 2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}
@article {pmid41354859,
year = {2025},
author = {Robas-Mora, M and Fernández-Pastrana, VM and González-Reguero, D and Probanza, A and Jiménez-Gómez, PA},
title = {Effect of PGPB-enriched organic fertilizer ORGAON[®]PK on the rhizospheric microbiota and biomass of Lupinus albus (L.): a sustainable alternative to chemical fertilizer.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00827-x},
pmid = {41354859},
issn = {2524-6372},
support = {TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON[®]PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.},
}
@article {pmid41354765,
year = {2025},
author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J},
title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09302-2},
pmid = {41354765},
issn = {2399-3642},
abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.},
}
@article {pmid41354674,
year = {2025},
author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L},
title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00879-4},
pmid = {41354674},
issn = {2055-5008},
support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; },
abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.},
}
@article {pmid41354462,
year = {2025},
author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C},
title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e12020},
doi = {10.1002/advs.202512020},
pmid = {41354462},
issn = {2198-3844},
support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.},
}
@article {pmid41354223,
year = {2025},
author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S},
title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113043},
doi = {10.1016/j.diabres.2025.113043},
pmid = {41354223},
issn = {1872-8227},
abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.},
}
@article {pmid41354039,
year = {2025},
author = {Meng, Y and Zhou, JX},
title = {Beyond technical feasibility: addressing practical hurdles for equitable wastewater metagenomic surveillance.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101311},
doi = {10.1016/j.lanmic.2025.101311},
pmid = {41354039},
issn = {2666-5247},
}
@article {pmid41353953,
year = {2025},
author = {Pan, Y and Tan, T and Meng, J and Guo, H and Dong, Y and Cui, Y and Yu, N and Jin, X and Zhang, Y and Zou, H and Bolan, N and Siddique, KHM},
title = {Biochar and moisture variability shape soil carbon pools via microbial carbon-degrading genes.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128157},
doi = {10.1016/j.jenvman.2025.128157},
pmid = {41353953},
issn = {1095-8630},
abstract = {Microbially derived organic carbon is a key component of the soil carbon pool. Shifts in microbial communities and their associated functional genes-triggered by moisture variability and biochar addition-can influence the composition and stability of soil organic carbon (SOC). However, the microbial processes involved in SOC formation and degradation under different biochar levels and moisture variability intensities remain clear. To address this, we conducted a 90-day microcosmic incubation using three levels of biochar addition (C0: 0, C1: 1 %, C2: 2 %, w/w) and three moisture regimes (W0: constant moisture, W1: high-intensity variability, W2: low-intensity variability) to analyzed microbial communities, carbohydrase activity, C-degrading genes, and C, N, and P enzyme activities to trace and characterize microbial contributions to SOC formation. The results showed a shift in the dominant soil microbial community from Actinomycetes to Ascomycetes with increasing moisture variability. Microbial biomass carbon increased by 158-900 % relative to C0W0, peaking under C2W1. This stimulation enhanced microbial carbon sequestration under high moisture variability while simultaneously accelerating the decomposition of both plant- and microbial-derived carbon. Biochar addition exerted only a marginal, non-significant inhibitory effect on the decomposition either carbon source (P > 0.05). Functional gene analysis revealed that 62 % of carbohydrate-active enzymes (CAZymes) targeted plant-derived components significantly exceeding the 38 % targeting microbial-derived components, indicating a significantly stronger degradation potential for plant residues under varying moisture conditions. This process was genetically regulated, as shown by the concurrent increase in of carbon-degrading gene abundance and corresponding enzyme activities. Consequently, microbial activity was efficiently modulated, with carbon use efficiency increasing by up to 767 % compared with the C0W0. Moisture variability and its interaction with biochar significantly (P < 0.05) or highly significantly (P < 0.01) affected these microbial indicators. This study reveals a moisture-driven microbial "carbon pump" operating through coordinating gene-enzyme-community regulation. Within this framework, up-regulated carbon-degrading genes align with enzyme activities to channel plant-derived carbon into stable SOC. The C2W1 treatment achieved the highest SOC stabilization, offering a theoretical basis for managing SOC under extreme climate conditions and advancing mechanistic understanding of microbe-mediated carbon dynamics.},
}
@article {pmid41353697,
year = {2025},
author = {Pandey, AK},
title = {Computational approach for identification and characterization of a glucose-tolerant thermostable β-glucosidase from marine metagenome.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {41353697},
issn = {1573-501X},
abstract = {Cellulase enzymes comprising endo-1,4-β-glucanase, exo-1,4-β-glucanase, and β-glucosidase mediate the degradation of cellulosic biomass and are frequently used in biofuel production from lignocellulose. β-glucosidases that convert cellobiose to glucose are sensitive to temperature and glucose concentration and thus often show limited catalytic efficiency. Several β-glucosidases having high temperature or glucose tolerance have been evaluated, but a potential candidate having high efficiency along with thermostability and glucose tolerance is yet to be identified. The present study focuses on marine metagenome investigation for the identification of high-potential β-glucosidase. Nine β-glucosidases of the GH 1 family having (β/α)8 barrel domains were observed. Six β-glucosidases were predicted to have a Tm value higher than 65 ℃, including ECV39653.1 β-glucosidase. Molecular docking of all identified β-glucosidases with cellobiose and glucose revealed that ECV39653.1 β-glucosidase has the highest negative binding energy of - 7.4 kcal/mol for cellobiose at the active site, while having insignificant binding of glucose with binding energy of -5.4 kcal/mol at a site different from the active site. The structural analysis showed an effective similarity of ECV39653.1 β-glucosidase with known thermostable and glucose-tolerant β-glucosidases. The prediction of kinetic parameters gave kcat/Km value of 989.08163 sec[-1] mM[-1] for cellobiose. In-depth MD simulation and free binding energy analysis showed highly effective binding of cellobiose over the 100 ns trajectory with an average total binding energy of - 17.45 kcal/mol. The PCA and analysis of free energy landscape showed less variance and conformational changes in ECV39653.1 β-glucosidase cellobiose complex form in comparison to apo-form and disclosed attainment of global minima, thus proving the high ECV39653.1 β-glucosidase-cellobiose complex stability. The analysis of the simulation trajectory revealed that glucose left the binding cavity during simulation, thus disclosing weak binding and, hence, effective glucose tolerance. Therefore, the present in-silico investigation provides a promising high-efficiency, thermostable, and glucose-tolerant ECV39653.1 β-glucosidase. Further studies can provide scope for its utilization in the development of effective technologies for large-scale biofuel production.},
}
@article {pmid41353545,
year = {2025},
author = {Briggs, P and Trimmell, L and Stiemsma, LT and Monzón, J},
title = {Sexual and regional differences in the microbiome and functional metagenome of the lone star tick, Amblyomma americanum.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00498-6},
pmid = {41353545},
issn = {2524-4671},
}
@article {pmid41353522,
year = {2025},
author = {Mugwanya, M and Mpingirika, EZ and AbdelMaksoud, Y and Eissa, RA and Sewilam, H},
title = {Assessment of sediment physiochemical properties, microbial and predicted functional diversity in mangrove eco-restoration sites of Hamata, Mangrove Bay, and Saffaga along the Egyptian Red Sea coast.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41353522},
issn = {1614-7499},
abstract = {Microbial communities perform important roles in nutrient cycling, degradation of environmental pollutants, and support of various life forms on Earth. Mangroves live in very harsh environments, and if not for the existence of several microbial species in their ecosystems, they would not survive. The Egyptian Red Sea coast is dominated by two mangrove species, Avicennia marina and Rhizophora mucronata, which serve as breeding grounds for marine organisms and aid in carbon sequestration. Despite their ecological significance, comparative studies examining the physiochemical properties and heavy metal concentration of mangrove sediments of two dominant species along the Egyptian Red Sea coast (Hamata, Mangrove Bay, and Saffaga) and their relationship to microbial and functional diversity are scarce. Our findings revealed significant differences in sodium ions, potassium ions, organic carbon, and bulk density at 30-50 cm depth across the locations. Heavy metal analysis revealed significantly lower concentrations of zinc and manganese and high concentrations of copper in sediment samples collected from Mangrove Bay at all sampling depths. Metagenomics analysis revealed that the dominant phyla across the three sites were Pseudomonadota, Bacillota, and Bacteroidota, along with Actenomycetota, and Chloroflexota, and unclassified bacteria. Within the phylum Bacillota, several major classes were identified, including Bacillota_A_368345, Bacillota_I, and Bacillota_C. Functional prediction revealed a higher abundance of microbes involved in energy metabolism and carbon cycle, whereas a lower abundance of microbes involved in sulfur and nitrogen cycles was noted across the sites. In conclusion, the identification of different microbial communities in sediments collected along the Egyptian Red Sea coastal areas suggests the role of different mangrove species and human activities in recruiting unique microbial species involved in promoting their survival under different environmental factors.},
}
@article {pmid41353382,
year = {2025},
author = {Kacnik, S and MacIntyre, C and Guarido, M and Venter, M},
title = {Identification of insect-specific viruses in mosquitoes collected from wildlife and rural areas in north-eastern parts of South Africa using a metagenomic RNA sequencing approach.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-025-00185-1},
pmid = {41353382},
issn = {2524-4655},
}
@article {pmid41353361,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67136-2},
pmid = {41353361},
issn = {2041-1723},
support = {UH2AI083264//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; },
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}
@article {pmid41353034,
year = {2025},
author = {McCone, N and Hosokawa, M},
title = {Recovering genomes from uncultured fungi with single-cell genomics.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.11.004},
pmid = {41353034},
issn = {1347-4421},
abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.},
}
@article {pmid41352820,
year = {2026},
author = {Chen, X and Tie, Y and Yang, Q and Wu, Z and Xu, W and Zhang, Z and Ju, F and Takamine, K and Zhang, W},
title = {Temporal metabolomic dynamics and microbial functional mechanisms unravel biomarkers for distinguishing maturation stages and types in medium- and high-temperature daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 1},
pages = {117916},
doi = {10.1016/j.foodres.2025.117916},
pmid = {41352820},
issn = {1873-7145},
mesh = {Biomarkers/analysis ; *Metabolomics/methods ; *Hot Temperature ; *Wine/analysis/microbiology ; *Bacteria/metabolism/classification/genetics ; *Alcoholic Beverages/microbiology/analysis ; },
abstract = {Daqu maturation is essential for developing the characteristic flavor profiles of Chinese Baijiu, yet the underlying microbial metabolic mechanisms remain incompletely understood. This study employed an integrated multi-omics approach to investigate metabolic heterogeneity and identify differential biomarkers during the aging of medium-temperature (MD) and high-temperature (HD) Daqu. Physicochemical analysis revealed MD exhibited higher saccharifying power, whereas HD showed increased esterifying power and dynamic acidity changes. Microbial succession and metagenomic analysis uncovered distinct succession patterns: MD was dominated by Saccharopolyspora and Bacillus, while HD featured thermophilic genera including Kroppenstedtia and Virgibacillus. Co-occurrence network analysis demonstrated higher connectivity and reduced modularity in HD, indicating functional adaptation to high temperatures. Combined VIP and OAV analysis identified key aroma biomarkers that distinctly define both Daqu type and maturation stage. Tetramethylpyrazine and acetic acid characterized MD, while benzaldehyde and methyl hexadecanoate marked HD. Non-targeted metabolomics further indicated MD was enriched in phenylpropanoids and branched-chain amino acid derivatives, whereas HD accumulated peptides and steroid-related compounds. Crucially, integrated analysis demonstrated that these metabolic shifts were directly driven by microbial enzymatic activities (e.g., EC 4.1.1.5, EC 3.1.1.3). These findings establish a causal link between temperature-driven microbial functional specialization and metabolic output, and provide a biomarker framework for precise quality assessment of Daqu.},
}
@article {pmid41352612,
year = {2025},
author = {Fishman, JA},
title = {Assuring Microbiological Safety in Clinical Xenotransplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2025.11.027},
pmid = {41352612},
issn = {1600-6143},
}
@article {pmid41352476,
year = {2025},
author = {Su, J and Zhao, K and Zhou, X and Pan, Z and Xia, C},
title = {Early-life exposure to linezolid caused gut microbiota dysbiosis can be inherited from parents to offspring.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111863},
doi = {10.1016/j.cbi.2025.111863},
pmid = {41352476},
issn = {1872-7786},
abstract = {BACKGROUND AND OBJECTIVES: Linezolid is a broad-spectrum antibiotic against Gram-positive bacterial infections. Widespread use of linezolid has brought about significant adverse effects and potential reproductive toxicity, but there is not yet any study regarding to the transgenerational impact.<br><br>METHODS: Gut microbiota and metabolites from the 12-weeks old male mice who were treated with one-week linezolid at 4 weeks of age, as well as those from their offsprings, were analyzed by metagenomics and metabolomics, respectively. Reproductivity of the male parents were monitored, including fertility, litter size, survival and weight gain of offsprings.<br><br>RESULTS: Offsprings survival from the linezolid-treated male parents was obviously decreased, although fertilities, litter size, or weight gain was not affected. The linezolid-induced gut microbiota perturbation in male parents was manifested as lower alpha diversity, distinguishing beta diversity, and the dramatically altered profiles of function genes and metabolites. Especially, linezolid exposure reversed the relationship between Dysosmobacter and butyrogenic species, and that between Dysosmobacter and inflammation-associated species. Interestingly, gut microbiota dysbiosis also existed in both female and male offsprings from the treated male parents. Moreover, it was found that the differential metabolites enriched in ABC transporter pathway were found male parents and offsprings, while those enriched in sphingolipid signaling pathway were only found in offsprings of both sexes CONCLUSIONS: The early-life short-term exposure to linezolid make long-term gut microbiota dysregulation, which was even inherited from parents to offsprings. These findings raised critical concern about the ecological consequences of early-life antibiotic exposure and clinical safety evaluations.},
}
@article {pmid41352467,
year = {2025},
author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS},
title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133774},
doi = {10.1016/j.biortech.2025.133774},
pmid = {41352467},
issn = {1873-2976},
abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.},
}
@article {pmid41352466,
year = {2025},
author = {Liu, Z and Gao, Y and Wang, J and Jing, X and Chen, X and Hu, W and Lu, X and Liu, M and He, X and Kumar, G and Zhen, G},
title = {Perfluorooctane sulfonate (PFOS) inhibits methane production during sludge anaerobic digestion by breaking the carbon-transfer bridge between methanogenesis and acidogenesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133775},
doi = {10.1016/j.biortech.2025.133775},
pmid = {41352466},
issn = {1873-2976},
abstract = {Per- or polyfluoroalkyl compounds (PFASs) are recognized as emerging contaminant, with perfluorooctane sulfonate (PFOS) being one of the most extensively utilized PFASs due to its great chemical stability. However, knowledge of the bio-chemical behavior, the toxicity of PFOS and its mechanisms of interfacial binding to microorganisms remain inadequately validated. In this study, the biotoxicity of PFOS and its molecular interfacial adsorption mechanism in anaerobic digestion were investigated. The results showed that the tightly bound EPS (TB-EPS) of anaerobic microorganisms could defend against the biotoxicity of PFOS to some extent by physical adsorption and chemical binding, the exposure to PFOS might produce a greater disturbance to methanogenic archaea. With the increase of PFOS, acid-producing bacteria (APB) and methanogenic archaea showed different resistance to PFOS, suppressing cumulative methane production by up to 91.64 %. On the contrary, APBs were more tolerant, and fatty acids accumulated up to 2194.27 mg/L. Metagenomics analysis further confirmed that functional genes associated with fatty acid biosynthesis (fas, FAS2, fabK, etc.) were significantly enriched (approximately 85.29 %) whereas the relative abundance of genes associated with methanogenesis (acs, comA, mcrB, etc.) were decreased (up to 65.96 %). Molecular docking results suggested a potential route for PFOS cellular entry, as it was observed to bind to the substrate-binding protein of the ATP-binding cassette (ABC) transporter and interact with key functional enzymes, which led to the inhibition of methanogens. This study provides novel insights into the molecular blocking mechanism by which PFOS disrupts carbon metabolic flux through the selective inhibition of methanogenic archaea, rather than through a general suppression of acidogenic bacteria.},
}
@article {pmid41352108,
year = {2025},
author = {Zeng, Z and Lei, T and Zhou, M and Wen, H and Li, S},
title = {Ciprofloxacin removal and antibiotic resistance genes response in the EGSB-AnMBR system treating swine wastewater: Performance, mechanism, and metagenomics.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128233},
doi = {10.1016/j.jenvman.2025.128233},
pmid = {41352108},
issn = {1095-8630},
abstract = {Ciprofloxacin (CIP), a veterinary antibiotic in swine wastewater is an emerging contaminant with low concentration but significant environmental risk. Its inhibitory effects on biological treatment systems and the proliferation of antibiotic resistance genes have raised widespread public concern. An expanded granular sludge bed reactor was coupled with an anaerobic membrane bioreactor (EGSB-AnMBR) to treat swine wastewater containing CIP. During 320 days operation, the EGSB-AnMBR system achieved over 98.6 % chemical oxygen demand (COD) removal efficiency and 61.4 %-100 % CIP removal efficiency. During the initial operation phase, sludge adsorption served as the primary mechanism for CIP removal, whereas biodegradation became dominant in the last operational phase. 16S rRNA gene high-throughput sequencing analysis revealed that under CIP stress, the abundance of CIP-resistant Spirochaetota increased from 4.7 % to 9.5 %, whereas Patescibacteria abundance progressively decreased from 72.7 % to 15.7 %. Metagenomic analysis demonstrated microbes in anaerobic granular sludge (AnGS) achieved "defense-efflux" by activating macB/evgS efflux pumps while suppressing tetA, whereas membrane biofilm (MB) developed a "storage-retention" strategy through synergistic effects of tetA and evgS. This EGSB-AnMBR system exhibits promising application potential for swine wastewater treatment and antibiotic control, providing significant support for livestock pollution management.},
}
@article {pmid41352011,
year = {2025},
author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X},
title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140640},
doi = {10.1016/j.jhazmat.2025.140640},
pmid = {41352011},
issn = {1873-3336},
abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.},
}
@article {pmid41351981,
year = {2025},
author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X},
title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157610},
doi = {10.1016/j.phymed.2025.157610},
pmid = {41351981},
issn = {1618-095X},
abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.<br><br>PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.<br><br>METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.<br><br>RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.<br><br>CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.},
}
@article {pmid41351872,
year = {2025},
author = {Mukherjee, I and Bulzu, PA and Boukheloua, R and Asghar, U and Park, H and Vieira, HH and Chiriac, MC and Kasalický, V and Znachor, P and Rychtecký, P and Šimek, K and Salcher, MM and Haber, M and Ghai, R},
title = {Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf271},
pmid = {41351872},
issn = {1751-7370},
abstract = {Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3-5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to cryptophytes that are characterised by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.},
}
@article {pmid41351776,
year = {2025},
author = {Hussain, B and Javed, K and Ali, M and Ullah, S and Sun, S and Idris, AM and Singh, S},
title = {Impact of nanoparticles on biogeochemical processes in soil-plant system under heavy metals stress; exploring remediation mechanism and plant health status.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {31},
pmid = {41351776},
issn = {1573-2983},
mesh = {*Metals, Heavy/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism/chemistry ; Soil/chemistry ; *Plants/drug effects/metabolism ; *Environmental Restoration and Remediation ; Biodegradation, Environmental ; Stress, Physiological ; *Metal Nanoparticles/chemistry/toxicity ; },
abstract = {Although, NPs have potential to improved plant resistance against abiotic stress, increased nutrient usage efficiency, and sustenance of agricultural production. However, reactions of NPs in soil matrices, particularly their movement, perseverance, and biogeochemical reactions in soil-plant system under heavy metals (HMs) were not well understood. Therefore, this review presents the latest research in order to clarify the molecular interactions, beneficial transformations, and detoxification processes of NPs in plants and evaluates their roles in these processes. It further aims to quantify the benefits and risks, and give future directions for NPs design and applications in environmental remediation and agriculture. NPs significantly enhanced agricultural outcomes through mechanisms such as regulating HMs uptake, boosting antioxidant enzyme activity (up to a 60% increase), altering soil properties, and optimizing physiological metabolism. NPs amendments raised crop output by 20-55% while reducing disease and nutrient leaching to 50% and 30%, respectively, and improving the soil's carbon sink by 15%. Meanwhile, green-synthesized nanomaterials offer eco-friendly alternatives in remediation through processes like adsorption, oxidation, coprecipitation, ion-exchange, photocatalysis, and nanophytoremediation, achieving 100% pollutant removal efficiency for elements like hexavalent chromium using iron NPs. However, challenges such as NPs accumulation in food chains, potential toxicity to non-target species, and physiological disruptions necessitate solutions like microbiome co-delivery and stimuli-responsive systems to balance safety and effectiveness. In order to increase the available resources and address the worldwide food safety issue, the use of NPs in agroecosystems might be a crucial step towards sustainable farming. Therefore, the influence of NPs on soil, and plant antioxidant defense systems and oxidative stress activation under HMs should be studied using molecular, physiological, and biochemical techniques. For this purpose, real-time polymerase chain reaction (RT-PCR) analysis, illumina MiSeq sequencing, pyrosequencing analysis, metagenomics, metabolomics, proteomics, and functional assays etc. could be most useful for NPs risk/benefit evaluation.},
}
@article {pmid41351708,
year = {2025},
author = {Campbell, KL and Armitage, AR and Labonté, JM},
title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02661-7},
pmid = {41351708},
issn = {1432-184X},
abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.},
}
@article {pmid41351628,
year = {2025},
author = {Liu, S and Liu, P and Deng, J and He, J and Xiang, Y and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z},
title = {C-arm-guided percutaneous biopsy combined with mNGS: a dual-modality strategy for op timizing diagnosis and targeted management of spinal infections.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41351628},
issn = {1432-0932},
support = {2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; },
}
@article {pmid41351142,
year = {2025},
author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A},
title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12365-4},
pmid = {41351142},
issn = {1471-2164},
abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.<br><br>RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.<br><br>CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.},
}
@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02236-1},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.<br><br>RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.<br><br>CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}
@article {pmid41350884,
year = {2025},
author = {De Sanctis, B and Mirchandani, C and Dong, H and Macleod, R and Corbett-Detig, R and Wang, Y},
title = {Bamdam: a post-mapping authentication toolkit for ancient metagenomics.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {413},
pmid = {41350884},
issn = {1474-760X},
support = {35GM128932./NH/NIH HHS/United States ; 35GM128932./NH/NIH HHS/United States ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; G10144//Social Sciences and Humanities Research Council of Canada/ ; },
mesh = {*Metagenomics/methods ; *Software ; Humans ; },
abstract = {Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for taxonomic identification. Here, we present bamdam, a lightweight post-mapping, post lowest common ancestor toolkit for eukaryotic or microbial metagenomics. Bamdam can shrink large metagenomics bam files, often by a factor of 10x or more, while retaining all informative reads and alignments, compute a suite of authentication metrics for each taxonomic node including k-mer duplicity, postmortem damage, and mean read complexity, and generate various visualizations including multi-sample deamination plots and damage-colored interactive Krona plots.},
}
@article {pmid41350579,
year = {2025},
author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M},
title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00868-7},
pmid = {41350579},
issn = {2055-5008},
abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.},
}
@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}
@article {pmid41350329,
year = {2025},
author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T},
title = {Differences in prokaryotic and viral community between rumen and feces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43232},
pmid = {41350329},
issn = {2045-2322},
mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; },
abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.},
}
@article {pmid40691354,
year = {2026},
author = {Roux, S and Coclet, C},
title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.},
journal = {Nature reviews. Genetics},
volume = {27},
number = {1},
pages = {32-46},
pmid = {40691354},
issn = {1471-0064},
mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; },
abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.},
}
@article {pmid41350265,
year = {2025},
author = {Tang, H and Liu, H and Yuan, L and Xie, M and Zheng, J and Wang, J and Zhou, J and Yang, B and Lou, B and Han, D},
title = {Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1919},
pmid = {41350265},
issn = {2052-4463},
support = {82472371//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Metagenomics ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; DNA Copy Number Variations ; },
abstract = {Metagenomic Next-Generation Sequencing (mNGS) enables simultaneous sequencing of both microbial and host nucleic acids in clinical samples. However, analytical approaches for interpreting complex mNGS datasets are seldom disclosed, limiting advancements in multimodal analysis and omics-driven research models built upon mNGS results. We present 402 high-quality bronchoalveolar lavage fluid mNGS DNA and RNA sequencing datasets for developing combined microbial-host metagenomic diagnostic approaches. Only the microbial (non-host) sequence reads have been deposited. We provide comprehensive descriptions of methods, tools, and pipelines used for mining microbial features (DNA/RNA microbial composition and bacteriophage abundances) and host response features (differential expression genes, transposable elements, cell-type composition, and copy number variation). These data processing pipelines set a standard for future multimodal omics diagnostic research, promoting the adoption of standardized practices in omics-based studies that integrate clinical data.},
}
@article {pmid41350118,
year = {2025},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70099},
pmid = {41350118},
issn = {1600-0714},
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}
@article {pmid41349993,
year = {2026},
author = {Zepernick, BN and Niknejad, DJ and Chase, EE and Abiodun, BA and Adler, MJ and Houghton, KA and Olavesen, JL and Sarumi, Q and Truchon, AR and Walton, JL and Cheshire, JH and Stanislawczyk, K and Hart, LN and Paerl, HW and Chaffin, JD and Boyer, GL and Castro, HF and Campagna, SR and Bullerjahn, GS and Wilhelm, SW},
title = {The ornithine-arginine cycle supported a toxic, metalimnic Planktothrix rubescens bloom.},
journal = {Harmful algae},
volume = {151},
number = {},
pages = {103008},
doi = {10.1016/j.hal.2025.103008},
pmid = {41349993},
issn = {1878-1470},
mesh = {*Cyanobacteria/metabolism/physiology/genetics ; *Arginine/metabolism ; *Ornithine/metabolism ; *Harmful Algal Bloom ; Metagenomics ; },
abstract = {Planktothrix rubescens is distinct from other cyanobacterial harmful algal bloom (cHAB) genera: the crimson-red cHAB thrives in the cold, low-light, nutrient-limited metalimnion. Studies have attributed this ecological success to buoyancy regulation, low-light adaptations, and the uptake of nitrogen-rich amino acids. Yet, it remains to be mechanistically determined how this cHAB maintains physiological nutrient quotas in the metalimnion due to limited in situ molecular studies. We employed metagenomics and metabolomics to generate hypotheses concerning a toxigenic P. rubescens bloom in Mead's Quarry (Knoxville, TN, USA) observed in two separate years. Our results suggest a perennial, metalimnic P. rubescens population may exist, with spring turnover facilitating seasonal migration to the epilimnion. Although P. rubescens dominated the epilimnion and metalimnion, intracellular metabolite pools grouped by depth and suggested depth-discrete partitioning of the arginine deiminase-mediated ornithine-arginine cycle (OAC, i.e., urea cycle) - while further indicating the presence of the arginine catabolic pathway. Though the arginine influx driving the OAC is unclear, we hypothesize this input is provided via the uptake of urea or nitrogen-rich amino acids. Further, we demonstrate arginine deiminase (agrE/argZ) is broadly distributed in Planktothrix genera and known microcystin producers, suggesting agrE/argZ-mediated arginine metabolism and the OAC may influence the fitness of toxigenic cHAB genera which require ample nitrogen to synthesize microcystins. Cumulatively, our results serve as a case study to provide insight on the metabolic pathways driving the ecological success of metalimnic P. rubescens blooms. On a broader scale, this work strengthens the case that alternative nitrogen metabolism - including urea utilization, amino acid catabolism, and the OAC - is a driver of toxigenic cHABs in fresh waters.},
}
@article {pmid41349311,
year = {2025},
author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A},
title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110820},
doi = {10.1016/j.vetmic.2025.110820},
pmid = {41349311},
issn = {1873-2542},
abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.},
}
@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
doi = {10.1371/journal.pone.0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}
@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf638},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}
@article {pmid41348453,
year = {2025},
author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z},
title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001493},
pmid = {41348453},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; },
abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.},
}
@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001574},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}
@article {pmid41347789,
year = {2025},
author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS},
title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0098825},
doi = {10.1128/aem.00988-25},
pmid = {41347789},
issn = {1098-5336},
abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.},
}
@article {pmid41347294,
year = {2026},
author = {McCaughan, KJ and Kniel, KE},
title = {Current Knowledge and Future Directions for Cyclospora cayetanensis Research and Its Surrogates.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70327},
doi = {10.1111/1541-4337.70327},
pmid = {41347294},
issn = {1541-4337},
support = {//National Institute of Food and Agriculture/ ; },
mesh = {*Cyclospora/genetics/isolation &amp; purification/physiology ; *Cyclosporiasis/parasitology/transmission ; Humans ; Animals ; Host-Parasite Interactions ; Oocysts ; Food Parasitology ; Cryptosporidium parvum ; },
abstract = {Cyclospora cayetanensis is a foodborne protozoan parasite that causes cyclosporiasis, a disease transmitted by the consumption of sporulated oocysts, often via contaminated produce. Since 2018, outbreaks traced back to domestically grown produce in the United States have raised growing concern. Despite its public health significance, research is hindered by methodological challenges, including inability to culture in vitro/in vivo and limited genomic characterization. This review examines current knowledge on its occurrence and transmission, detection methods, host-parasite interactions, genetics, and remediation strategies, while also evaluating use of surrogate organisms (Eimeria spp. and Cryptosporidium parvum) to address research gaps. Detection remains challenging due to low oocyst concentrations in environmental and food matrices, requiring highly sensitive molecular assays. Additionally, the lack of standardized sampling methods that are representative of an entire batch of produces further complicates reliable detection and surveillance efforts. The recently implemented Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 19c method has improved sensitivity but still requires refinement. Although Eimeria spp. offer insight into sporulation and environmental behaviors and C. parvum has supported methodological development, neither fully replicates C. cayetanensis biology; limiting the translatability of surrogate-based research. Remediation strategies are underexplored, though research on related coccidia suggests significant resistances to conventional sanitizers. Genomic advancements, including the identification of distinct C. cayetanensis lineages, provide useful insights, though gaps in genome assemblies limit phylogenetic and functional analyses. Emerging tools, such as metagenomics, single-cell sequencing, and AI-driven bioinformatics, may overcome persistent barriers. Addressing these challenges is essential for improving detection, risk assessment, and guiding policy, all of which will mitigate the public health burden of cyclosporiasis.},
}
@article {pmid41346779,
year = {2025},
author = {Orsud, H and Zoughbor, S and AlDhaheri, F and Hajissa, K and Refaey, M and Ajab, S and Alswaider, K and Mohamed, N and Alkaabi, O and Al Rasbi, Z},
title = {Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1690766},
pmid = {41346779},
issn = {2673-7647},
abstract = {BACKGROUND: Gut fungi play crucial roles in human health. The profiling of the human gut mycobiome continues to progress. However, adjustments in the selection of ribosomal DNA marker regions can substantially affect the taxonomic resolution of a population. In particular, the impact of using primers' combinations is insufficiently defined. In this study, we investigated the performance of three targeted sequencing regions, ITS1, ITS2 and 18S rRNA, separately and in combination.<br><br>METHODS: Eight fecal samples from healthy individuals (n = 4) and cancer patients (n = 4) were selected as proof of principle for amplicon-based sequencing conducted with the DNBSEQ&#x2122; sequencing system. Quality-filtered reads were grouped into operational taxonomic units (OTUs) via USEARCH and categorized using the SILVA (18S) and UNITE (ITS) databases. Downstream bioinformatics encompassed diversity analyses, principal component analysis (PCA), and biomarker detection via linear discriminant analysis effect size (LEfSe). To improve taxonomic coverage and compositional understanding, data were examined using ALDEx2 with centered log-ratio (CLR) transformation, facilitating reliable differential abundance and effect size assessment in small sample metagenomic contexts.<br><br>RESULTS AND DISCUSSION: Among primers, ITS2 and ITS1 enhanced the coverage of identified taxa, with operational taxonomic unit quantities of 183 and 158, respectively, compared to 58 OTUs of 18S. Accordingly, among primer combinations tested, the triple integration of ITS1-ITS2-18S produced the highest fungal richness, while the dual ITS1-ITS2 combined datasets enhanced group discrimination analysis, showing enrichment of Candida albicans and scarcity of Penicillium sp. in cancer patients. Our findings based on ITS sequencing and the combination of ITS1 and ITS2 provide instructive information on the composition and dynamics of gut fungi in our initial test subjects, enhancing our understanding of their roles in gut homeostasis and the microbial shifts associated with cancer. Despite our approach being conducted with a limited cohort to establish methodological feasibility, it brings attention to multi-marker strategies, demonstrating that integrated primer datasets surpass traditional single-marker methods in both taxonomic coverage and biomarker detection sensitivity in low-biomass fecal samples. Our research provides a reliable starting point for future studies on gut mycobiome in both healthy and diseased individuals, which could lead to better diagnostics and treatments based on microbiome profiles.},
}
@article {pmid41346662,
year = {2025},
author = {Ren, M and Liao, Q},
title = {Diagnosis of Salmonella enterica-induced septic arthritis in a healthy child using metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1704234},
pmid = {41346662},
issn = {2296-2360},
abstract = {Salmonella enterica-induced arthritis frequently manifests in children with malignancies, sickle cell disease, immunodeficiency, or undergoing immunosuppressive therapy; however, its incidence in healthy children is rare. Here, we present a case of septic arthritis resulting from S. enterica infection in a previously healthy child, diagnosed utilizing metagenomic next-generation sequencing (mNGS). This case underscores the utility of mNGS in the clinical identification of S. enterica arthritis. Particularly in scenarios where the causative pathogen remains unidentified, mNGS emerges as a pivotal adjunctive diagnostic modality for uncommon pathogens.},
}
@article {pmid41346360,
year = {2025},
author = {Huang, J and Li, S and Jiang, C and Wang, L and Pan, Z and Zhang, Z and Zhu, J and Chen, W and Hu, X},
title = {Targeted next-generation sequencing for respiratory infections in patients with haematological malignancies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1678858},
pmid = {41346360},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Male ; Adult ; Aged ; Immunocompromised Host ; Sensitivity and Specificity ; Metagenomics/methods ; Young Adult ; Aged, 80 and over ; Adolescent ; Bacteria/genetics/isolation &amp; purification/classification ; },
abstract = {BACKGROUND: Patients with haematological malignancies are immunocompromised and prone to respiratory infections, but identification of causative pathogens is challenging. The aim of this study was to analyse the ability of targeted next-generation sequencing (tNGS) to detect pathogens in immunocompromised patients.<br><br>METHODS: tNGS and conventional microbiological tests (CMT) were performed on samples from the respiratory tract of 99 patients with suspected respiratory infections. Metagenomic next-generation sequencing (mNGS) was conducted in parallel in 43 patients. Comparative analysis was conducted using the Pearson &#x3c7;2 test and Fisher's exact test, as appropriate.<br><br>RESULTS: The overall microbial detection rates for tNGS were 100% (23/23) in the upper respiratory tract and 96.1% (99/103) in the lower respiratory tract. Microorganism colonization was detected by tNGS in 80.8% (97/120) of cases. The sensitivity of tNGS was approximately 30% higher than that of CMT (87.7% vs. 52.5%; P <&#xa0;0.001), but tNGS had a lower specificity (33.3% vs. 83.3%; P&#xa0;=&#xa0;0.242). tNGS improved the overall treatment success rate by 69.7% (69/99 cases) in CMT true-negative or CMT-partially matched cases. In the paired respiratory tNGS and mNGS cases, tNGS verified 73.3% (11/15) cases of infection, while mNGS only verified 40% (P&#xa0;=&#xa0;0.139).<br><br>CONCLUSIONS: Most immunosuppressed patients are colonized by microorganisms, and require prompt identification of the cause of any infections. tNGS has promising diagnostic potential and offers valuable information for optimizing antibiotic therapy, especially when compared to CMT.},
}
@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022//&#x2003;Department of Biotechnology/ ; //&#x2003;Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}
@article {pmid41346299,
year = {2025},
author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z},
title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11806},
pmid = {41346299},
issn = {1520-5851},
abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.},
}
@article {pmid41345980,
year = {2025},
author = {Jiang, Y and Che, L and Li, SC},
title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02273-w},
pmid = {41345980},
issn = {2049-2618},
support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.<br><br>RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.<br><br>CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.},
}
@article {pmid41345979,
year = {2025},
author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M},
title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02256-x},
pmid = {41345979},
issn = {2049-2618},
support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.<br><br>RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.<br><br>CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.},
}
@article {pmid41345977,
year = {2025},
author = {Saati-Santamaría, Z and González-Dominici, LI and Jiménez-Gómez, A and Morais, D and Tláskal, V and Frontela, I and Benada, O and Qi, L and Sheng, Y and Rivas, R and Baldrian, P and García-Fraile, P},
title = {Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02277-6},
pmid = {41345977},
issn = {2049-2618},
support = {101090267//HORIZON-TMA-MSCA-PF-EF/ ; PID2023-150384NB-I00//European Union NextGenerationEU/PRTR/ ; TED2021-129157B-100//MICIU/AEI/10.1309/501100011033/ ; CLU-2025-2-04//Escalera de Excelencia - Consejer&#xed;a de Educaci&#xf3;n de Castilla y Le&#xf3;n - ERDF/ ; RYC2023-045204-I//MCIU/AEI/10.13039/501100011033 and ESF+/ ; 750795//EUROPEAN UNION'S HORIZON 2020/ ; },
abstract = {BACKGROUND: Microorganisms play important ecological roles during interactions with plants, with some strains promoting plant performance. However, the molecular basis of bacterial adaptation to the plant environment remains poorly understood. Microbial plant growth promotion is a complex process that likely involves numerous bacterial genes, many of which remain uncharacterized. In this study, we aimed to identify genes tightly associated with the bacterial adaptation to plant hosts by integrating transcriptomic data from bacteria colonizing roots with comparative genomic and metagenomic analyses.<br><br>RESULTS: Here, we identified a set of bacterial genes that were significantly upregulated during root colonization and are more abundant in rhizosphere communities than in bulk soils. Many of these genes had not been previously linked to plant-bacteria interactions. Comparative genomic analyses revealed some of these genes as more prevalent in plant-associated Pseudomonas genomes than in genomes from other environments. We argue that these genes may play relevant biological roles in this host, although only a few have been previously associated with plant colonization. Among them, we focused on a gene homologous to yafL, which encodes a cysteine peptidase of the NlpC/P60 family, known for its role in peptidoglycan remodelling. This gene is more abundant in rhizosphere microbiomes than in bulk soils, and it showed induced expression on the root surface, supporting its ecological relevance in root-associated environments. Functional validation using a knockout mutant confirmed its contribution to plant-bacteria interactions by affecting root architecture and plant growth.<br><br>CONCLUSIONS: This study provides new insights into the genetic basis of bacterial adaptation to the plant root environment. By integrating transcriptomic and comparative genomic analyses, we identified numerous genes upregulated during root colonization that are enriched in plant-associated Pseudomonas genomes. Our findings highlight previously overlooked bacterial functions with potential roles in plant-microbe interactions. The functional validation of a protein of the NlpC/P60 family supports its involvement in plant-bacteria interactions and underscores the importance of uncharacterized genes in shaping beneficial associations in the rhizosphere. Video Abstract.},
}
@article {pmid41345889,
year = {2025},
author = {Bessière, P and Hayes, B and Fusade-Boyer, M and Sécula, A and Rous, G and Brun, J and Marchand, A and Croville, G and Cadiergues, MC and Guérin, JL},
title = {Seroprevalence and genetic diversity of feline immunodeficiency virus in outdoor cats in France.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01672-z},
pmid = {41345889},
issn = {1297-9716},
abstract = {Feline immunodeficiency virus (FIV) is a retrovirus that causes lifelong infections in cats and may lead to immune dysfunction. Despite its importance for feline health, there is limited FIV data from France. This study investigated samples collected from stray and owned cats with outdoor access across France between December 2023 and January 2025 to estimate FIV seroprevalence, identify seropositivity predictors and analyse the genetic diversity of circulating strains. Serological screening was performed using a commercial ELISA. Polymerase chain reaction (PCR) was conducted on ELISA-positive sera, with selected samples analysed by Sanger sequencing for phylogenetic inference. One sample underwent metagenomic shotgun sequencing using Oxford Nanopore technology. The national seroprevalence, estimated using a Bayesian hierarchical model, was 16% (95% credible interval: 8.4-20%) overall, then 31% (21-42%) among intact male cats, 18% (CrI: 10.6-25.2%) among neutered male cats and 8.4% (CrI: 1.8-14%) among female cats. Outdoor exposure, sex and neuter status were strong predictors of seropositivity. Among strays, predicted probability of seropositivity exceeded 50% by 5 years of age. All sequenced viruses were classified as subtype A. However, the phylogenetic analysis revealed notable genetic variability, indicating at least two independent introductions of FIV into France. While related to other European strains, several isolates appeared to share distinct ancestral lineages. The metagenomic dataset yielded approximately 100,000 FIV reads among 2 million total reads, enabling full genome recovery. These findings highlight the ongoing circulation of FIV in France and provide valuable data for veterinary practitioners and future surveillance efforts in Europe.},
}
@article {pmid41345831,
year = {2025},
author = {Bu, Y and Sun, F and Liu, L and He, X and Wang, H and Chen, Z and He, T and Xu, S and Zhao, X and Meng, X},
title = {Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12392-1},
pmid = {41345831},
issn = {1471-2164},
support = {CX23YQ31//Heilongjiang Agricultural Science and Technology Innovation Leapfrog Project/ ; CARS-37//Supported by China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Understanding the rumen microbiota's development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.<br><br>METHODS: Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).<br><br>RESULTS: The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P&#x2009;<&#x2009;0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P&#x2009;<&#x2009;0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid41345737,
year = {2025},
author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H},
title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02291-8},
pmid = {41345737},
issn = {2049-2618},
support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; },
abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.<br><br>RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.<br><br>CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.},
}
@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07285-4},
pmid = {41345617},
issn = {1472-6831},
}
@article {pmid41345487,
year = {2025},
author = {Karnachuk, OV and Panova, IA and Rusanov, II and Avakyan, MR and Lukina, AP and Ikkert, OP and Kijar, N and Kadnikov, VV and Beletsky, AV and Danilova, EV and Kopitsyn, DS and Pimenov, NV and Shcherbakova, VA and Ravin, NV},
title = {Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28271-4},
pmid = {41345487},
issn = {2045-2322},
support = {24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; },
abstract = {Dissimilatory sulfate reduction is the main microbial process that detoxifies metals and increases pH in acid mine drainage. Acidophilic, copper-resistant Desulfosporosinus sp. BG and Desulfosporosinus sp. OT were previously isolated from acidic metalliferous tailings of the Bom-Gorkhon mine in Transbaikalia and Norilsk, respectively. To understand the role of sulfate-reducing bacteria (SRB) in mine tailings, we returned to the Bom-Gorkhon site to measure sulfate-reduction rate (SRR) with radioactive tracer and to estimate the proportion of SRB in the microbial community using 16 SrRNA gene profiling and metagenomic analysis. The SRR measured under ambient temperature conditions was high, reaching 9.86 ± 0.89 µmol SO4 cm[- 3] day[- 1]. Unexpectedly for a temperate biotope, SRR values of the same order of magnitude were recorded at 60 °C. Thermophilic spore-forming Desulfotomaculum and Desulfofundulus are likely involved in the thermophilic process. The spores of thermophilic Desulfofundulus germinating at 20 °C may input into sulfate reduction at in-situ temperature conditions. Metagenomic analysis by dsr gene mapping and 16 S rRNA gene profiling revealed low abundance of Desulfosporosinus and other SRBs, indicating that geochemically important active sulfate reduction in acidic wetland sediments is carried out by a "rare biosphere" consortium. The cultivated BG[T] and OT strains are described as Desulfosporosinus cupriresistens sp. nov.},
}
@article {pmid41345261,
year = {2025},
author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I},
title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41345261},
issn = {2058-5276},
support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; },
abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.},
}
@article {pmid41345243,
year = {2025},
author = {Ste Marie, J and Mays, C and Guo, B and Radniecki, TS and Waite-Cusic, J and Navab-Daneshmand, T},
title = {Longitudinal replicated metagenomic analysis of biosolids-amended soils reveals enrichment of ARGs, virulence factors, and ESKAPE pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {96},
pmid = {41345243},
issn = {2731-8745},
support = {2018-67017-27631//USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, Agriculture Economics and Rural Communities/ ; },
abstract = {Biosolids land application introduces antibiotic resistance genes (ARGs) and clinically relevant pathogens into agricultural soils, raising concerns about long-term environmental and public health impacts. Despite growing interest in biosolids reuse, there remains a critical need for replicated, longitudinal studies to assess how biosolids amendments shape soil microbiomes and resistomes during crop cultivation. In this replicated longitudinal greenhouse study, we used shotgun metagenomics to characterize the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation. Biosolids-amended soils exhibited increased richness of microbial genera (e.g., Rhodanobacter, Dyella, and Thermomonas), ARG subtypes (resistance to sulfonamide, tetracycline, fosmidomycin, and macrolides), and virulence factors compared to pristine controls. Notably, all six ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., were detected at elevated relative abundances (1.4- and 3.4-fold) in biosolids-amended soils and remained detectable throughout the 11-week cultivation period. Network analysis revealed statistically supported co-occurrences between microbial taxa and ARGs (with resistance to tetracyclines, beta-lactams, chloramphenicol, and multidrugs), suggesting possible host associations. These findings underscore the ecological and clinical relevance of biosolids amendment and highlight the need for integrated surveillance frameworks to mitigate antimicrobial resistance dissemination in agricultural environments.},
}
@article {pmid41345146,
year = {2025},
author = {Kar, S and Reddy, MK and Asthana, R and Srivastava, P and Dhaarani, R and Reddy, KVNS and Meghamala, V and Koduru, JR and Karri, RR},
title = {Synergistic effects of syzygium cumini sawdust biochar and poultry manure on soil quality enhancement, nitrogen, organic carbon dynamics, and Amaranthus cruentus growth.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25003-6},
pmid = {41345146},
issn = {2045-2322},
support = {Ref. No-2022/0149//GITAM Research Seed Grants/ ; },
abstract = {The study aimed to evaluate the potential of incorporating biochar with poultry manure to address the constant challenges of sandy, loam soils due to poor water retention and low soil fertility, and their influence on the growth and yield of Amaranthus cruentus during the Rabi and Kharif seasons. The combined effect of manures on soil health over different seasons was unexplored, so the current research has been taken up to understand the impact of different treatments on physical, chemical, and microbial dynamics in the Rabi and Kharif seasons. Advanced statistical analysis was used to measure the soil and plant factor variations across seasons. Pre- and post-harvest results showed substantial progress in the soil bulk density, water-holding capacity (WHC), and nutrient retention in KR5 (biochar + poultry manure) treatment, where WHC displayed a strong positive correlation with organic matter (r > 0.82). Even chemical analysis indicated increased soil nitrogen, phosphorus, potassium, and carbon levels. Metagenomic analysis implied microbial diversity and abundance promoting nitrogen fixation and decomposition of organic matter. FTIR and SEM also revealed structural improvements that are beneficial for microbial colonization and nutrient retention. The combination of biochar and poultry manure showed higher growth, increasing plant height by 40 cm and yielding over 550 g/m[2] during the Kharif season. The results have revealed that the combination of biochar and poultry manure has improved soil fertility, microbial diversity, and yield of Amaranthus cruentus grown in sandy loam soils.},
}
@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}
@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}
@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}
@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteriophages/genetics/classification/isolation &amp; purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}
@article {pmid41344758,
year = {2026},
author = {Okoye, CO and Ezenwanne, BC and Olalowo, OO and Ajanwachukwu, OJ and Chukwudozie, KI},
title = {Microbial-mycotoxin interactions in food: A review of ecotoxicological implications and omics approaches for understanding detoxification mechanisms.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104955},
doi = {10.1016/j.fm.2025.104955},
pmid = {41344758},
issn = {1095-9998},
mesh = {*Mycotoxins/metabolism/toxicity ; *Food Contamination/analysis ; *Fungi/metabolism/genetics ; *Food Microbiology ; Ecotoxicology ; Inactivation, Metabolic ; Animals ; Humans ; Genomics ; },
abstract = {Mycotoxins, toxic secondary metabolites produced by fungi such as Aspergillus, Fusarium, and Penicillium, frequently contaminate food supplies, posing risks to human health, animal welfare, and ecosystem stability. Mycotoxins like aflatoxins, ochratoxin A, fumonisins, trichothecenes, and zearalenone disrupt microbial communities, food chains, and environmental matrices, with synergistic interactions amplifying their toxicity. This review explores microbial-mycotoxin interactions in food systems, focusing on ecotoxicological implications and omics approaches for elucidating detoxification mechanisms. Microbial detoxification, through adsorption by cell wall components (e.g., β-glucans) or enzymatic biodegradation (e.g., lactonases, oxidoreductases), offers a sustainable alternative to physical and chemical methods. However, challenges include variable detoxification efficiency, mechanistic uncertainties, regulatory hurdles, and the detection of masked mycotoxins in complex food matrices. Omics technologies such as metagenomics, genomics, transcriptomics, and their integration provide comprehensive insights into microbial diversity, gene expression, enzyme activity, and metabolite transformations. In addition, omics integration enhances understanding of microbial-mycotoxin dynamics, supporting targeted biocontrol strategies. Future prospects include leveraging synthetic biology, CRISPR-based gene editing, and machine learning-assisted bioinformatics to optimize microbial strains and predict detoxification outcomes. By addressing these challenges, omics-driven approaches can mitigate mycotoxin contamination, ensure food safety, and reduce ecotoxicological impacts across global food systems.},
}
@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}
@article {pmid41344255,
year = {2025},
author = {Chen, X and Wu, Y and Xue, B and You, Y and Yin, L and Wang, S and Zheng, J},
title = {Mechanism of flavor formation in Suansun fermented by Lactiplantibacillus plantarum during a three-stage flavor formation model.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147316},
doi = {10.1016/j.foodchem.2025.147316},
pmid = {41344255},
issn = {1873-7072},
abstract = {This study employed an integrated multi-omics approach-metagenomics, metatranscriptomics, and metabolomics-to elucidate the flavor formation mechanism in Suansun, leading to the proposal of a three-stage flavor formation model. In the initial stage, Lactiplantibacillus plantarum dominates pyruvate metabolism, rapidly producing lactic acid and creating an acidic environment that drives microbial succession. This pH shift initiates the key flavor-forming stage, during which peak levels of Weissella cibaria align with linalool biosynthesis, suggesting strong temporal coordination. During the mid-to-late stages, the abundance of Clostridium species was strongly correlated with p-cresol generation via tyrosine catabolism, while Lactococcus and related taxa produce nonanal and ketones through fatty acid β-oxidation. Overall, the starter culture actively restructures the fermentation niche, sequentially activating metabolic pathways in successive microbial communities to shape a stable flavor profile. This staged model of flavor evolution provides a scientific foundation for optimizing and controlling Suansun fermentation quality.},
}
@article {pmid41344131,
year = {2025},
author = {Liu, T and Li, L and Chen, J and Cai, G and Meng, F and Jiao, Y and Mao, Y and Wang, Z and Zuo, W and Tian, Y and Sun, H},
title = {Real-world aged microplastics exacerbate antibiotic resistance genes dissemination in anaerobic sludge digestion via enhancing microbial metabolite communication-driven pilus conjugative transfer.},
journal = {Water research},
volume = {290},
number = {},
pages = {125056},
doi = {10.1016/j.watres.2025.125056},
pmid = {41344131},
issn = {1879-2448},
abstract = {The dissemination of antibiotic resistance genes (ARGs) facilitated by coexisting microplastics (MPs) in the "source-sink" hotspots of waste activated sludge (WAS) raises great concern. Despite real-world MPs undergoing aging, whether and how naturally aged microplastics (AMPs) affect ARG dissemination during sludge treatment remains largely unknown. Herein, we systematically explored the evolved effects and underlying mechanisms of environmentally relevant MPs (0, 3, and 30 mg/kg TS) aging on ARG propagation in anaerobic sludge digestion via multi-omics analyses. Specifically, microplastic exposure increased total ARG abundance by 2.59-15.31 % with enriched mobile genetic elements (MGEs, 0.22-16.71 %). These effects were escalated at higher microplastic dosages and aging degrees. Mechanistically, metagenomic and metaproteomic analyses revealed the drivers for ARG amplification in the sludge digester evolved from the pristine microplastics (PMPs)-induced higher oxidative stress and membrane permeability to AMPs-induced higher multidrug efflux coupled with pilus-mediated conjugation. Subsequently, metagenomic binning identified key multidrug-resistant hosts of Sedimentibacter, Alicycliphilus, and Sulfuricurvum genera. Moreover, high-resolution metabolomics and reactomics network analysis uncovered that AMPs stimulated microbial metabolite turnover, particularly of nitrogenous and sulfurous compounds, and enhanced the complexity and communication frequency of molecular transformation networks centered on lignin and protein nodes, thereby promoting ARG exchange. Finally, Mantel tests reconfirmed that reactive oxygen species level (Mantel's r = 0.93, p = 0.04) and metabolite network connectivity (Mantel's r = 0.82, p = 0.04) are paramount drivers of ARG spread. These findings offer novel insights into the ARG amplification risk driven by MPs aging, guiding targeted strategies to mitigate ARG spread and improve resource recovery in sludge bioengineering systems.},
}
@article {pmid41344128,
year = {2025},
author = {Xie, X and Li, E and Jiang, H and Pi, K and Yan, L and Shen, S},
title = {Methane biogeochemical turnover constrains arsenic transformation in groundwater systems: Organic molecular signatures and microbial functional networks.},
journal = {Water research},
volume = {290},
number = {},
pages = {125083},
doi = {10.1016/j.watres.2025.125083},
pmid = {41344128},
issn = {1879-2448},
abstract = {Arsenic (As) contamination of groundwater is primarily driven by microbially mediated redox processes and the dynamic evolution of dissolved organic matter (DOM). The influence of cycled methanogenesis and methane oxidation processes on As species transformation in geogenic As-contaminated groundwater, however, remain mechanistically elusive. In this study, quantitative relationships among DOM molecular characteristics, microbial functional networks, and As speciation were established using sediment microcosm experiments, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and metagenomic sequencing. The results indicate that rates of methanogenesis and methane oxidation are regulated by thermodynamic properties of DOM. Labile DOM promoted As(III) mobilization at a rate of 1.04 μg kg[-1] d[-1] through methyl-related metabolism. Remarkably, enhanced methane oxidation further elevated the As(III) generation rate to 3.30 μg kg[-1] d[-1], underscoring the accelerating effect of methane cycling on As release. In contrast, humified DOM decoupled the geochemical linkage between iron and As. Microbial succession governed the redox transitions, as the proliferation of methanogens substantially increased methane production (up to 7.23 mg kg[-1] d[-1]), while methanotrophs enhanced oxidation rates from 94.99 to 190.76 mg kg[-1] d[-1]. This microbial progression coupled sulfate and As(V) reduction through the up-regulation of key functional genes (dsrAB, arsC). Energy conversion during DOM biodegradation governs As migration stages. These findings highlight the interactive constraints on As speciation dynamics by molecular characteristics of DOM and microbial functional networks during methane biotransformation processes in groundwater systems. This research provides new mechanistic insights into As biogeochemical cycling in geogenic contaminated groundwater.},
}
@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf118},
pmid = {41342600},
issn = {1574-6941},
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}
@article {pmid41341964,
year = {2025},
author = {Yao, J and Zhang, J and Zheng, L and Fang, W and Lang, Y},
title = {Coxiella burnetii Should Not Be Ignored: Two Cases of Q Fever Pneumonia Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6227-6239},
pmid = {41341964},
issn = {1178-6973},
abstract = {BACKGROUND: Q fever is a globally distributed zoonotic disease caused by Coxiella burnetii (C. burnetii). As an obligate intracellular bacterium, C. burnetii is primarily transmitted from domestic animals to humans, with ticks also serving as potential vectors. The clinical manifestations of Q fever are often nonspecific and highly variable, making its diagnosis particularly challenging.<br><br>CASE PRESENTATION: Two male pneumonia patients were hospitalized in Deqing People's Hospital, one was 73 years old, and the other one was 30 years old, both of them presented with hyperpyrexia without a clear epidemiological history. However, initial empirical treatment was ineffective and microbiological cultures were all negative, then bronchoscopy was conducted for them and bronchoalveolar lavage fluid (BALF) was sent for metagenomic next-generation sequencing (mNGS) test. Ultimately, two patients were diagnosed with Q fever pneumonia, and the symptoms of patients were significantly improved after timely treatment with the special drug doxycycline and moxifloxacin, and lung inflammation in both patients were effectively absorbed in the subsequent follow-up examination.<br><br>CONCLUSION: Two cases of Q fever pneumonia were diagnosed through mNGS. As a new detection method, mNGS has advantages in the diagnosis of unknown infectious pathogens. As a zoonotic pathogen, C. burnetii should not be ignored. The One Health approach may be suitable for Q fever prevention and control.},
}
@article {pmid41341958,
year = {2025},
author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M},
title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1701570},
pmid = {41341958},
issn = {2235-2988},
mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; },
abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.},
}
@article {pmid41341954,
year = {2025},
author = {Fang, XZ and Liu, ZH and Duan, LM and Yao, L and Xu, JQ and Yang, XB and Ren, LH and Jiang, YX and Sun, SW and Shang, Y and Yuan, Y},
title = {Clinical features, pathogens, and prognosis of immunocompromised host pneumonia in patients with malignancies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646513},
pmid = {41341954},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; Male ; *Neoplasms/complications ; Female ; Middle Aged ; Prospective Studies ; Aged ; Prognosis ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/mortality/diagnosis ; Coinfection/microbiology ; Adult ; Bacteria/isolation &amp; purification/classification ; Metagenomics ; COVID-19 ; Aged, 80 and over ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Cancer patients face elevated risks of severe pulmonary infections due to malignancy-related immunosuppression and anti-neoplastic therapy. Comprehensive data on the etiology and prognostic factors remain limited.<br><br>METHODS: This prospective cohort study enrolled 115 patients with malignancies and immunocompromised host pneumonia (ICHP) from July 2023 to July 2024. Pathogens were identified using clinical metagenomics of bronchoalveolar lavage fluid (BALF), supported by CT imaging and clinical evaluation.<br><br>RESULTS: Pathogens were detected in 92 patients (80.0%), with 158 potential pathogens detected. Etiologic diagnoses were established by BALF mNGS alone in 68 (73.9%), by combined mNGS plus standard microbiologic testing (SMT) in 24 (26.1%), and by SMT alone in 1 (1.1%). Pneumocystis jirovecii (32, 20.3%), SARS-CoV-2 (14, 8.9%), Aspergillus fumigatus (13, 8.2%), Klebsiella pneumoniae (12, 7.6%) and Haemophilus influenzae (10, 6.3%) were the five most common pathogens. Coinfections occurred in 36.5% of all enrolled patients. Death at 28 days, ICU admission, Death at ICU was more frequent among patients with polymicrobial infections than single pathogen infection, though this difference was not statistically significant. Use rate of vasoactive drugs was significantly higher in patients with coinfection than in patients with single-pathogen infection (39.1% vs. 16.0%). invasive mechanical ventilation (IMV) (OR = 22.86, p=0.047), vasopressor use (OR = 72.69, p=0.039), and higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores (OR = 1.46, p=0.016) were associated with increased 28-day all-cause mortality.<br><br>CONCLUSION: Patients with malignancies and evaluated for pulmonary infection were found to have unique microbiological profiles detected by BAL metagenomic sequencing. Co-detection of potential pathogens was high, and associated with high 28-day all-cause mortality.},
}
@article {pmid41341823,
year = {2025},
author = {Huang, W and Lai, HP and Yu, L and Jin, L and Lei, W},
title = {Case Report: Chronic Q fever mimicking malignancy and tuberculosis in a hemodialysis patient: multidisciplinary diagnosis guided by metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1656891},
pmid = {41341823},
issn = {2296-858X},
abstract = {BACKGROUND: Q fever, caused by Coxiella burnetii, is a rare zoonosis whose clinical presentation is highly heterogeneous. Chronic Q fever can present with atypical systemic masses, creating significant diagnostic challenges as it lacks distinctive imaging features, often leading to misdiagnosis.<br><br>CASE PRESENTATION: We report a case of a 50-year-old woman on maintenance hemodialysis who presented with a one-month history of generalized myalgia and abdominal discomfort. Initial PET-CT imaging revealed multiple hypermetabolic abdominal lesions (SUV&#x223c;max&#x223c; 7.1), mimicking metastatic malignancy. Histopathology of abdominal biopsies showed granulomatous inflammation with necrosis but lacked definitive microbiological evidence. Empirical anti-tuberculosis therapy was initiated based on clinical suspicion. Despite initial clinical improvement, the patient experienced recurrence of symptoms and radiological progression after 1 year. Re-evaluation with transesophageal echocardiography suggested the possibility of infective endocarditis. Crucially, metagenomic next-generation sequencing (mNGS) of a repeat biopsy identified Coxiella burnetii, confirming chronic Q fever. Targeted doxycycline therapy resulted in sustained clinical and radiological improvement, with lesion resolution confirmed at the 14-month follow-up.<br><br>CONCLUSION: This case underscores the diagnostic difficulty of chronic Q fever due to its non-specific presentation and imaging characteristics. PET-CT may suggest malignancy, but incorporating advanced molecular diagnostics such as mNGS is critical for accurate pathogen identification. Recognizing atypical manifestations and utilizing integrative diagnostic approaches can facilitate timely, targeted therapy, improving clinical outcomes in rare infectious diseases like Q fever.},
}
@article {pmid41341819,
year = {2025},
author = {Kong, M and Sun, J},
title = {Case Report: A case of Nocardia otitidiscaviarum pneumonia diagnosed by application of metagenome next-generation sequencing and a narrow literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1646940},
pmid = {41341819},
issn = {2296-858X},
abstract = {Nocardia is an opportunistic pathogen with relatively low incidence but high mortality. Recently, reports of Nocardia infections have increased; however, infections caused by Nocardia otitidiscaviarum (N. otitidiscaviarum) remain relatively rare. Due to its non-specific clinical manifestations and imaging features, N. ototidiscaviarum infections are frequently misdiagnosed or underdiagnosed, and no standardized guidelines currently exist for their diagnosis and treatment. In this study, we report a case of pulmonary infection caused by N. otitidiscaviarum, which was diagnosed using a combination of traditional microbial morphology and second-generation sequencing, and subsequently showed improvement following treatment with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid. Additionally, we conducted a comprehensive literature review using PubMed to provide insights for improving the diagnosis and treatment of N. otitidiscaviarum infections.},
}
@article {pmid41341716,
year = {2025},
author = {Leutert, A and Zeckanovic, A and Huber, M and Meyer Sauteur, PM and Morscher, RJ},
title = {Recurrent vaccine-strain varicella zoster virus reactivation in a child with acute lymphatic leukemia.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02422},
pmid = {41341716},
issn = {2214-2509},
abstract = {This case illustrates recurrent herpes zoster (HZ) in a child with acute lymphatic leukemia. Interestingly, vaccine-strain HZ was confirmed by identifying the live-attenuated Oka vaccine strain (vOka) using metagenomic sequencing and sequence comparison at three loci that distinguish vOka from wild-type varicella zoster virus (VZV). Although vaccine-strain HZ is generally milder than HZ caused by wild-type VZV, prompt recognition and initiation of antiviral treatment is essential in immunocompromised patients, as fatal varicella due to disseminated vaccine-strain VZV has been reported in this high risk group.},
}
@article {pmid41341658,
year = {2025},
author = {Kriem, LS and King, N and Niemann, S and Vainshtein, Y and Sonntag, M},
title = {Molecular Identification of Human and Plant Pathogens in Municipal Domestic Wastewater for Hydroponic System Applications.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {6958575},
pmid = {41341658},
issn = {1687-918X},
abstract = {Water is essential for human survival and socioeconomic development, yet its overconsumption threatens global food security and ecosystem integrity. This necessitates a 60% increase in food production, further straining water resources. Hydroponic systems represent a promising solution, utilizing up to 90% less water than traditional methods while providing optimal growing conditions for crops. This study was aimed at developing a PCR-based detection system for main human and plant pathogens in hydroponic systems using treated domestic wastewater. Metagenomic analysis of wastewater samples revealed significant microbial diversity, identifying human pathogens such as Pseudomonas aeruginosa and Yersinia enterocolitica, alongside plant pathogens including Rhodococcus fascians. Specific primer pairs for the most abundant species found in a domestic municipal wastewater sample of target pathogens (Streptococcus mutans, P. aeruginosa, Acinetobacter baumannii, Y. enterocolitica, Enterococcus faecalis, Pseudomonas viridiflava, R. fascians, Xanthomonas vesicatoria, and Pseudomonas syringae) were designed and validated, ensuring high specificity and efficiency. Future research should focus on enhancing detection methods and optimizing DNA extraction techniques to improve pathogen quantification and management in hydroponic systems. This approach is crucial for sustainable agricultural practices that minimize water usage while ensuring food safety and environmental health.},
}
@article {pmid41341495,
year = {2025},
author = {Rana, TS and Bansode, RR and Rana, JP and Williams, LL},
title = {A systematic review: polyphenol's effect on food allergy via microbiome modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673472},
pmid = {41341495},
issn = {1664-302X},
abstract = {INTRODUCTION: Food allergy is an increasing health concern worldwide. Microbes, food allergies, and polyphenols are found to be interrelated. However, studies relating polyphenols' effect on food allergy via microbiome modulation are scarce, and there is a lack of common signature microbiome modulation patterns. Thus, this review aims to summarize the effect of polyphenols on food allergy via microbiome modulation.<br><br>METHODS: Research articles were searched from Scopus, PubMed, ScienceDirect, and Web of Science database. The in vivo and in vitro studies were assessed via SYRCLE risk of bias and modified CONSORT checklist, respectively. The population characteristics and experimental details were extracted, and the data were synthesized narratively.<br><br>RESULTS: The included studies were free of selective reporting of results. The allergy of egg (ovalbumin), milk (&#x1d6fd;-lactoglobulin), soybean (&#x1d6fd;-conglycinin), and shrimp allergy contributed to 54%, 23%, 15%, and 8% of the total included studies, respectively. The used compounds were a different source or types of polyphenols such as cocoa, cyanidin-3-O-glucoside (C3G), avenanthramide's (AVA), rosmarinic acid (RA), neohesperidin, and fermented apple juice for egg allergy, luteolin, and green tea polyphenol (GTP) for soybean allergy, and flavonoids (Luteolin, myricetin and hyperoside), ferulic acid, and luteolin for milk allergy. Allergies of milk, egg, wheat, and shrimp occurred with the reduction of Lactobacillus, Alistipes, Odaribactor, Akkermansia, Bacteroides, and Lachnospiraceae_NK4A136_group and an increase of Prevotella, Alloprevotella, Faecalibaculum, Helicobactor, Blautia, Clostridium, and Staphylococcus. The polyphenols modulated these microbes in order to attenuate the food allergies.<br><br>DISCUSSION: The types of polyphenols, food allergies, animal model used, and taxonomic resolution of the microbiome studies lead to variation in the results. Thus, by increasing the studies on effect of polyphenols on individual food allergies, and combining with higher taxonomic resolution techniques such as shotgun metagenomics along with metabolomics would increase reliability of the results of the future studies.},
}
@article {pmid41341171,
year = {2025},
author = {Khan, N and Nasir, MM and Mushtaq, A and Kayani, MUR},
title = {SNPraefentia: a toolkit to prioritize microbial genome variants linked to health and disease.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf297},
pmid = {41341171},
issn = {2635-0041},
abstract = {MOTIVATION: Analysis of genomic variation in microbial genomes is crucial for understanding how microbes adapt, interact with their hosts, and influence health and disease. In metagenomic studies, where genetic material from entire microbial communities is sequenced, thousands of single-nucleotide polymorphisms can be detected across species and samples. However, identifying which of these variations has biologically or functionally relevant impacts remains a significant challenge.<br><br>RESULTS: To address this, we present SNPraefentia, a Python-based toolkit for prioritizing microbial SNPs based on their predicted functional relevance. The tool integrates multiple biologically meaningful parameters, including sequencing depth, physicochemical impact of amino acid substitutions, and the structural and functional context of mutations within annotated protein domains. SNPraefentia extracts variation depth and amino acid changes, annotates protein domains using UniProt, and computes individual impact scores. These are then integrated into a composite prioritization score that reflects the potential biological importance of each variant. Overall, SNPraefentia provides researchers with a systematic and reproducible approach to filter and rank microbial variants for downstream functional analysis or experimental validation.<br><br>The toolkit and test data are freely available at https://github.com/muneebdev7/SNPraefentia.},
}
@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
doi = {10.1080/19490976.2025.2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Vegans ; Metagenome ; Multiomics ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}
@article {pmid41340249,
year = {2025},
author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER},
title = {Molecular insights into the gut-thyroid Axis: microbiota-driven biomarkers and diagnostic applications.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2599225},
pmid = {41340249},
issn = {1744-8352},
abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.<br><br>AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.<br><br>EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.},
}
@article {pmid41340151,
year = {2025},
author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE},
title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-025-00794-5},
pmid = {41340151},
issn = {2042-6410},
support = {R01MH105447-01/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.<br><br>METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.<br><br>RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.<br><br>CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.},
}
@article {pmid41340071,
year = {2025},
author = {Peng, J and Liu, X and Wang, J and Meng, N and Cai, R and Peng, Y and Han, Y and Liao, J and Li, C and Rubin-Blum, M and Ma, Q and Dong, X},
title = {Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02280-x},
pmid = {41340071},
issn = {2049-2618},
support = {1359/23//Israel Science Foundation/ ; 32170121//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; 3502Z202373076//Natural Science Foundation Project of Xiamen City/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; },
abstract = {BACKGROUND: Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. However, its contribution in deep-sea cold seep ecosystems, where diverse microbial communities and frequent communication occur, remains poorly understood. In this study, we aimed to elucidate the occurrence and potential ecological roles of quorum sensing in cold seeps.<br><br>RESULTS: We analyzed 170 metagenomes and 33 metatranscriptomes from 17 global cold seep sites, identifying 299,355 quorum sensing genes from the cold seep non-redundant gene catalog. These genes represent 34 types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. A total of 32,500 quorum sensing genes were identified in 3576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs, and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles in cold seeps. Phylogenetic analysis and protein domain identification highlighted the involvement of key quorum sensing-related proteins (e.g., PDE, RpfC/G, CahR, and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression further confirmed the activity of representative LuxI-R pairs, and metabolomic profiling suggested the presence of putative quorum sensing inhibitors in cold seep sediments.<br><br>CONCLUSIONS: Overall, these findings highlight the complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere. Video Abstract.},
}
@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.<br><br>RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.<br><br>CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}
@article {pmid41339959,
year = {2025},
author = {McAdams, ZL and Campbell, EJ and Dorfmeyer, RA and Turner, G and Shaffer, S and Ford, T and Lawson, J and Terry, J and Raju, M and Coghill, L and Cresci, L and Lascola, K and Pridgen, T and Blikslager, A and Barrell, E and Banse, H and Paul, L and Gillen, A and Nott, S and VandeCandelaere, M and van Galen, G and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC},
title = {A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {124},
pmid = {41339959},
issn = {2524-4671},
abstract = {BACKGROUND: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.<br><br>RESULTS: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.<br><br>CONCLUSIONS: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.},
}
@article {pmid41339940,
year = {2025},
author = {Parwin, N and Dixit, S and Das, S and Sahoo, RK and Subudhi, E},
title = {Metagenomic analysis of microbiome spatial dynamics in urban river confluence affected by city wastewater.},
journal = {Genomics &amp; informatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s44342-025-00054-3},
pmid = {41339940},
issn = {1598-866X},
abstract = {BACKGROUND: Environmental pollutants have a profound impact on microbial dynamics. This study highlights the influence of anthropogenic activity on the shift in bacterial diversity in the catchment area compared to upstream and downstream at Kathajodi, using a metagenomic approach for the first time in River Kathajodi.<br><br>METHODS: Water samples were collected from upstream, catchment, and downstream locations and transported at 4&#xb0;C to the laboratory for DNA extraction, library preparation, sequencing, and physicochemical analysis employing inductively coupled plasma. The extracted DNA was sequenced via the Illumina HiSeq platform and analyzed through MG-RAST for taxonomic and functional classification using KEGG and COG annotations. Statistical diversity analysis, including rarefaction curves, alpha- and beta-diversity indices, and Venn diagrams, provided insights into microbial composition and community variations across sites.<br><br>RESULTS: A significant abundance of pollution indicator members of phylum Bacteroidetes (29.82%) in the catchment (CM), highly contaminated with metals, fecal, and other organic pollutants, could be attributed to their high metabolic capabilities to degrade them. The pristine upstream (US) exhibited an abundance of Shewanella (25.04%), Pseudomonas (17.35%), and Synechococcus (5.62%). The CM, influenced by high anthropogenic activity, showed higher abundances of Flavobacterium (5.20%), Arcobacter (4.05%), and Bacteroides (3.88%). In contrast, downstream (DS), with fewer anthropogenic activities, displayed higher abundances of Aeromonas (4.40%), Acidovorax (0.52%), and Acidimicrobium (0.32%). The highest bacterial diversity of CM could be due to the influence of the physicochemical properties of city waste effluent. From the Venn diagram, 73 common OTUs at the genera level were observed in all three sites, which indicates that the native microflora of the river water niche remains unaffected irrespective of the temporary changes in the vicinity. The functional profiling through KEGG and COG revealed that CM was enriched in carbohydrate metabolism (12.11%), while DS exhibited higher contributions to amino acid metabolism, along with the highest relative abundance of general function prediction (R) (12.89%), all indicative of stress adaptation and metabolic flexibility under polluted conditions. The clean upstream is home to oxygen-loving helpful bacteria, the catchment supports nutrient-hungry and sewage-linked microbes, while the downstream is dominated by metal-tolerant and possibly harmful bacteria, showing the clear impact of human activities along the river.<br><br>CONCLUSIONS: The marked shift in bacterial diversity between US, CM, and DS regions highlights the ecological consequences of anthropogenic impact. These findings emphasize the need for effective environmental management to safeguard water quality and prevent undesirable health issues.},
}
@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04546-8},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.<br><br>METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.<br><br>RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score&#x2009;>&#x2009;5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r&#x2009;=&#x2009;-0.46, P&#x2009;=&#x2009;0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P&#x2009;<&#x2009;0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.<br><br>CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}
@article {pmid41339548,
year = {2025},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41339548},
issn = {1476-4687},
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}
@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}
@article {pmid41339358,
year = {2025},
author = {Li, H and Cao, Y and Liu, X and Ke, Z and Chen, L and Siame, BA and Yaron, S and Leung, KY},
title = {Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1896},
pmid = {41339358},
issn = {2052-4463},
support = {32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; },
mesh = {*Caves/microbiology ; *Metagenome ; *Archaea/genetics/classification ; *Genome, Bacterial ; *Genome, Archaeal ; *Bacteria/genetics/classification ; },
abstract = {Cave microorganisms represent unique extremophiles that have evolved in isolated, nutrient-limited environments and harbor exceptional metabolic capabilities. However, knowledge of cave microbial diversity at genomic level remains limited. Previous studies have focused on individual caves and do not give a global picture. Here, we present the first prokaryotic cave metagenomic catalog from 37 geographical diverse cave environments. We employed an optimized genome reconstruction pipeline to recover 3,837 medium-to-high quality cave metagenome-assembled genomes (MAGs). These MAGs were dereplicated into 1,979 species-level representative clusters that spanned 67 phyla of Bacteria (n = 1,858) and Archaea (n = 121) domains. Classification of representative species showed that 98.7% did not match any existing genome taxonomy classification of named species at ≥ 95% average nucleotide identity (ANI). Most representative genomes harbored putative biosynthetic gene clusters (BGCs) (98.0%) and enzymatic antibiotic resistance genes (ARGs) (95.0%). This comprehensive MAGs catalog provides a foundational resource for exploring cave microbial diversity, secondary metabolism, and the evolutionary origins of antibiotic resistance in subterranean ecosystems.},
}
@article {pmid41339349,
year = {2025},
author = {Coe, A and Mullet, JI and Vo, NN and Berube, PM and Anjur-Dietrich, MI and Salcedo, E and Parker, SM and VonEmster, K and Bliem, C and Arellano, AA and Castro, KG and Becker, JW and Chisholm, SW},
title = {A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1895},
pmid = {41339349},
issn = {2052-4463},
support = {OCE-2048470//National Science Foundation (NSF)/ ; OCE-1153588//National Science Foundation (NSF)/ ; DBI-0424599//National Science Foundation (NSF)/ ; 984601//Simons Foundation/ ; 337262//Simons Foundation/ ; 329108//Simons Foundation/ ; GBMF495//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
mesh = {*Synechococcus/classification/genetics ; *Prochlorococcus/classification/genetics ; *Metagenome ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacterial Proteins/genetics ; },
abstract = {Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.},
}
@article {pmid41339341,
year = {2025},
author = {Bellankimath, AB and Branders, S and Kegel, I and Ali, J and Asadi, F and Johansen, TEB and Imirzalioglu, C and Hain, T and Wagenlehner, F and Ahmad, R},
title = {Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66865-8},
pmid = {41339341},
issn = {2041-1723},
support = {336420 and 352514//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; },
abstract = {Urinary tract infections (UTIs) affect 405 million people worldwide. Current diagnostics rely on cultures, which can take 2 to 4 days. This study evaluates eleven culture-independent methods for sample preparation from 78 complicated UTI patients, followed by real-time nanopore sequencing and data analysis. The metagenomic results are highly consistent with culture-based clinical routines (MALDI-TOF/VITEK-2). The optimized method demonstrated an accuracy score of 99% (100/101) for pathogen identification and 90% (589/653) for antimicrobial susceptibility profiling with 95% specificity. The method's robustness is highlighted by its ability to accurately identify pathogens with as few as 32 bacterial cells/µL and a low bacterial-to-host cell ratio limit of 0.5. Additionally, mNGS identified 13 pathogens that routine diagnostics missed, which were subsequently confirmed by Vivalytic or PCR. This method is up to 30% more economical than published studies and commercial kits. DNA yield and flow cytometry can be used for pre-screening to reduce costs, which is crucial for clinical adoption. This research highlights the rapid diagnosis of clinical UTIs using a cost-effective and scalable method that requires around four hours from sample collection to informed decision-making. Furthermore, it aims to improve antimicrobial and diagnostic stewardship by reducing empirical treatment and ensuring more judicious antibiotic use.},
}
@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age <one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants had greater alpha diversity and significant differences in bacterial beta diversity, with 114 species and 38 genera differing in abundance. Indigenous infants almost exclusively had higher carriage of Megaspaera, Streptococcus, Caecibacter, Parolsenella and Prevotella species, and markedly higher numbers of gut viruses and fungi. Bifidobacteria ssp. were dominant in Indigenous infants. Despite encroaching Westernisation, the gut microbiome of Indigenous infants retains key features of traditional societies worldwide, attesting to the dominant influence of remote environment and traditional lifestyle in maintaining microbiome diversity.},
}
@article {pmid41338553,
year = {2025},
author = {, and , },
title = {[The Chinese guidelines for the diagnosis and treatment of invasive fungal disease in patients with hematological disorders and cancers (the seventh revision)].},
journal = {Zhonghua nei ke za zhi},
volume = {64},
number = {12},
pages = {1155-1168},
doi = {10.3760/cma.j.cn112138-20250808-00468},
pmid = {41338553},
issn = {0578-1426},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis/therapy/drug therapy ; *Hematologic Diseases/complications ; Antifungal Agents/therapeutic use ; *Neoplasms/complications ; Hematologic Neoplasms/complications ; *Mycoses/diagnosis/therapy ; China ; },
abstract = {In 2005, the Chinese Invasive Fungal Infection Working Group published the first guidelines for the diagnosis and treatment of invasive fungal disease (IFD) in patients with hematological disorders and cancers, with the sixth revision released in 2020. Numerous advances in the fields of hematological oncology treatment and the diagnosis and management of IFD have significantly influenced the corresponding strategies. Therefore, the Chinese Invasive Fungal Infection Working Group has reviewed key research advances from 2020 to 2024 and released the seventh revision of the Chinese guidelines. Major revisions include: changes in the epidemiology of IFD; evaluation of novel diagnostic methods (especially PCR and metagenomic next-generation sequencing); updated recommendations on therapeutic drug monitoring and in vitro drug sensitivity test; management of breakthrough IFD; targeted therapy of Pneumocystis jiroveci pneumonia and cryptococcosis; and updated recommendation on the duration of antifungal therapy.},
}
@article {pmid41338123,
year = {2025},
author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y},
title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.},
journal = {Journal of psychiatric research},
volume = {193},
number = {},
pages = {223-235},
doi = {10.1016/j.jpsychires.2025.11.029},
pmid = {41338123},
issn = {1879-1379},
abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.},
}
@article {pmid41339745,
year = {2025},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}
@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09306-y},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}
@article {pmid41338426,
year = {2025},
author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y},
title = {Decoding Microbial-Mediated Sulfur Transformation Pathways in Mangrove Wetland: Metagenomic and Hydrogeochemical Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123472},
doi = {10.1016/j.envres.2025.123472},
pmid = {41338426},
issn = {1096-0953},
abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07%) and Salmonella prevailing in mudflat sediments (23.87-60.98%). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.},
}
@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}
@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation &amp; purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}
@article {pmid41335476,
year = {2025},
author = {Docter, J and Mansfeldt, C},
title = {Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00618},
pmid = {41335476},
issn = {2161-5063},
abstract = {Engineered microorganisms in biotechnology present biosafety and environmental management challenges. As the synthetic biology market develops and deploys new technologies, these engineered organisms may escape into unintended environments. Improved predictive computational tools are necessary to assess the potential establishment risk and environmental location of these escaped engineered microorganisms, assisting their design and management. Here, we present EnCen, a risk assessment Python software package that predicts the environmental range of engineered microorganisms through annotated functional one-hot-encoded similarity between the engineered microorganism and resident microorganisms of a given environment. EnCen utilizes publicly available composite metagenomes as representatives of microbial environments that occur along an agriculture-water cycle and can be customized for any additional target environment. This tool was deployed against case studies reported in the literature and to reassess commercially available bacterial biopesticides, highlighting both the successful recapture of previously reported dynamics and the identification of select commercial products that pose a wider establishment risk in multiple environments. When further utilizing EnCen to investigate the receiving environments comprising the central database, key enzyme classes are mapped as characteristics to select environments, prioritizing certain modifications likely leading to a greater risk (or effectiveness) of establishment. The results demonstrate that EnCen meaningfully summarizes publicly available metagenomic data, prioritizes environments to monitor for adverse effects, and analyzes potential impacts on microbial community composition and functioning. Overall, this study demonstrates a computational approach to managing engineered microorganisms, aiding in the safe deployment and benefit of industrial synthetic biology.},
}
@article {pmid41335362,
year = {2025},
author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Wang, H and Huang, Y and Liu, Y and Chen, P and Peng, J},
title = {Astragalin attenuates caerulein-induced acute pancreatitis by targeting the NLRP3 signaling pathway and gut microbiota.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {139},
pmid = {41335362},
issn = {2197-4365},
support = {82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 2025JJ60669//Hunan Provincial Natural Science Foundation of China/ ; 2024M763719//China Postdoctoral Science Foundation/ ; GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) has caused great concern worldwide due to its serious threat to human health. Astragalin is a bioactive natural flavonoid compound with several pharmacological activities, but it remains unclear about its effect on AP. The objective of this experiment was to explore the mitigating efficacy of astragalin on caerulein-induced AP model and examine the underlying mechanisms.<br><br>METHODS: Following the assessment of astragalin's direct effects on pancreatic acinar cells using an in vitro AP model, an in vivo mouse model was established to further validate its efficacy and elucidate the underlying mechanisms. Pancreatic histopathology, amylase, and lipase levels of mice were observed to determine the optimal therapeutic dose of astragalin. The network pharmacology and RNA sequencing technology were used to reveal the possible targets and pathways. Subsequent molecular docking and western blot were conducted to validate the association between astragalin and key target molecules, as well as the NLRP3 signaling pathway. Combined with metagenomics and metabolomics analysis, the astragalin effective gut microbiota-metabolite-gene network was constructed. Moreover, fecal microbiota transplantation experiments were performed to clarify the importance of gut microbiota in astragalin-mediated alleviation of AP.<br><br>RESULTS: The results showed that astragalin attenuated caerulein-induced injury in AR42J cells in vitro. Consistent with these findings, in vivo experiments revealed that astragalin treatment significantly improved pancreatic pathological injury, cell apoptosis, and systemic inflammatory response in AP mice, particularly at high doses. The integrated analysis of network pharmacology and transcriptomics revealed that the NLRP3 signaling pathway was a key molecular pathway, which was further validated using western blot. Docking analysis showed that 12 target genes had good docking activity with astragalin. More intriguingly, it was found that astragalin could reverse gut microbiota dysbiosis by restoring microbial diversity, altering bacterial community composition, and modulating key metabolic pathways. Specifically, astragalin-effective correlation networks were constructed with Lachnoclostridium sp. YL32, Roseburia intestinalis, Ruminococcus gnavus, Lachnospiraceae bacterium Choco86, Anaerobutyricum hallii, etc. as the core strains, 22 metabolites, including 5-Methoxytryptophan, D-Serine, L-Tryptophan, L-Methionine, etc. as core metabolites, and NLRP3 pathway-related genes as the main regulatory targets. Furthermore, fecal microbiota transplantation experiments confirmed the involvement of gut microbiota in AP remission.<br><br>CONCLUSION: Collectively, these findings identify astragalin as a promising therapeutic agent for AP, targeting both the NLRP3 signaling cascade and gut microbial homeostasis.},
}
@article {pmid41334926,
year = {2025},
author = {Shulman, HB and Pyle, JAM and Classen, AT and Inouye, DW and Simberloff, R and Sorensen, PO and Thomas, W and Rudgers, JA and Kivlin, SN},
title = {Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0052325},
doi = {10.1128/msystems.00523-25},
pmid = {41334926},
issn = {2379-5077},
abstract = {In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO4[3-]). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO4[3-] from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO4[3-] and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO4[3][-]. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.},
}
@article {pmid41334911,
year = {2025},
author = {Kandathil, AJ and Clipman, SJ and Anantharam, R and Duchen, D and Cox, AL and Larman, HB and Thomas, DL},
title = {Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0161225},
doi = {10.1128/jvi.01612-25},
pmid = {41334911},
issn = {1098-5514},
abstract = {Infections with viruses belonging to the family Anelloviridae are widespread among humans. Although generally considered a commensal, there is evidence to suggest that these infections may be controlled by host immune responses. However, the mechanism of immune control remains unclear. Previous research has also suggested a possible role of anellovirus capsid spikes in immune evasion. To investigate the role of antibodies in controlling infection, we used AnelloScan to profile plasma collected every 6 months over 2 years from 10 persons who inject drugs (PWID). Participants were selected based on viremia patterns: persistent (n = 6) versus intermittent (n = 4). Long-read metagenomic sequencing revealed a higher median number of alphatorquevirus (TTV) species in participants with persistent viremia compared to those with intermittent viremia (P < 0.0001). AnelloScan detected TTV-specific antibodies among all study participants. No significant differences were observed between the two groups when all antibody-reactive peptides located in the capsid were included. However, among participants with intermittent viremia, antibodies were more frequently reactive to peptides located in the amino acid variable region of the capsid spike domain (P = 0.0429). These findings suggest that among PWID, antibodies targeting the sequence variable region of the spike domain appear to be associated with control of anellovirus infection. Additionally, anelloviruses might be susceptible to pre-existing immunity, and the amino acid variable region of the spike protein may play a role in viral infectivity.IMPORTANCEAnelloviruses are highly diverse and are recognized as the major component of the blood virome in healthy humans. Despite this, little is known about their interactions with their hosts. In this study, we found that anelloviruses can elicit antibody responses. Notably, antibodies that targeted a sequence variable region on spikes present on viral capsids were associated with truncation of plasma viremia. These data suggest a possible mechanism of immune control of anellovirus infections while also indicating a role of the capsid spikes in viral infectivity.},
}
@article {pmid41334589,
year = {2025},
author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H},
title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593119},
doi = {10.1080/19490976.2025.2593119},
pmid = {41334589},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.},
}
@article {pmid41334206,
year = {2025},
author = {Yang, L and Liu, Y and Guo, S and Li, T and Nie, Q and Zhang, Y and Zeng, S and Wang, F and Liu, L},
title = {Mechanism of tobacco-sweet potato intercropping in suppressing Ralstonia solanacearum in flue-cured tobacco.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1688379},
pmid = {41334206},
issn = {1664-462X},
abstract = {Tobacco bacterial wilt (Ralstonia solanacearum) is a fatal pathogen of tobacco, causing severe losses annually. Intercropping has been proposed as a sustainable strategy to mitigate soil-borne pathogens through rhizosphere interactions. However, the mechanisms by which tobacco-sweet potato intercropping specifically affects the microecological environment and suppresses R. solanacearum remain poorly understood. To investigate the effect of the TSP model on the soil-borne pathogen of bacterial wilt (Ralstonia solanacearum) in tobacco-growing soil, this study compared and analyzed the characteristics and differences in bacterial wilt incidence, Ralstonia solanacearum content, phenolic acid components, metabolome, and metagenome between (T) and (TSP) systems. The results showed that compared to the T treatment, the TSP treatment reduced the incidence of bacterial wilt in flue-cured tobacco and significantly decreased the abundance of R. solanacearum in the soil by 21.4%, while increasing the total phenolic acid content by 21.9%. The total phenolic content in the TSP soil was increased by 21.9% compared to T. Differentially abundant metabolites between TSP and T were primarily enriched in carbohydrate metabolic pathways, such as nucleotide sugar biosynthesis, fructose, and mannose metabolism. The content of substances such as rhamnose, D-allose, and mannitol in T-treated soil was 2.14-6.62 times higher than that in TSP-treated soil, with new tobacco alkaloids being up to 91.09 times higher. Compared to the T treatment, the TSP treatment significantly increased the relative abundances of Acidobacteriota, Chloroflexota, Bradyrhizobium, Pseudolabrys, and Sphingomonas by 64.08%, 18.86%, 23.55%, 21.80%, and 12.98%, respectively. The content of Ralstonia solanacearum in the soil was positively correlated with differential metabolites such as mannitol, rhamnose, and D-allose (r = 0.8), while negatively correlated with phenolic acids such as syringic acid, ferulic acid, caffeic acid, and gallic acid, as well as microorganisms such as Chloroflexota, Gemmatimonadota, Acidobacteriota, and Sphingomonas. In summary, TSP can regulate soil metabolites, phenolic acids, and beneficial microorganisms, forming a synergistic network to suppress the content of Ralstonia solanacearum and reduce the risk of tobacco bacterial wilt. This provides a theoretical basis for regulating soil microecology and enhancing crop disease resistance in intercropping systems.},
}
@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.<br><br>RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.<br><br>CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}
@article {pmid41333777,
year = {2025},
author = {Zhang, Q and Gong, Q and Sun, X and Zhu, H},
title = {Massive hemoptysis as the sentinel symptom: a case report of pulmonary nocardiosis in an immunocompetent patient.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1677156},
pmid = {41333777},
issn = {2296-858X},
abstract = {Pulmonary nocardiosis is frequently missed or misdiagnosed due to its atypical clinical symptoms and non-specific imaging findings. Moreover, delayed diagnosis and treatment can lead to high mortality rates, underscoring the need to enhance etiological diagnosis. Here, we report a 55-year-old immunocompetent woman who developed pulmonary Nocardia cyriacigeorgica infection with massive hemoptysis as the initial symptom. The patient had no history of chronic respiratory diseases. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid collected via bronchoscopy was performed, which confirmed the diagnosis. After targeted therapy with oral sulfamethoxazole-trimethoprim and linezolid, the patient achieved significant symptomatic and radiological improvement, accompanied by normalization of white blood cell count and neutrophil count. No recurrence was observed during follow-up.},
}
@article {pmid41333773,
year = {2025},
author = {Li, Q and Sun, X and Lei, W and Zhu, Y and Du, W and Jiang, X and Su, N},
title = {Psittacosis chlamydia pneumonia complicated with organizing pneumonia: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1670456},
pmid = {41333773},
issn = {2296-858X},
abstract = {BACKGROUND: Secondary organizing pneumonia (SOP) may develop following infections. Psittacosis, caused by Chlamydia psittaci (C. psittaci), is a zoonotic disease transmitted from birds to humans. It can present with a wide spectrum of symptoms, ranging from mild flu-like illness to life-threatening severe pneumonia. Cases of C. psittaci infection complicated by organizing pneumonia (OP) are rarely reported, and delayed treatment may pose a life-threatening risk.<br><br>METHODS: We report a case of C. psittaci pneumonia complicated by OP. To identify additional cases and clarify the clinical features of this condition, a literature search was conducted using the PubMed and Embase databases for the period from January 1995 to May 2025. The search included the following keywords: "psittacosis," "Chlamydia psittaci," "chlamydia," "organizing pneumonia," and "bronchiolitis obliterans with organizing pneumonia."<br><br>RESULTS: A 66-year-old male with a history of poultry farming presented with fever, cough, sputum production, and hemoptysis. Empirical antimicrobial therapy with ceftizoxime was ineffective. To identify the etiology of the pulmonary lesions, bronchoscopy was performed, and C. psittaci infection was confirmed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Although the lesions partially resolved after moxifloxacin therapy, the patient experienced recurrent episodes. Chest CT revealed migratory lesions, which are uncommon in C. psittaci pneumonia. Further pathological examination of the specimen confirmed the diagnosis of OP. The patient's condition improved following corticosteroid therapy. A review of the literature indicated that none of the three previously reported cases were definitively diagnosed at initial admission; all presented primarily with fever and cough. One case progressed to severe pneumonia and resulted in death.<br><br>CONCLUSION: OP caused by C. psittaci pneumonia presents with non-specific symptoms and signs, making early diagnosis challenging. During treatment of C. psittaci pneumonia, if empirical anti-infective therapy shows no response after three days, or if imaging reveals features such as consolidation, migratory lesions, or a reverse halo sign, the possibility of concurrent OP should be considered. Pathological examination is recommended in such cases to avoid missed diagnosis and to ensure timely intervention.},
}
@article {pmid41333054,
year = {2025},
author = {Kravchuk, OI and Finoshin, AD and Nikishina, YO and Melnikova, VI and Kublanov, IV and Sutormin, DA and Rusanova, AN and Ri, MT and Isaev, AB and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Anashkina, AA and Ignatyuk, VM and Gornostaev, NG and Voronezhskaya, EE and Sokolova, AM and Mikhailov, VS and Lyupina, YV},
title = {Evolutionary conservation of dopamine-mediated cellular plasticity in Arctic sponges (Porifera).},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1671771},
pmid = {41333054},
issn = {2296-889X},
abstract = {Dopamine is an evolutionarily ancient signaling molecule implicated in stress responses across the tree of life. The role of dopamine is well-documented in the nervous system of animals, yet in the early-branching animal lineage of sponges its utility is poorly understood. Arctic marine sponges inhabiting the tidal zone of the White Sea, with fluctuating seasonal ice cover and solute concentrations, exhibit remarkable physiological plasticity, making them ideal models for studying conserved stress-response mechanisms. We investigated the dopamine signaling in two sponge species, Sycon ciliatum (class Calcarea) and Halisarca dujardini (class Demospongiae), using metagenomics, transcriptomics, high performance liquid chromatography, mass spectrometry, molecular docking, and immunofluorescence. S. ciliatum expresses an aromatic amino acid decarboxylase-like enzyme and efficiently converts L-DOPA to dopamine, whereas H. dujardini lacks this canonical biosynthetic enzyme, but accumulates dopamine, likely via its symbionts. During morphogenetic transitions in H. dujardini, genes involved in dopamine turnover, including tyrosinase, dopamine β-hydroxylase, and G protein-coupled receptors (GPCRs), showed dynamic expression. Molecular docking revealed that GPCR affinity for dopamine is modulated by cellular redox status. Notably, we report the first evidence of post-translational dopaminylation of cytoskeleton proteins in a non-bilaterian animal. Fluctuations in cellular dopamine levels and actin dopaminylation correlated with structural remodeling of the aquiferous system throughout the sponge life cycle. These findings demonstrate that dopamine regulates cellular plasticity through both transcriptional and post-translational mechanisms. The discovery of dopaminylation in sponges expands the evolutionary scope of catecholamine signaling and underscores the ancient role of dopamine in the regulatory interactions of animal cells.},
}
@article {pmid41332906,
year = {2025},
author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X},
title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.},
journal = {Biochemistry and biophysics reports},
volume = {44},
number = {},
pages = {102361},
pmid = {41332906},
issn = {2405-5808},
abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.<br><br>OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.<br><br>METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.<br><br>RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375&#x202f;&#xb1;&#x202f;1.302 and 46&#x202f;&#xb1;&#x202f;9.75 respectively) vs healthy controls (3.425&#x202f;&#xb1;&#x202f;1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p&#x202f;<&#x202f;0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P&#x202f;<&#x202f;0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P&#x202f;<&#x202f;0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P&#x202f;<&#x202f;0.05).<br><br>CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.},
}
@article {pmid41332561,
year = {2025},
author = {Ahmed, MA and John, J and Campbell, BJ},
title = {Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689735},
pmid = {41332561},
issn = {2692-8205},
abstract = {Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems.},
}
@article {pmid41332430,
year = {2025},
author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML},
title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593076},
doi = {10.1080/19490976.2025.2593076},
pmid = {41332430},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; },
abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.},
}
@article {pmid41331875,
year = {2025},
author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S},
title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02290-9},
pmid = {41331875},
issn = {2049-2618},
support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.<br><br>RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20&#xa0;&#xb5;M pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.<br><br>CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.},
}
@article {pmid41331807,
year = {2025},
author = {Rouzban, T and Goudarzi, R and Motamedi, E and Ghollasi, M and Zeinalabedini, M and Ariaeenejad, S},
title = {Metagenomic laccase-catalyzed crosslinking of wheat proteins for enhanced soybean meal nutritional value: applications in poultry feed and food industry.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01081-2},
pmid = {41331807},
issn = {1472-6750},
support = {0//Agricultural Biotechnology Research Institute of Iran (ABRII)/ ; },
}
@article {pmid41331687,
year = {2025},
author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H},
title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.},
journal = {Genomics &amp; informatics},
volume = {23},
number = {1},
pages = {25},
pmid = {41331687},
issn = {1598-866X},
abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.<br><br>RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.<br><br>CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.},
}
@article {pmid41331561,
year = {2025},
author = {Tian, J and Wang, X and Zhu, Y and Kong, F and Sun, J},
title = {Diagnosis of esophageal pleural fistula via metagenomic next-generation sequencing of pleural effusion: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1689},
pmid = {41331561},
issn = {1471-2334},
}
@article {pmid41331462,
year = {2025},
author = {Xu, W and Wang, W and Liu, Q},
title = {Identification of a novel pegivirus in reindeer (Rangifer tarandus valentinae) in Northeastern China.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05167-z},
pmid = {41331462},
issn = {1746-6148},
support = {2024YFD1800103//This study was financially supported by the National Key Research and Development Program of China ./ ; },
abstract = {BACKGROUND: Pegiviruses (family Flaviviridae), associated with persistent infections in diverse mammalian and avian hosts, are increasingly recognized for their evolutionary significance. Reindeer (Rangifer tarandus valentinae), semi-domesticated in northeastern China's Greater Khingan Mountains, are critical reservoirs for zoonotic pathogens and face growing human contact due to tourism. This study aims to investigate the viral diversity in reindeer, identify potential viruses of public health or veterinary significance, and highlight the need for viral surveillance at the human-animal interface.<br><br>RESULTS: The metagenomic sequencing analysis identified a novel pegivirus, Rangifer tarandus pegivirus (RPgV), in reindeer serum from Inner Mongolia. The near-complete genome (10,367 nucleotides; GenBank OQ164633) encodes a polyprotein (3,249 amino acids) processed into four structural (Y, E1, E2, X) and six non-structural (NS2-NS5B) proteins. RPgV shares 57.3% nucleotide and 60.6% amino acid identity with its closest relative, equine pegivirus (EPgV), but exceeds species demarcation thresholds for NS3 (p-distance: 0.340) and NS5B (p-distance: 0.408). Phylogenetic analyses placed RPgV within the equine pegivirus clade, while cophylogenetic models revealed strong host specificity and co-divergence over evolutionary timescales. With a 9.5% prevalence (2/21) in sampled reindeer, RPgV represents the first pegivirus detected in Cervidae, underscoring its potential role in wildlife virome dynamics.<br><br>CONCLUSION: This study identified a novel pegivirus, which expands its host range, geographic distribution, and genetic diversity. This discovery highlights the need for enhanced surveillance of understudied viral families in regions where human-wildlife interfaces amplify zoonotic risks.},
}
@article {pmid41331251,
year = {2025},
author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z},
title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66596-w},
pmid = {41331251},
issn = {2041-1723},
support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.},
}
@article {pmid41333904,
year = {2024},
author = {Choi, CH and Lee, M and Lee, SE and Shin, H and Choi, MM and Kim, JW and Yi, H and Chung, YS},
title = {[Monkeypox Virus Genomic Analysis in the Republic of Korea: A Comparison of Metagenomic- and Probe Hybridization Capture Sequencing Methods].},
journal = {Jugan geon-gang gwa jilbyeong},
volume = {17},
number = {20},
pages = {859-873},
pmid = {41333904},
issn = {2586-0860},
abstract = {Monkeypox virus (MPXV) whole-genome from specimens of individuals diagnosed with mpox in the Republic of Korea (ROK) between May 2022 and November 2023 was analyzed comprehensively. An infectious disease originating in Africa, mpox gained global significance after the first case was confirmed in the UK in May 2022, subsequently spreading worldwide. In the ROK, 155 infection cases were recorded, predominantly transmitted through close contact with symptomatic individuals. MPXV, consisting of approximately 197,000 base pairs of double-stranded DNA, encompasses approximately 191 genes consisting of inverted terminal repeats at both ends and a central conserved region. The virus is categorized as Clade I (Central African type) and Clade II (West African type), with Clade I and II reporting fatality rates of 1-10% and less than 1%, respectively. Two sequencing methods, metagenomic and hybridization capture sequencing, were used to perform a thorough whole-genome analysis. Compared to metagenomic sequencing, hybridization capture sequencing demonstrated superior efficiency in generating MPXV read sequences. The proportion of virus reads varied based on specimen type, informing the selection of targets for whole-genome analysis. Genomic phylogenetic analysis revealed that the MPXV in the ROK belonged to lineage C.1, indicating sustained domestic transmission and providing crucial insights for national and international responses to MPXV variants. This information will contribute to understanding infection pathways and improving strategies for disease response and prevention.},
}
@article {pmid41330454,
year = {2025},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, J and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}
@article {pmid41330298,
year = {2025},
author = {Huang, Y and Li, R and Dai, Y and Ren, Z and Wu, J},
title = {Migration characteristics of ARGs from pig manure in compost - soil - lettuce.},
journal = {Ecotoxicology and environmental safety},
volume = {308},
number = {},
pages = {119447},
doi = {10.1016/j.ecoenv.2025.119447},
pmid = {41330298},
issn = {1090-2414},
abstract = {This study aims to reveal the contamination patterns, persistence characteristics, and fate dynamics of ARGs during aerobic composting of swine manure with different carbon-nitrogen ratios (C/N = 15:1, 25:1, 35:1) and their subsequent dissemination in soil-plant systems following fertilization. The absolute abundances of 101 ARGs of six categories ranged from 10[5] to 10[14] copies/g during the composting process. The tetracyclines, macrolides and β-lactams ARGs were effectively reduced by the maturation phase. Among them, the β-lactam ARGs had the highest abatement efficiency (73-89 %). Quinolones, aminoglycosides and sulfonamides ARGs had relatively high residues during the maturation phase. Composting treatments with higher C/N (25:1 and 35:1) exhibited superior performance in ARGs reduction. Metagenomic analysis revealed the compost microbial community succession from Firmicutes to Proteobacteria and Actinobacteria. Luteimonas may be potential hosts for high-residual ARGs in compost, while Acinetobacter exhibited strong associations with β-lactam and macrolide ARGs that can be easily reduced. The ARGs in the fertilized soil increased significantly. ARGs such as floR, tetG-01, sul1 and sul2 have the highest abundance in the soil where lettuce is grown. The ARGs reduction is better in C/N 25:1 group, and the ARGs abundance of the soil is lower after fertilization with compost products. The sulfonamide sul1 and sul2 genes have always maintained a high abundance in compost, soil and lettuce. This study provides a theoretical basis for controlling the residue and spread of ARGs by regulating the C/N of compost to drive changes in microbial community.},
}
@article {pmid41330199,
year = {2025},
author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ},
title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128411},
doi = {10.1016/j.micres.2025.128411},
pmid = {41330199},
issn = {1618-0623},
abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.},
}
@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}
@article {pmid41329990,
year = {2025},
author = {Choi, HI and Cha, JM},
title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.},
journal = {Clinical endoscopy},
volume = {},
number = {},
pages = {},
doi = {10.5946/ce.2025.246},
pmid = {41329990},
issn = {2234-2400},
abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.},
}
@article {pmid41328758,
year = {2026},
author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA},
title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70086},
doi = {10.1111/1755-0998.70086},
pmid = {41328758},
issn = {1755-0998},
support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; },
abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.},
}
@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
doi = {10.1080/19490976.2025.2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics/growth &amp; development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.<br><br>METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at&#x2009;<&#x2009;33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.<br><br>RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).<br><br>CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}
@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}
@article {pmid41328415,
year = {2025},
author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X},
title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72565},
pmid = {41328415},
issn = {2045-7758},
abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.},
}
@article {pmid41328248,
year = {2025},
author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN},
title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {3},
pages = {717-727},
pmid = {41328248},
issn = {2311-7710},
abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.<br><br>MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.<br><br>RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.<br><br>CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.},
}
@article {pmid41328030,
year = {2025},
author = {Hickman, B and Korpela, K},
title = {Impact of data compositionality on the detection of microbiota responses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590841},
doi = {10.1080/19490976.2025.2590841},
pmid = {41328030},
issn = {1949-0984},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; },
abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.},
}
@article {pmid41328016,
year = {2025},
author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O},
title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587968},
doi = {10.1080/19490976.2025.2587968},
pmid = {41328016},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; },
abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).},
}
@article {pmid41327872,
year = {2025},
author = {Zhang, Y and Zhang, Z and Chen, Z and Yang, B and Cai, S and Chen, J and Guo, J and Zhang, W},
title = {2-line Ferrihydrite Enhance Microbial Synthesis of Plant Biostimulants in Composted Biosolid by Regulating Phyla Pseudomonadota and Actinomycetota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e06502},
doi = {10.1002/advs.202506502},
pmid = {41327872},
issn = {2198-3844},
support = {U24A20193,52270141//The National Natural Science Foundation of China/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; 122-G1323522145//Fundamental Research Funds for the central Universities, China University of Geosciences/ ; },
abstract = {The discovery of plant biostimulants (PBs) in sewage sludge offers a promising avenue for biosolids valorization. Here, the study investigates how two mineral additives, including 2-line ferrihydrite (a disordered iron oxide) and disordered birnessite (a manganese oxide), modulate microbial activity and molecular pathways to enhance PB production during aerobic sludge composting. Application of 2-line ferrihydrite significantly promotes the synthesis of growth-promoting PBs, including arginine, valine, decanoic acid, and indoleacetic acid (IAA), while disordered birnessite primarily enhances resistance-related PBs, such as decanoic acid, L-pyroglutamate, and trans-aconitic acid. In pot trials, composted biosolids amended with 2-line ferrihydrite significantly improve plant biomass and leaf area compared to mineral-free and birnessite treatments. Metagenomic profiling reveals that PB biosynthesis is dominated by members of the phyla Pseudomonadota and Actinomycetota, with temporal niche partitioning across the thermophilic and maturation stages. 2-line ferrihydrite enhances the abundance of critical biosynthetic genes (e.g., trpA/C/D/E/F), particularly within taxa such as Xanthomonadaceae, Sphingomonadaceae, and Streptosporangiaceae. Additionally, genes involved in IAA and indole biosysnthesis (ALDH, DDC, and tnaA) are enriched, supporting enhanced tryptophan-to-IAA conversion. This study provides a mechanistic link between iron oxide-mediated microbial modulation and PB production in composted biosolids, offering a sustainable approach for upgrading waste into high-value agricultural inputs.},
}
@article {pmid41327491,
year = {2025},
author = {Wu, H and Sun, Z and Chen, B and Hu, X and Li, Y},
title = {Enhanced nitrogen load improved soil phosphorus availability by regulating P-cycling microbial genes in a typical subtropical estuary (Min River), Southeast China.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {151},
pmid = {41327491},
issn = {2524-6372},
support = {No. 42371105//the National Natural Science Foundation of China/ ; No. 2023J02012//the Key Program of Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND: Enhanced nitrogen (N) load was considered a critical factor influencing phosphorus (P) availability and P-cycling in marsh soils. However, information on the links between soil P availability and microbial genes involved in P-cycling processes under N enrichment conditions remains scarce.<br><br>METHODS: A field N load experiment with four treatments (N0, Nlow, Nmedium, and Nhigh) was conducted in Cyperus malaccensis marsh of the Min River estuary, and soil P availability, the relative abundances of P-cycling functional genes and their regulatory roles on P availability were investigated.<br><br>RESULTS: The total phosphorus (TP) contents in soils were significantly positively correlated with N load levels (p&#x2009;<&#x2009;0.05). Compared with the N0 treatment, the TP in the Nlow, Nmedium and Nhigh treatments increased by 8.97%, 17.34% and 15.21%, respectively. With increasing N load levels, the proportions of easily- and moderately-available P in TP contents noticeably increased, suggesting that N additions enhanced soil P availability. Metagenomic sequence analyses showed that N enrichment markedly altered the relative abundances of P-cycling functional genes. Briefly, the abundances of inorganic P solubilization genes (particularly ppa and ppx) increased substantially with increasing N load levels. The total abundances of organic P mineralization genes in the Nlow and Nmedium treatments decreased markedly, while those in the Nhigh treatment increased greatly. The abundances of genes coding for phytase (phy and appA) markedly increased with increasing N load levels, implying that phytase was more sensitive to N enrichment. Furthermore, enhanced N load noticeably reduced the abundances of genes participated in P transportation (particularly ugpABEC) and those involved in P-assimilating process (e.g., phoR, phoB, pstABCS and pit). As affected by enhanced N load, the contents of easily-available P showed strong correlations with the abundances of genes involved in inorganic P solubilization while those of moderately-available P (particularly Sonic-Pi, Sonic-Po and NaOH-Pi) were positively correlated with the abundances of genes involved in P regulation and transportation, indicating strong linkages between P-cycling functional genes and soil P availability.<br><br>CONCLUSIONS: This paper found that, under N enrichment conditions, the increased inorganic P solubilization potential and the weakened microbial P immobilization capacity were beneficial to increasing soil P availability.},
}
@article {pmid41327449,
year = {2025},
author = {Zhao, Y and Duanmu, X and Hu, Z and Fan, Y and Mao, R and Zhang, Y and Zhang, X},
title = {Temperature seasonality constrains soil T4-like bacteriophage abundance at large spatial scale.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00824-0},
pmid = {41327449},
issn = {2524-6372},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; },
abstract = {BACKGROUND: Viruses play key roles in regulating soil microbial dynamics and biogeochemical cycles. T4-like bacteriophages, one of the best-studied viral groups, are abundant in soils, but their biogeographical patterns and ecological drivers remain poorly understood. In this study, we performed the first large-scale assessment of soil T4-like bacteriophages based on metagenomic data using viral hallmark genes, revealing broad spatial structure, identifying dominant environmental factors, and projecting shifts under future climate scenarios.<br><br>RESULTS: We analyzed two viral hallmark genes, gene 20 (g20) and gene 23 (g23), retrieved from global soil metagenomes, and National Center for Biotechnology Information (NCBI) reference sequences, yielding 2,385 and 2,928 full-length sequences clustered into 1,211 and 1,269 operational taxonomic units (OTUs), respectively. Phylogenetic analysis revealed that only a small fraction of soil-derived sequences could be assigned to established viral families, with most remaining unclassified below the class Caudoviricetes. The relative abundances of g20 and g23 were assessed at 116 sites spanning 14 biomes across six continents. Consistent biogeographic patterns were observed for both genes, with higher relative abundance in tropical climates and lower levels in polar and dry regions, indicating strong climatic influence. Temperature seasonality (BIO4) was identified as the primary environmental driver, showing a significant negative correlation with the relative abundance of both genes. Using an extreme gradient boosting (XGBoost) model, we predicted global distribution patterns based on extrapolation, revealing concordant global trends, with lower relative abundances in regions with greater seasonal temperature variation. Future projections of BIO4 and viral gene abundance further supported this significant negative correlation.<br><br>CONCLUSIONS: Our findings reveal that temperature seasonality constrains the abundance of soil T4-like bacteriophages, which serve as sensitive indicators of climate-driven environmental shifts and play important ecological roles within soil microbial communities.},
}
@article {pmid41327428,
year = {2025},
author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I},
title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02238-z},
pmid = {41327428},
issn = {2049-2618},
support = {ISF 1947/19//Israel Science Foundation/ ; ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; },
abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.<br><br>RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy&#xa0;number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.<br><br>CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.},
}
@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02287-4},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&amp;D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.<br><br>RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.<br><br>CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}
@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02275-8},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.<br><br>RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.<br><br>CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}
@article {pmid41327286,
year = {2025},
author = {Xu, W and Top, J and Viveen, MC and Slyzkyi, A and Hermans, N and van Erp, S and Eiloz, D and Anthony, R and Kremer, K and Schürch, AC},
title = {Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-025-02272-8},
pmid = {41327286},
issn = {1755-8794},
support = {LSHM22031//Health~Holland/ ; },
abstract = {BACKGROUND: Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target data output. NAS promises up to 5-10 × enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS for profiling clinical sputum metagenomes.<br><br>METHODS: We sequenced DNA extracted from clinical sputa and spike-in controls of a mock community of bacterial respiratory pathogens, using the current R10.4.1 MinION flowcell chemistry.<br><br>RESULTS: We achieved at best 3.1&#x2009;&#xd7;&#x2009;enrichment of bacterial sequence output with NAS due to the shorter read lengths (~&#x2009;2.5&#xa0;kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors.<br><br>CONCLUSIONS: We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.},
}
@article {pmid41327021,
year = {2025},
author = {Chen, B and Shu, W and Le, J and Jin, D},
title = {Application of metagenomic next-generation sequencing technology in hematologic malignancy patients with sepsis following antibiotic use.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1678},
pmid = {41327021},
issn = {1471-2334},
}
@article {pmid41327018,
year = {2025},
author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D},
title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07781-3},
pmid = {41327018},
issn = {1471-2229},
support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; },
}
@article {pmid41326768,
year = {2025},
author = {Polizel, GHG and Cánovas, &#xc1; and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, &#xc9; and de Almeida Santana, MH},
title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {8},
pmid = {41326768},
issn = {1573-3890},
support = {23/09113-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 17/12105-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; },
abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.<br><br>OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.<br><br>METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).<br><br>RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.<br><br>CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.},
}
@article {pmid41326588,
year = {2025},
author = {Yadav, MK and Ranjan, R and Verma, P and Sharma, R},
title = {Discovery and characterization of an enantioselective family VIII esterase from effluent treatment plant sludge metagenome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29625-8},
pmid = {41326588},
issn = {2045-2322},
support = {BSC0124//Council of Scientific and Industrial Research (CSIR), India/ ; },
}
@article {pmid41326129,
year = {2026},
author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S},
title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106807},
doi = {10.1016/j.pestbp.2025.106807},
pmid = {41326129},
issn = {1095-9939},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; },
abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.},
}
@article {pmid41325946,
year = {2025},
author = {Yin, Z and Ma, J and Bian, R and Wang, Y and Zhang, K and Ma, Y and Zhang, X and Ye, L},
title = {Xenobiotic degradation promotes enrichment but not dissemination of antibiotic resistance genes in activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133748},
doi = {10.1016/j.biortech.2025.133748},
pmid = {41325946},
issn = {1873-2976},
abstract = {Activated sludge in wastewater treatment bioreactors plays a pivotal role in xenobiotic degradation but is also regarded as a hotspot for the dissemination of antibiotic resistance genes (ARGs). Yet, it remains unclear whether pollutant degradation itself also creates conditions that facilitate ARG spread. To address this, we developed a xenobiotic degradation gene (XDG) database covering 22 degradation pathways. Using this database, we analyzed over 30,000 complete bacterial genomes and identified widespread co-occurrence of ARGs and XDGs, particularly within Pseudomonadota and Campylobacterota. Metagenomic profiling of 119 activated sludge samples further revealed strong positive correlations (Pearson's r > 0.8) between XDG and intrinsic ARGs, especially, modules involved in aromatic ring cleavage showed the highest correlations with ARGs. However, only 30.9 % of ARG-HGT events were found in MAGs carrying XDGs, and genome-level proximity analysis indicated that such microorganisms did not exhibit higher horizontal transfer potential. Cultivation-based experiments revealed that Pseudomonas strains with high degradation capacity carried intrinsic but not mobile ARGs. Together, these results demonstrate that xenobiotic degradation promotes ARG enrichment primarily through shifts in community composition rather than by enhancing gene mobility, highlighting that environmental AMR risk assessments based solely on ARG abundance may be misleading, and should avoid misestimation in future research.},
}
@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf252},
pmid = {41324463},
issn = {1751-7370},
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}
@article {pmid41324436,
year = {2025},
author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G},
title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages and ecological strategies on local and regional scales.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf264},
pmid = {41324436},
issn = {1751-7370},
abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.},
}
@article {pmid41324077,
year = {2025},
author = {Mah, JK and Hogan, JI and Kothadia, S and Keenan, JE and Berger, J and Carugati, M},
title = {Application of plasma cell-free metagenomic next-generation sequencing for the identification of Aspergillus fumigatus donor-derived infections among solid organ transplant recipients.},
journal = {Medical mycology case reports},
volume = {50},
number = {},
pages = {100751},
pmid = {41324077},
issn = {2211-7539},
abstract = {A cluster of Aspergillus fumigatus donor-derived infections (DDI) was rapidly diagnosed using plasma metagenomic next-generation sequencing (mNGS) among solid organ transplant recipients. The heart recipient, experiencing marginal hemodynamics, underwent an endomyocardial biopsy, which was concerning for a fungal infection on histopathology. Plasma mNGS was performed, identifying A. fumigatus two days prior to conventional diagnostics. This timely diagnosis enabled prompt nephrectomies in the kidney recipients, who survived. This report represents the first published use of mNGS in the diagnosis of Aspergillus fumigatus DDI, highlighting the utility of this novel, underutilized assay for early diagnosis of donor-derived infections.},
}
@article {pmid41323881,
year = {2025},
author = {Aini, N and Wahyuningsih, SPA and Achhlam, DH and Fatimah, and Amin, MHF and Do, HDK},
title = {Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo-Strain Probiotics in African Catfish (Clarias gariepinus) Challenged With Aeromonas hydrophila.},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {6624613},
pmid = {41323881},
issn = {1365-2095},
abstract = {This study aimed to determine the effect of dual-strains probiotic (DSP) consisting of Lactobacillus casei and Bacillus subtilis on bacterial metagenomic profile, gut physiology, and digestive enzyme levels of African catfish (Clarias gariepinus) infected by Aeromonas hydrophila. The ratio between L. casei and B. subtilis was 1:1 each with a density of 10[8] CFU/mL. Catfish (n = 8 fish per tank, three replicates per treatment) were fed diets supplemented with 0%, 5%, 10%, or 15% DSP for 42 days. On the 35th day, selected groups were intraperitoneally challenged with A. hydrophila at a dose of 0.1 mL × 10[8] CFU/mL. The observed parameters included bacterial counts and microbial profile in the gastrointestinal tract (analyzed using next-generation sequencing [NGS]), gut physiology, and digestive enzyme levels (amylase, lipase, and protease). The results showed that DSP supplementation increased both the abundance and diversity of gastrointestinal microbes, elevated digestive enzyme levels, and enhanced the number of goblet cells in the intestinal lining. The dominant microbial phyla observed in the control group were Fusobacteria and Pseudomonadota.},
}
@article {pmid41323829,
year = {2025},
author = {Luo, A and Liu, L and Shi, S and Liu, X and Hu, B},
title = {Analysis of Microbial Community Structure and Functional Genes for Volatile Flavor in Stinky Tofu.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {12},
pages = {e71257},
pmid = {41323829},
issn = {2048-7177},
abstract = {The distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high-quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy-annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α-acetolactate synthase genes) and 3-methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short-chain fatty acid production via α-keto acid dehydrogenase complexes (55 genes). A total of 410,231 non-redundant genes were identified, annotated to 4690 microbial species, establishing a multi-layered microbial-gene-metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.},
}
@article {pmid41323686,
year = {2025},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Multiomics analysis of microbial succession and flavor formation mechanism during the fermentation process of Maotai-flavour Baijiu.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103236},
pmid = {41323686},
issn = {2590-1575},
abstract = {This study employed metagenomics and metabolomics techniques to investigate the complex relationship between microbial succession and the formation of flavor compounds during the fermentation process of Maotai-flavour Baijiu. Results demonstrated that stacking fermentation, characterized by Weissella, Pichia, and Aspergillus, which secreted amylases and proteases to hydrolyze starch and proteins. Pitting fermentation facilitated the enrichment of anaerobic microbes such as Acetilactobacillus and Pichia, significantly promoting the synthesis of key flavor compounds, including esters, alcohols, and acids, through Glycosyltransferase and Esterification activities. Volatile compound analysis revealed distinct stage-specific profiles, with acids, alcohols, and esters accumulating predominantly in pitting fermentation. These findings elucidate the stage-specific microbial metabolic networks and synergistic mechanisms underlying flavor formation, providing a scientific basis for optimizing traditional Baijiu fermentation processes.},
}
@article {pmid41323679,
year = {2025},
author = {He, Y and Qiao, M and Zhang, H and Xiao, D and Guo, X},
title = {Microbial community, metabolic, and flavor differences among high-temperature Daqu with varying Douchi aroma intensities: a comprehensive metagenomic and metabolomic analysis.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103265},
pmid = {41323679},
issn = {2590-1575},
abstract = {The Douchi aroma is widely regarded as a key quality marker of high-quality high-temperature Daqu, but the compounds related to Douchi aroma formation and the key aroma-producing microorganisms remain unclear, which this study seeks to clarify. Therefore, metagenomic and metabolomic approaches were employed to decode the characteristic compounds and core microbial contributors in high-temperature Daqu samples no (NF), light (LF), and strong (SF) Douchi aroma. Esters were the most abundant volatiles across all groups, while acids increased with aroma intensity. Lentibacillus daqui, enriched in SF, showed strong positive correlations with isocetic, phenylacetic, and nonanoic acids. In contrast, Lichtheimia ramosa and Monascus purpureus were dominant in NF and LF, respectively. Furthermore, functional prediction and KEGG analysis further revealed potential biosynthetic pathways for phenylacetic and acetic acid. These findings clarify the molecular and microbial basis of Douchi aroma formation and provide a scientific reference for targeted quality regulation in Daqu production.},
}
@article {pmid41322275,
year = {2025},
author = {Dong, R and Liu, Y and Wang, N and Tan, KKY and Ji, M},
title = {The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.},
journal = {Marine life science &amp; technology},
volume = {7},
number = {4},
pages = {978-988},
pmid = {41322275},
issn = {2662-1746},
abstract = {UNLABELLED: Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00323-8.},
}
@article {pmid41322254,
year = {2025},
author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q},
title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.},
journal = {Marine life science &amp; technology},
volume = {7},
number = {4},
pages = {670-681},
pmid = {41322254},
issn = {2662-1746},
abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.},
}
@article {pmid41322233,
year = {2025},
author = {Chen, X and Yu, X and Deng, J and Yang, J and Chen, P},
title = {Case Report: Blood and cerebrospinal fluid mNGS-assisted diagnosis Toxoplasma gondii infection-associated with hemophagocytic syndrome and systemic lupus erythematosus.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1674391},
pmid = {41322233},
issn = {2296-858X},
abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more prevalent than primary infection in patients with autoimmune diseases. We present a rare case of systemic lupus erythematosus (SLE) and hemophagocytic syndrome (HPS) associated with T. gondii infection.<br><br>CASE PRESENTATION: We describe the case of a young girl with SLE and HPS who presented with fever, dyspnea, and pancytopenia. The patient's T. gondii infection was diagnosed through the detection of double-positive IgM and IgG antibodies. Metagenomic next-generation sequencing (mNGS) analysis of both plasma and cerebrospinal fluid (CSF) samples revealed a high concentration of T. gondii DNA. The patient demonstrated a positive response to a combined treatment regimen consisting of anti-Toxoplasma medications and glucocorticoids.<br><br>CONCLUSIONS: Co-infection with uncommon pathogens is not uncommon in patients with autoimmune diseases. In individuals with immune disorders and positive T. gondii IgM antibodies, mNGS analysis of peripheral blood samples proves valuable in diagnosing disseminated T. gondii infection.},
}
@article {pmid41322208,
year = {2025},
author = {Duan, J and Li, X and Hu, Y and Pang, F and Cao, Y and You, Z},
title = {Case Report: Next-generation metagenomic sequencing in the diagnosis of Brucella-associated joint infections-a case series analysis and comprehensive literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1688037},
pmid = {41322208},
issn = {2296-858X},
abstract = {BACKGROUND: The application of next-generation metagenomic sequencing (mNGS) in the diagnosis of human brucellosis, particularly in cases of joint brucellosis infection, remains under-explored, with rarely no case reports available in the literature. We present the first case series focusing on the application of mNGS in the diagnosis of Brucella joint infections. The results indicate that mNGS plays a crucial role in diagnosing Brucella joint infections, serving as a valuable complement, particularly for culture-negative patients.<br><br>CASE PRESENTATION: This study presents a comprehensive analysis of four cases of human joint brucellosis diagnosed using mNGS on the BGI sequencing platform, involving three male and one female patients aged from 42 to 63&#x202f;years, all of whom had documented epidemiological exposure histories. mNGS successfully identified Brucella sequences in all cases, with additional diagnostic findings including a positive Brucella agglutination test in Patient 1, positive joint fluid cultures in Patients 3 and 4, and no positive results in Patient 2. Following surgery and targeted antibiotic therapy, all patients exhibited clinical improvement and favorable follow-up outcomes.<br><br>CONCLUSION: These findings underscore the utility of mNGS as a critical diagnostic tool for joint brucellosis infections and highlight its potential as a complementary approach in cases of culture-negative joint infections. In cases where clinical suspicion of joint infection persists despite the absence of identifiable etiological evidence, the implementation of mNGS is strongly advised to facilitate timely and accurate clinical decision-making.},
}
@article {pmid41321514,
year = {2025},
author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z},
title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {396-414},
pmid = {41321514},
issn = {2405-6383},
abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.},
}
@article {pmid41321463,
year = {2025},
author = {Wang, W and Jiang, X and Wu, W and Zhang, L},
title = {Case Report: Primary segmental volvulus in an infant.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1707716},
pmid = {41321463},
issn = {2296-2360},
abstract = {Primary segmental volvulus (PSV) is a rare cause of acute abdomen in infants. It is characterized by a form of strangulated intestinal obstruction requiring prompt diagnosis and surgical intervention. This study aimed to report a case of PSV in an infant, which was managed successfully through early recognition, close clinical monitoring, and timely surgical treatment. Although both blood and ascitic fluid cultures were negative postoperatively, metagenomic next-generation sequencing (mNGS) identified the same pathogen in both specimens, enabling targeted antibiotic therapy. This case highlights the importance of including PSV in the differential diagnosis of infants presenting with unexplained abdominal distension and bilious vomiting, particularly when accompanied by anemia. Additionally, the elevated level of the coagulation system biomarker thrombin-antithrombin complex (TAT) may serve as a useful marker for monitoring coagulation status in the perioperative period. The integration of TAT assessment and mNGS-based pathogen identification provides a novel framework for individualized perioperative management in PSV.},
}
@article {pmid41321415,
year = {2025},
author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D},
title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf199},
pmid = {41321415},
issn = {2730-6151},
abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.},
}
@article {pmid41320762,
year = {2025},
author = {Peng, S and Liu, Z and Song, Z and Wang, C and Yu, Z and Zhao, N and Lu, W and Ning, Z and Lyu, A},
title = {Vinegar-processed frankincense extracts alleviate colorectal cancer by butyric acid mediating M1 tumor-associated macrophage pyroptosis.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {208},
pmid = {41320762},
issn = {1749-8546},
support = {CI2021A04201//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 82003950//the National Natural Science Foundation Committee of China/ ; YZX-202334//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ14-YQ-035//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
abstract = {BACKGROUND: Olibanum (RF), a traditional Chinese medicinal resin, shows efficacy in colorectal cancer (CRC) treatment. Its vinegar-processed form (PF) is clinically recognized for enhanced therapeutic effects, with prior mechanistic studies focusing on lipophilic components like boswellic acids. Yet, the regulatory mechanisms of PF's aqueous extracts remain unclear.<br><br>METHODS: The aqueous extracts of RF and PF were characterized and compared through transmission electron microscopy (TEM), nanoparticle analysis, and protein profiling. The accumulation of these fractions in feces was confirmed using DiR dye labeling. A mouse CRC model was employed to evaluate and compare the therapeutic effects of RF and PF. The composition of butyric acid-producing microbiota was analyzed using 16S rRNA gene sequencing and metagenomics. Butyric acid levels were quantified using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-TQ-MS). Macrophage phenotypes were assessed via flow cytometry, while mRNA and protein expression levels were determined through RT-qPCR and western blot analysis.<br><br>RESULTS: PF aqueous extracts exhibited distinct morphology, particle size, and protein content and had a superior therapeutic effect in alleviating CRC compared to RF. Further analysis confirmed that both RF and PF accumulated in feces and modulated the butyric acid metabolism of gut microbiota. The increased levels of butyric acid contributed to CRC alleviation by promoting the polarization of M1 tumor-associated macrophages (TAMs) and suppressing the pyroptosis of M1 TAMs.<br><br>CONCLUSION: The study confirmed that vinegar-processed frankincense enhances its therapeutic effect on CRC by modulating M1 tumor-associated macrophages, which may provide efficient treatment of CRC from the perspective of host-gut metabolic interactions.},
}
@article {pmid41320324,
year = {2025},
author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P},
title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335627},
pmid = {41320324},
issn = {1468-3288},
abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.<br><br>OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.<br><br>DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.<br><br>RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.<br><br>CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.},
}
@article {pmid41319631,
year = {2025},
author = {Wang, J and Tian, Y and Zhang, G and Li, Y and Chen, L},
title = {Metagenomic insights into nitrogen and phosphorus metabolisms of bacteria in lakes with distinct nutrient conditions.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128121},
doi = {10.1016/j.jenvman.2025.128121},
pmid = {41319631},
issn = {1095-8630},
abstract = {Nitrogen (N) and phosphorus (P) cycling are crucial for preserving ecosystem functioning in lakes, yet our comprehension of the dynamics of N/P cycling genes and microorganisms under diverse nutrient levels is still limited. Herein, we conducted a comprehensive investigation into the profiles of N/P cycling genes and bacteria across three lakes with distinct nutrient levels. We found that N and P cycling genes were most abundant in the high-nutrient lake, particularly those involved in ammonification, assimilatory nitrate reduction, P regulation, and P transportation. Bacteria responsible for mediating most N/P cycling processes (excluding nitrogen fixation and P regulation) were predominant in the high-nutrient lake and mainly affiliated with Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidota. Furthermore, a potential biogeochemical hotspot for the co-metabolism of N and P was identified in the high-nutrient lake, consolidated by the most intricate co-occurrence pattern between N and P cycling genes. More importantly, these versatile bacteria capable of N/P metabolisms, primarily influenced by total nitrogen, total phosphorus, Secchi depth, and total dissolved solids, played important roles in maintaining the stability of bacterial communities in lakes. These findings offer significant insights into microbial-mediated N and P biogeochemical cycling in lakes with varying nutrient conditions, improving our understanding of utilizing N/P co-metabolism microbes to regulate ecosystem function and service amid the challenges of global lake eutrophication.},
}
@article {pmid41319542,
year = {2025},
author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W},
title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147314},
doi = {10.1016/j.foodchem.2025.147314},
pmid = {41319542},
issn = {1873-7072},
abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.},
}
@article {pmid41319383,
year = {2025},
author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L},
title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.},
journal = {Water research},
volume = {290},
number = {},
pages = {125031},
doi = {10.1016/j.watres.2025.125031},
pmid = {41319383},
issn = {1879-2448},
abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.},
}
@article {pmid41318814,
year = {2025},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41318814},
issn = {1532-1827},
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.<br><br>METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.<br><br>RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P&#x2009;<&#x2009;0.001) and overall survival (OS) (3.9 vs. 9.5 months; P&#x2009;<&#x2009;0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.<br><br>CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.<br><br>TRIAL REGISTRATION: NCT03874897.},
}
@article {pmid41318497,
year = {2025},
author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X},
title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07423-0},
pmid = {41318497},
issn = {1479-5876},
support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; },
}
@article {pmid41317994,
year = {2025},
author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM},
title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101129},
doi = {10.1016/j.ajcnut.2025.101129},
pmid = {41317994},
issn = {1938-3207},
abstract = {BACKGROUND: BMD explains fractures incompletely; studies relating lifestyle to bone quality are lacking.<br><br>OBJECTIVES: To examine associations of diet quality with bone measures (BMSi, TBS, BMD); evaluate moderation by inflammation; identify gut microbiome features linked to diet quality; and quantify diet-microbiome-bone relationships.<br><br>METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored FFQ, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score.. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with MaAsLin regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).<br><br>RESULTS: DASH score was not associated with BMSi (&#x3b2; = -0.10; 95% CI: -0.46, 0.27; P = 0.60), TBS (&#x3b2; = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (&#x3b2; = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (&#x3b2; = 0.002; 95% CI: -0.003, 0.006, P = 0.52 but was at total hip (&#x3b2; = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (&#x3b2; = -0.0001, P = 0.89). Lachnospira eligens was one of 4 taxa positively associated with DASH score, and BMD. No microbial pathways were associated with the DASH score.<br><br>CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes, and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.},
}
@article {pmid41317922,
year = {2025},
author = {Yang, G and Zhen, Z and Zhang, K and Yin, J and Zhong, X and Li, X and Li, Q and Nie, K and Miao, X and Lin, Z and Zhang, D},
title = {Biochar accelerated soil atrazine degradation by promoting dechlorination pathway: A novel mechanism revealed by DNA stable isotope probing (DNA-SIP).},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133722},
doi = {10.1016/j.biortech.2025.133722},
pmid = {41317922},
issn = {1873-2976},
abstract = {Biochar can accelerate atrazine degradation in soils, with surface modification being a widely accepted method to improve the performance. Nevertheless, the underlying mechanisms remain unclear. This study explored the efficiency of modified biochar in facilitating soil atrazine biodegradation with the aid of DNA stable isotope probing (DNA-SIP) and metabolite profiling. DNA-SIP results confirmed the involvement of ten bacterial genera and six atrazine degradation-related genes in atrazine metabolism in situ. Among them, Candidatus Nitrososphaera, Pedosphaera and Conexibacter were reported to be associated with atrazine degradation for the first time. FeCl3-modified biochar significantly accelerated atrazine degradation (85%) by improving soil physicochemical properties (pH, soil organic matter and humus) and enriching the active atrazine degraders. Notably, atrazine dechlorination pathway was preferentially promoted by modified biochar. The findings suggested that DNA-SIP enabled the discovery of the active atrazine degraders and degradation-related genes in biochar-amended soils, providing novel insights into the mechanisms of biochar-facilitated atrazine removal.},
}
@article {pmid41317625,
year = {2025},
author = {Kharaillah, A and Zhong, M and Soriano, JD and Gambardella, N and Sanz-Sáez, I and Yan, D and Bertilsson, S and Björn, E and Bravo, AG and Capo, E},
title = {Low-oxygen freshwaters as ecological niches for mercury methylators.},
journal = {Water research},
volume = {290},
number = {},
pages = {125014},
doi = {10.1016/j.watres.2025.125014},
pmid = {41317625},
issn = {1879-2448},
abstract = {Methylmercury (MeHg) is a hazardous neurotoxin, predominantly formed by microbial transformation of inorganic mercury in oxygen-depleted aquatic and terrestrial ecosystems. The ongoing deoxygenation of aquatic ecosystems due to global warming is likely to expand microbial niches for MeHg production. Although mercury methylators have also been reported to thrive in oxyge-deficients conditions in a few marine and freshwater ecosystems, there is a lack of comprehensive understanding of how they are distributed in freshwater systems. In this study, we retrieved hgcA genes, genomic marker for mercury methylation potential, from 586 metagenomes from the water column of 186 freshwater systems. Overall, hgcA genes were detected in the water column of 30 lakes, with the highest richness and abundance being detected in anoxic (0 mg O2l[-1]) and hypoxic (>0-2 mg O2l[-1]) compared to oxic conditions (>2 mg O2l[-1]). Although Desulfobacterota had the highest hgcA gene richness across most freshwater systems, certain systems were dominated by hgcA genes from Bacteroidales and Kiritimatiellales, implying metabolic and ecological versatility of mercury methylators as a group. Our findings suggest that projected expanding deoxygenation may lead to new niches for mercury methylators in inland waters.},
}
@article {pmid41317490,
year = {2025},
author = {Qin, Y and Xie, X and Li, D and Wu, Z and Liu, J and Li, W and Tang, D and Chen, S and Zhang, Y and Liu, N and Zhang, Q and Chen, Y},
title = {NADH-driven bioreductive degradation of azo dyes: Mechanisms of high NADH production, electron transfer, and microbial responses.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {140559},
doi = {10.1016/j.jhazmat.2025.140559},
pmid = {41317490},
issn = {1873-3336},
abstract = {Bioreductive co-metabolic degradation of azo dyes represents a promising green technology for addressing the environmental pollution caused by azo dyes. This study investigated the impact of co-metabolized substances on NADH production in microbial systems, focusing on the production of reducing power, electron transfer, and the synergistic effects of microbial communities and associated mechanisms during azo dye degradation. A culture system was developed to maximize NADH production at 3 g/L yeast extract, and it was observed that the system exhibited a significant increase in reducing power, with NADH concentration reaching 909.48 pg/mL (60 h). The electron transfer process in this system primarily depended on factors such as redox mediators, azoreductase, and formic acid. Azo dye reductive degradation and decolorization occurred through an indirect electron transfer pathway. Flavin-based redox mediators (riboflavin and flavin mononucleotide) played a key role in the system, with the application of riboflavin and flavin mononucleotide increasing the system's dye reduction ratio by 14.45 % and 14.40 %, respectively. They were endogenously expressed by the system and facilitated efficient electron transfer by synergizing with specific reductases, particularly when the electron transport chain was inhibited, and alternative pathways ensured the continuation of the reduction reaction. NADH production primarily occurred through glycolysis, the TCA cycle, and fatty acid β-oxidation, with glycolysis contributing the most. Microorganisms such as Enterococcus, Burkholderia, and Escherichia within the microbial community played a crucial role in NADH production while regulating community behavior through a quorum sensing system, thereby enhancing the stability and efficiency of dye degradation. This study investigated the bioreduction of azo dyes in terms of reducing power, offering a theoretical foundation and practical guidance for optimizing the microbial system and enhancing the biodegradation efficiency of azo dyes.},
}
@article {pmid41317467,
year = {2025},
author = {Huang, S and Yu, X and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Unveiling the metabolic mechanism of pesticide in food fermentation through metagenomics and metabolomics: A case study of β-cypermethrin in Pixian broad-bean paste.},
journal = {Food chemistry},
volume = {498},
number = {Pt 2},
pages = {147299},
doi = {10.1016/j.foodchem.2025.147299},
pmid = {41317467},
issn = {1873-7072},
abstract = {Fermented foods contain less chemical pollutants, such as pesticide residues, than raw materials. In this study, using Pixian broad-bean paste as a model system, the pesticide degradation during food fermentation was comprehensively elucidated through metagenomic and metabolomics analyses. As a result, β-cypermethrin (β-CY) at 5 mg/kg was almost completely degraded, with a half-life of 6.1 d. β-CY caused flavor changes in fermented products, reducing esters and increasing ketones. Metagenomic analysis revealed that β-CY promoted bacteria phyla Bacteroidota, Pseudomonadota, and enriched the genes of xenobiotic degradation pathways, which is beneficial to its degradation. Microbial-metabolite correlation analysis identified Cyclobacteriaceae, Sulfurovaceae, FEN-1099 and Rhodocyclaceae as key drivers in the synthesis and metabolism of aromatic compounds following β-CY degradation during PBP fermentation. This dual mechanism offers a crucial theoretical foundation for understanding microbial community adaptability and β-CY detoxification in the process.},
}
@article {pmid41316964,
year = {2025},
author = {Puchol-Royo, R and Pascual, J and Ortega-Legarreta, A and Otto, P and Tideman, J and de Vries, SJ and Abendroth, C and Tanner, K and Porcar, M and Latorre-Perez, A},
title = {Metagenomic Insights Into the Ecology, Taxonomy and Metabolic Capabilities of 'Candidatus Darwinibacteriales' Ord. Nov. (Formerly MBA03), a Potential Key Player in Anaerobic Digestion.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70258},
doi = {10.1111/1751-7915.70258},
pmid = {41316964},
issn = {1751-7915},
support = {101000470//European Union's Horizon 2020/ ; },
mesh = {Anaerobiosis ; Phylogeny ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Metagenome ; Biofuels ; Sequence Analysis, DNA ; },
abstract = {Biogas, a mix of CO2, CH4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www.micro4biogas.eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota, was very prevalent and abundant in industrial full-scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as 'Candidatus Darwinibacteriales' ord. nov., which includes 'Candidatus Darwinibacter acetoxidans' gen. nov., sp. nov. of 'Candidatus Darwinibacteriaceae' fam. nov., along with 'Candidatus Wallacebacter cryptica' gen. nov., sp. nov. of the 'Candidatus Wallacebacteriaceae' fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of 'Candidatus Darwinibacteriales'. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate-oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present 'Candidatus Darwinibacteriales' as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.},
}
@article {pmid41316759,
year = {2025},
author = {Li, RX and Qiu, CS and Li, F and Xu, F and Liu, NN and Chen, X and Qi, L and Wang, CC and Wang, D and Wang, SP},
title = {[Effects of Thermal-alkaline and Thermal Hydrolysis Treatments on Antibiotic Resistance Genes in Sludge].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {11},
pages = {6940-6947},
doi = {10.13227/j.hjkx.202410028},
pmid = {41316759},
issn = {0250-3301},
mesh = {*Sewage/microbiology/chemistry ; Hydrolysis ; *Waste Disposal, Fluid/methods ; *Drug Resistance, Microbial/genetics ; Hot Temperature ; Wastewater/microbiology ; Genes, Bacterial ; },
abstract = {Sewage sludge from urban wastewater treatment plants is an important source of antibiotic resistance gene (ARGs) dissemination into various environmental media. In this study, two treatment methods were employed to treat sewage sludge: thermal-alkaline lysis (60-100℃, pH 10-12) and thermal hydrolysis (140-200℃, 60-120 min). Through metagenomic sequencing and quantitative polymerase chain reaction technology (qPCR), the effects of different treatment conditions on the physicochemical properties of sludge and the removal of ARGs were systematically investigated. In addition, the correlation between ARGs, intI1, and the physicochemical properties of sludge was analyzed in detail. The results indicated that both thermal-alkaline lysis and thermal hydrolysis treatments could break sludge cells, with thermal hydrolysis showing a more significant effect. Moreover, both treatment methods could effectively reduce the abundance of ARGs in sludge under certain conditions. Under thermal hydrolysis conditions at 200℃ for 120 mins, the absolute abundance of ARGs in sludge reached its lowest level of 4.08×10[6] copies·g[-1], and the absolute abundance of intI1 also achieved its minimum value of 1.83×10[6] copies·g[-1] under these conditions. Correlation analysis revealed a significant positive correlation (P < 0.05) between soluble polysaccharides and intI1 under thermal-alkaline lysis conditions. However, under thermal hydrolysis conditions, multiple ARGs and intI1 exhibited significant negative correlations (P < 0.05) with physicochemical indicators such as soluble chemical oxygen demand (SCOD), soluble proteins, and soluble polysaccharides. The removal of ARGs by these different treatment methods was mainly influenced by the treatment conditions and the degree of microbial cell disruption in the sludge.},
}
@article {pmid41316756,
year = {2025},
author = {Huang, W and Zhu, C and Yang, YJ and Zhang, HZ and Hu, SG and Wu, K and Cui, KP and Chen, YH},
title = {[Distribution Characteristics and Driving Mechanism of Antibiotic Resistance Genes in a Water Source in Hefei, China].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {11},
pages = {6906-6916},
doi = {10.13227/j.hjkx.202409265},
pmid = {41316756},
issn = {0250-3301},
mesh = {China ; *Drug Resistance, Microbial/genetics ; *Water Microbiology ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Water Supply ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Drinking Water/microbiology ; },
abstract = {One of the important water sources in Hefei serves as a crucial water supplier, playing a vital role in water provisioning. Its water quality is related to both drinking water safety and ecological water safety. To elucidate the distribution characteristics and influencing factors of antibiotic resistance genes (ARGs) within the water source, water, sediment, and soil samples were collected in July 2021 and December 2021. Metagenomic sequencing was employed to identify and characterize ARGs, mobile genetic elements (MGEs), and bacterial communities in the samples. The correlations between ARGs and physical-chemical properties, antibiotics, MGEs, and bacterial communities were also analyzed. Lastly, the factors were categorized into physical-chemical and biological factors, and their degrees of influence on ARGs were analyzed. The results showed that a total of 544 subtypes of ARGs were detected in the water source, which were classified into 26 major categories. Multidrug, bacitracin, β-lactam, and polymyxin resistance genes were the dominant types of ARGs in all three media, with the subtype bacA exhibiting the highest abundance across all. The numbers of certain classifications of ARGs tended to be higher in soil compared to those in sediment and water, and the abundance of ARGs in the soil was also significantly higher than that in the sediment. PCoA analysis showed significant differences in the structural composition of ARGs among the three media. Correlation analyses showed that TP, pH, LINs, and FQs in the water and SAs in the sediment were significantly correlated with ARGs. Additionally, strong correlations were observed between MGEs and bacterial communities and ARGs in the three media. The VPA results indicated that biological factors played a pivotal role in influencing ARGs in water, whereas physical-chemical factors exerted a stronger influence in soil. However, the synergistic effect of both physical-chemical and biological factors on ARGs in all three media was not negligible.},
}
@article {pmid41316726,
year = {2025},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1225},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}
@article {pmid41316344,
year = {2025},
author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J},
title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02257-w},
pmid = {41316344},
issn = {2049-2618},
support = {82171317//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.<br><br>RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation.&#xa0;Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects.&#xa0;In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.<br><br>CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.},
}
@article {pmid41316248,
year = {2025},
author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N},
title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07443-w},
pmid = {41316248},
issn = {1479-5876},
}
@article {pmid41316012,
year = {2025},
author = {Ye, X and Li, JA and Wang, S and Luan, S and Zheng, J and Lv, S and Zheng, G and Jiang, W and Huang, X and Xu, J and Zhu, L and Niu, B},
title = {Submandibular infection in a healthy child caused by Legionella maceachernii.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12203-8},
pmid = {41316012},
issn = {1471-2334},
}
@article {pmid41315949,
year = {2025},
author = {Chen, Y and Hu, Y and Liang, H and Xia, J and Tang, L and Zhang, S},
title = {Embolism of coronary, cerebral, and limb arteries resulting from infective endocarditis of a prosthetic aortic valve: a clinical case report.},
journal = {BMC cardiovascular disorders},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12872-025-05287-2},
pmid = {41315949},
issn = {1471-2261},
abstract = {BACKGROUND: Infective endocarditis (IE) involving prosthetic valves is a critical cardiac condition that can lead to complications such as structural heart damage, heart failure, and arterial embolism, with a high associated mortality rate. This report describes an uncommon instance of infective endocarditis of a prosthetic aortic valve leading to multiorgan embolism.<br><br>CASE PRESENTATION: A 52-year-old male with a history of Bentall surgery and prosthetic aortic valve replacement presented with chest pain and dyspnea. Coronary angiography demonstrated blockage of the distal left anterior descending artery, which was addressed with balloon angioplasty. A transesophageal echocardiogram (TEE) detected vegetation on the prosthetic valve, and metagenomic next-generation sequencing of blood confirmed infection with Cardiobacterium hominis. During treatment, he experienced acute ischaemia in the right lower limb necessitating thrombectomy, and MRI disclosed numerous tiny infarct foci in the brain. Following a period of six weeks of antibiotic treatment, the patient was discharged in a better condition. However, the valve dysfunction persisted and regular follow-up was required in order to determine whether to perform a further operation.<br><br>CONCLUSION: This case underscores the risk of multi-organ embolic consequences in prosthetic valve infective endocarditis, highlighting the necessity for prompt identification, antimicrobial treatment, and surgical intervention where warranted.},
}
@article {pmid41315849,
year = {2025},
author = {Zhang, R and Wang, M and Liu, X and Yang, F and Xu, X and Zi, L and Liang, Z and Liu, X and Gao, H and Chen, X and Zhou, G},
title = {The bacterial spectrum of spinal infections based on blood culture, tissue culture, and molecular methods: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28576-4},
pmid = {41315849},
issn = {2045-2322},
support = {CB23059C065A//Yunnan Fundamental Research Projects/ ; },
abstract = {Spinal infections (SI) are on the rise due to an aging population and the prevalence of more invasive procedures. This study aims to systematically review the microbiological spectrum of SI to enhance diagnostic accuracy and inform effective antibiotic treatment strategies. The last search was conducted on May 9th, 2024, from databases including EMBASE, PubMed, and Web of Science. The outcome variable is infection rate, and the detection method used should be blood culture, tissue culture, or molecular biology method. Two researchers independently extracted research data and evaluated its quality using the JBI Critical Appraisal Tools. Out of 14,639 identified records, 156 studies (encompassing 13,539 patients) were included. Staphylococcus aureus was identified as the most prevalent pathogen, with pooled infection rates of 17.6% (95%CI: 12.8-22.9%; I[2]=93%) in blood culture, 16.8% (95%CI: 14.0-19.8%; I[2]=96%) in tissue culture, and 12.0% (95%CI: 9.3-15.0%; I[2]=35%) in molecular methods. The bacterial spectrum also featured Staphylococcus epidermidis, Escherichia coli, and Mycobacterium tuberculosis (MTB). Molecular methods, particularly metagenomic next-generation sequencing (mNGS), demonstrated markedly superior sensitivity for MTB detection, with a pooled rate of 9.7% (95%CI: 4.6-16.3%; I[2]=90%) compared to 1.3% (95%CI: 0.6-2.1%; I[2]=86%) by tissue culture. The odds ratio for MTB detection with mNGS versus conventional culture was 4.24 (95%CI: 1.68-10.73). This review confirms that a core group of pathogens, including Staphylococcus aureus, Staphylococcus epidermidis, MTB, and Escherichia coli. Our findings underscore that tissue culture is fundamental for common pyogenic bacteria, while metagenomic next-generation sequencing is indispensable for detecting fastidious organisms like MTB. Trial registration: The protocol was registered with PROSPERO (No. CRD42023427429). Registered on May 28, 2023.},
}
@article {pmid41315738,
year = {2025},
author = {Medvedeva, S and Guyet, U and Pelletier, E and Ruscheweyh, HJ and Sunagawa, S and Ogata, H and Aylward, FO and Gaïa, M and Yutin, N and Koonin, EV and Krupovic, M and Delmont, TO},
title = {Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41315738},
issn = {2058-5276},
support = {ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0022//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes. Mirusviricota comprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, major Mirusviricota lineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses.},
}
@article {pmid41315665,
year = {2025},
author = {Goraj, W and Kagan, K and Kuźniar, A and Banach, A and Jurczyk, S and Podlewski, J and Wolińska, A},
title = {Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30318-5},
pmid = {41315665},
issn = {2045-2322},
abstract = {Biofilms in historic buildings represent stable microbial ecosystems shaped by long-term environmental filtering. We investigated bacterial and fungal communities forming biofilms on walls and ceilings in a 19th-century cheese ripening cellar in Poland, characterized by low temperature, high humidity, and minimal light - conditions resembling natural subterranean habitats. Using high-throughput 16 S rRNA and ITS sequencing, we revealed distinct taxonomic and predicted functional profiles associated with surface type (wall vs. ceiling) and material (brick vs. stone). The wall biofilms exhibited greater taxonomic and functional diversity, with enrichment in heterotrophic, fermentative, and polymer-degrading taxa and pathways, whereas ceiling biofilms showed predicted enrichment in aerobic, stress-tolerant, and potentially methanogenic lineages. The co-occurrence network analysis revealed more complex and tightly connected associations in wall biofilms, dominated by Actinobacteriota (21-97%) and Ascomycota (60-97%), suggesting stable ecological organization despite the limited sample size. Environmental factors, such as pH, redox potential, and electrolytical conductivity, explained a substantial proportion of the variance in the microbial diversity and predicted functional traits. Overall, this study highlights traditional ripening cellars as semi-natural built ecosystems that sustain specialized, spatially structured microbiomes. The results provide new insights into microbial adaptation, functional potential, and ecological resilience in heritage food environments.},
}
@article {pmid41315430,
year = {2025},
author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D},
title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42704},
pmid = {41315430},
issn = {2045-2322},
support = {R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; },
mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; },
abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).},
}
@article {pmid41060580,
year = {2025},
author = {Vega-Carranza, AS and Escamilla-Montes, R and Luna-González, A and Diarte-Plata, G and Fierro-Coronado, JA and García-Gutiérrez, C and Ceseña, CE},
title = {Investigating the effects of synbiotics, postbiotics and bacilli in the modulation of gut microbiota and the survival of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {4},
pages = {2845-2854},
pmid = {41060580},
issn = {1678-4405},
abstract = {The effect of feed and water additives was evaluated on the gut microbiota and survival of white shrimp challenged with V. parahaemolyticus. Bacillus licheniformis BCR 4 − 3 and vibrio cultures were spray dried. Inulin, probiotics, and postbiotics of bacilli (SPB) and postbiotics of vibrios (PVp) were added to commercial feed. Viable bacilli cells were added to water. An experiment with four treatments in triplicate was performed to determine the effect of diet on survival and the intestinal microbiota by sequencing the V3 region of the bacterial 16S ribosomal gene. Metagenomic analysis was performed on the Shaman, MicrobiomeAnalyst, and Ivikodak platforms. The growth was not affected by the additives but survival of animals in treatments was significantly higher as compared to control group. The phyla and genera that predominated in the white shrimp intestine were Proteobacteria, Bacteroidetes, Firmicutes, Vibrio, Agarivorans, Tropicibacter, and Roseovarius. The Vibrio genus increased in treatments with bacilli in feed and water and decreased in PVp in feed. The control and treatments shared 219 Operational Taxonomic Units. No changes were observed in the bacterial diversity (richness and relative abundance of species). In the bacterial community of the shrimp intestine (species replacement) changes were observed. Bacterial functional profile (Lipid, amino acid, and energy metabolism and digestive and immune systems) was modulated in treatments. Synbiotics, postbiotics, and bacilli in water enhance survival rates and modulated the gut microbiota of L. vannamei.},
}
@article {pmid41315421,
year = {2025},
author = {Thystrup, C and Gobena, T and Salvador, EM and Fayemi, OE and Kumburu, H and Buys, EM and Gichure, J and Moiane, BT and Belina, D and Hugho, EA and Faife, S and Ogunbiyi, TS and Akanni, G and Ayolabi, CI and Mmbaga, B and Thomas, KM and Pires, SM and Njage, PMK and Hald, T},
title = {Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66400-9},
pmid = {41315421},
issn = {2041-1723},
support = {OPP1195617//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; },
abstract = {Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.},
}
@article {pmid41315331,
year = {2025},
author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S},
title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {223},
pmid = {41315331},
issn = {2055-5008},
support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; },
mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; },
abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.},
}
@article {pmid41315266,
year = {2025},
author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P},
title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10777},
pmid = {41315266},
issn = {2041-1723},
support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Zea mays/microbiology/genetics/growth &amp; development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; },
abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.},
}
@article {pmid41315190,
year = {2025},
author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and , and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M},
title = {Unveiling the global urban virome through wastewater metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10707},
pmid = {41315190},
issn = {2041-1723},
support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; },
mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; Cities ; Animals ; Metagenome ; },
abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.},
}
@article {pmid41314968,
year = {2025},
author = {Li, YX and Wang, RY},
title = {Autoimmune glial fibrillary acidic protein astrocytopathy following human herpesvirus-7 infection: a case report.},
journal = {Brain injury},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/02699052.2025.2596225},
pmid = {41314968},
issn = {1362-301X},
abstract = {OBJECTIVE: Human herpesvirus-7 encephalitis (HHV7E) is exceedingly rare in immunocompetent adults, and the subsequent development of autoimmune glial fibrillary acidic protein astrocytopathy (GFAP-A) following HHV7E is even rarer. We present the inaugural Chinese case of GFAP-A triggered by HHV7E, confirmed via metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: A 37-year-old male initially presented with fever and significant memory impairment. Brain magnetic resonance imaging (MRI) revealed T2/fluid-attenuated inversion recovery (FLAIR) hyperintensity in the right temporal lobe. The diagnosis of HHV7E was confirmed by the detection of HHV7 in the cerebrospinal fluid (CSF) via mNGS. His symptoms improved significantly following acyclovir treatment. However, five weeks post-discharge, he experienced acute neurological deterioration, with symptoms including bifrontal headaches, vomiting, memory impairment, and visual hallucinations. Repeat brain MRI revealed new bilateral punctate and patchy T2/FLAIR hyperintensities in the periventricular white matter. Contrast-enhanced MRI demonstrated bilateral linear radial perivascular enhancements. A cell-based assay detected GFAP antibodies in CSF at a titer of 1:100, establishing a diagnosis of postinfectious GFAP-A. The patient responded well to combined intravenous steroid and immunoglobulin therapy.<br><br>CONCLUSIONS: This case highlights the importance of considering autoimmune encephalitis in patients with new or recurrent neurological symptoms after HHV7E recovery. Systematic mNGS and neuronal antibody testing are essential for timely diagnosis, and early aggressive immunotherapy may improve outcomes in post-HHV7E GFAP-A.},
}
@article {pmid41314430,
year = {2025},
author = {Gabbay, U and Carmi, D},
title = {The Paradox of Rapid and Synchronized Propagation of Seasonal Influenza 'A' Outbreaks in Contrast with COVID-19: a Testable Hypothesis.},
journal = {Virus research},
volume = {},
number = {},
pages = {199670},
doi = {10.1016/j.virusres.2025.199670},
pmid = {41314430},
issn = {1872-7492},
abstract = {Seasonal influenza A virus (SIAV) apparently exhibits a paradoxical pattern: despite a lower basic reproduction number (R0) than SARS-CoV-2, it propagates across the Northern Hemisphere with remarkable speed and synchronicity. We propose a testable hypothesis, developed in two conceptual steps to explain this phenomenon. First, we discuss what may explain the rapid, near-synchronous propagation of SIAV seasonal outbreak. We suggest that it may result from parallel seeding from multiple sources, rather than emerging from a singular origin, as observed with COVID-19. Second, we examined potential mechanisms for parallel seeding. The hypothesis is testable through genomic and metagenomic methods. Sequencing viruses from humans and migratory birds across regions may be evaluated to reveal identical viral lineages. The hypothesis may highlight the potential role of ecological reservoirs in global influenza propagation dynamics. If validated, this framework would advance understanding of influenza seasonality and may guide integrated surveillance strategies linking avian ecology with human epidemiology.},
}
@article {pmid41314145,
year = {2025},
author = {Li, X and Lin, X and Dong, Z and Zhou, R and Niu, Q},
title = {Biomass ratio regulates methane conversion and carbon fixation in a methanotrophs-microalgae symbiotic system: Efficiency optimization and mechanisms driven by co-metabolism.},
journal = {Water research},
volume = {290},
number = {},
pages = {125016},
doi = {10.1016/j.watres.2025.125016},
pmid = {41314145},
issn = {1879-2448},
abstract = {The methanotrophs-microalgae symbiotic system for greenhouse gas treatment is a novel biological carbon fixation technology. However, practical applications are limited by low conversion efficiency, which arises from metabolic heterogeneity in growth rates and carbon-nitrogen resource utilization within the system. To improve metabolic stability of such symbiotic systems, this study systematically assessed CH4 metabolic fluxes by regulating the methanotrophs-microalgae biomass ratio, and further revealed synergistic mechanisms that enhance system stability. Experimental results indicated that at a methanotrophs to microalgae ratio of 1:5, the CH4 consumption rate peaked at 1.1 L CH4/d/g biomass. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the laser confocal revealed that the co-aggregation force of methanotrophs and microalgae was significantly enhanced at the optimal ratio. This enhancement was crucial for regulating the spatial mutualistic growth and metabolic interactions within the methanotrophs-microalgae symbiotic community. Structural equation modeling (SEM) indicated that poly-β-hydroxybutyrate (PHB) exerts a significant negative effect on methane consumption (-0.68***). Metagenomics results indicated that at the optimal methanotrophs-microalgae ratio, the relative abundance of genes associated with the methane oxidation center metabolic pathway increased by 1.38 times. This significantly enriched Type I methanotrophs (1.89 times) and Type II methanotrophs (1.51 times), while the relative abundance of genes involved in the PHB production pathway decreased by 16 %. This change accelerated the conversion and assimilation of methane carbon, ultimately improving the carbon fixation efficiency by 16 %. This study provided theoretical foundations and technical support for advancing the engineering application of methanotrophs and microalgae symbionts to achieve efficient, stable methane conversion and simultaneous carbon sequestration.},
}
@article {pmid41314069,
year = {2025},
author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK},
title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181062},
doi = {10.1016/j.scitotenv.2025.181062},
pmid = {41314069},
issn = {1879-1026},
abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.},
}
@article {pmid41313993,
year = {2025},
author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y},
title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128135},
doi = {10.1016/j.jenvman.2025.128135},
pmid = {41313993},
issn = {1095-8630},
abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.},
}
@article {pmid41313912,
year = {2025},
author = {Li, Y and Tang, C and Qin, X and Qin, W and Fu, Y and Shi, D and Lan, W and Tang, Y and Wu, R and Yu, F},
title = {Rhizosphere nutrient dynamics and physiological responses of Oryza sativa L. under polyethylene terephthalate microplastic stress.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt E},
pages = {110797},
doi = {10.1016/j.plaphy.2025.110797},
pmid = {41313912},
issn = {1873-2690},
abstract = {Polyethylene terephthalate microplastics (PET-MPs), as emerging environmental contaminants, pose growing threats to agricultural ecosystems. This study investigated the impacts of PET-MPs on key physiological traits of Oryza sativa L. and the abundance of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling within rhizosphere soils. Results demonstrated that PET-MPs were absorbed by rice roots and translocated to aerial tissues, significantly inhibiting chlorophyll biosynthesis (p < 0.05). Exposure to PET-MPs induced oxidative stress, with the 2.5 g kg[-1] treatment elevating root malondialdehyde levels by 175.3 %, and reducing plant height and biomass by 15.8 % and 44.6 %, respectively. Metagenomic analysis revealed a marked increase in the denitrification gene narI, while genes associated with C fixation (korB, korA), methanogenesis (mch), organic N metabolism (glnA), and P transport (ugpC) were significantly suppressed, indicating disruptions to soil nutrient cycling. Actinomycetota and Pseudomonadota were identified as predominant microbial hosts of these functional genes. Pearson correlation analysis showed significant positive associations (p < 0.05) between plant growth parameters and the abundance of korA, korB, IDH1, mch, glnA, and ugpC. These findings advance our understanding of the ecological risks posed by PET-MPs in terrestrial environments and underscore their potential to compromise soil fertility and sustainable rice production.},
}
@article {pmid41313659,
year = {2025},
author = {Sun, W and Pan, J and Gao, X},
title = {Research on the influence mechanism of low-temperature storage on nitrifying bacteria.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {10},
pages = {1426-1440},
pmid = {41313659},
issn = {0273-1223},
support = {2022JH1/10800006//Science and Technology Program of Guizhou Province/ ; },
mesh = {*Nitrification ; *Bacteria/metabolism/genetics ; Sewage/microbiology ; *Cold Temperature ; Nitrites/metabolism ; Ammonia/metabolism ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; },
abstract = {To develop a more cost-effective nitrogen removal strategy, this study investigated the impact of low-temperature storage methods on nitrifying bacterial activity. Sludge was stored under laboratory-scale static batch conditions in three media: (1) distilled water, (2) nutrient solution, and (3) nutrient solution supplemented with hydroxylamine (NH2OH). Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) activity, sludge properties, and microbial characteristics were examined. Results revealed that all storage methods inhibited both AOB and NOB activity. Notably, nutrient solution storage demonstrated the most significant effect: it suppressed NOB activity by 86.6% and reduced its relative abundance by 20%, while maintaining high extracellular polymeric substance content (43.5 mg/g VSS) and AOB relative abundance (0.18%). This method substantially shortened the required storage duration (from 8 months to 60 days) and better preserved AOB activity and sludge stability. Metagenomic analysis indicated strong inhibition of the NOB functional gene nitrite oxidoreductase across all methods, while nutrient solution storage specifically elevated the abundance of the AMO gene. Although NH2OH supplementation exhibited inhibitory effects on microorganisms, the concurrent addition of nutrient solution effectively mitigated this impact. Consequently, sludge properties and functional microbiota abundance showed no significant difference between the NH2OH-supplemented nutrient solution method and distilled water storage.},
}
@article {pmid41313651,
year = {2025},
author = {Zhang, Q and Jiang, X and Xi, Y and Ma, X and Zhang, W},
title = {Complete genome sequences of two Cressdnaviricota viruses identified in respiratory tract samples from forest musk deer in China.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063225},
doi = {10.1128/mra.00632-25},
pmid = {41313651},
issn = {2576-098X},
abstract = {We identified two circular single-stranded DNA viruses from forest musk deer in China through metagenomic analysis. Phylogenetic results suggest they represent unclassified Cressdnaviricota lineages. This study highlights the diversity of the deer's respiratory virome and underscores the importance of wildlife virus surveillance for conservation and public health.},
}
@article {pmid41313537,
year = {2025},
author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS},
title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41313537},
issn = {1867-1314},
abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.},
}
@article {pmid41313246,
year = {2025},
author = {Rigonato, J and Lozano, JC and Vergé, V and Jaillon, O and Bouget, FY},
title = {Latitudinal Diversity in Circadian and Light-Sensing Genes in an Ecologically Vital Group of Marine Picoeukaryote Algae.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf263},
pmid = {41313246},
issn = {1751-7370},
abstract = {Organismal life cycles are influenced by Earth's rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms' ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.},
}
@article {pmid41313177,
year = {2025},
author = {Hoque, MN and Rahman, MS},
title = {Bacteriome and resistome dysbiosis in subclinical mastitis and antibiotic-treated milk of dairy cows.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0107025},
doi = {10.1128/mra.01070-25},
pmid = {41313177},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct bacteriome profiles in subclinical mastitis, antibiotic-treated, and healthy cow milk, with enriched resistance repertoires in diseased and treated samples. Findings highlighted the need for better diagnostics, precision antimicrobial use, and antibiotic alternatives to ensure milk safety and address antimicrobial resistance in dairy farming.},
}
@article {pmid41313018,
year = {2025},
author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0086225},
doi = {10.1128/msystems.00862-25},
pmid = {41313018},
issn = {2379-5077},
abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.<br><br>IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.},
}
@article {pmid41313013,
year = {2025},
author = {Babb, PL and Akhund-Zade, J and Spacek, D and Brick, K and Christians, FC and Portnoy, V and Tsai, M-S and Jarman, KH and Bercovici, S and Vilfan, ID and Blauwkamp, TA},
title = {In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/jcm.00944-25},
pmid = {41313013},
issn = {1098-660X},
abstract = {Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel microbial biomarkers for disease. However, widespread implementation of this approach is limited by lengthy and complex workflows, high host background cfDNA leading to high sequencing costs, and prevalent environmental DNA contamination risks. Addressing these barriers is critical for scalable deployment in both centralized and decentralized settings. To overcome these limitations, we developed Karius Helion-4 Chemistry (Helion-4), an in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, to serve as a platform for mcfDNA sequencing applications in infectious disease, microbiome analyses, and disease biomarker discovery. We compared Helion-4 to two widely used metagenomic extraction-based sequencing workflows, as well as to the prior Karius chemistry platform (Digital Culture-3), using 36 clinical plasma specimens. Helion-4 enables end-to-end sequencing library construction for up to 96 samples in 5.25-6.1 h, including setup and final quality control evaluation, with 2.25 h of hands-on time when using automated liquid handling robots. Compared to the other methods, Helion-4 recovered 58-fold to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating 1.8-fold to 6-fold lower exogenous background DNA contamination, likely due to the absence of DNA extraction. The fraction of mcfDNA reads among total reads was enriched by 60-fold to 164-fold for Helion-4 compared to current state-of-the-art methods, significantly lowering sequencing costs required for applications built on the Helion-4 platform vs other platforms. Collectively, these advances enable routine processing of small specimen volumes and provide a simple, efficient, and scalable approach for mcfDNA sequencing applications.IMPORTANCEMetagenomic sequencing of microbial cell-free DNA (mcfDNA) enables the identification and quantification of diverse pathogens from blood and other biofluids, providing minimally invasive and rapid diagnosis of deep-seated infectious disease. However, widespread implementation of this approach is limited by complex workflows, high sequencing costs, and prevalent contamination risks. Karius Helion-4 Chemistry, the first in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, overcomes these limitations. Compared to the other methods, Helion-4 is faster, cleaner, and more sensitive. Helion-4 recovered up to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating up to sixfold lower exogenous background DNA contamination. The fraction of mcfDNA reads among total reads was enriched by up to 164-fold for Helion-4, lowering sequencing costs. These advances by Helion-4 technology enable a simple, efficient, and scalable approach for mcfDNA sequencing applications and bring us closer to widespread, high-resolution, and real-time microbial profiling across diverse healthcare settings.},
}
@article {pmid41312992,
year = {2025},
author = {D'Amico González, G and Rodríguez, MM and Penzotti, P and Brunetti, F and Ghiglione, B and Moe, LA and Centrón, D and Gutkind, G and Gao, L and Haider, S and Powers, RA and Klinke, S and Power, P},
title = {Proposal of metagenomic-origin LRA-5 as a precursor of active β-lactamases through Tyr69Gln and Val166Glu amino acid substitutions: a functional and structural analysis.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0067525},
doi = {10.1128/aac.00675-25},
pmid = {41312992},
issn = {1098-6596},
abstract = {Wild-type LRA-5, recovered from Alaskan soil samples, shares no more than 33% amino acid sequence identity with enzymes from pathogens like PER β-lactamases. Recombinant E. coli expressing wild-type LRA-5 and its engineered variants LRA-5[Y69Q] and LRA-5[V166E] showed MIC values equivalent to control strains. However, LRA-5[Y69Q/V166E] displayed MICs above the resistant breakpoint for some β-lactams. Kinetic parameters correlated with the MICs, showing that the catalytic efficiency of LRA-5[Y69Q/V166E] was comparable to those from class A β-lactamases, such as CTX-M-15, PER-2, and KPC-2. LRA-5[Y69Q/V166E] exhibited kcat/Km values up to 11,000-fold higher compared to wild-type LRA-5, which is associated with the presence of Glu166. The X-ray crystallographic structure of wild-type LRA-5 (1.80 Å; PDB 8EO5) shows that the lack of both Glu166 and a deacylation water molecule contributes to a biologically insignificant activity. Interactions observed between LRA-5 and ceftazidime (2.35 Å; PDB 8EO6) show structural conservation with other β-lactamases. In contrast, the crystallographic structure of LRA-5[Y69Q/V166E] (2.15 Å; PDB 8EO7) bears a deacylation water molecule that is associated with the increase in catalytic activity compared to the wild-type variant. Circular dichroism results confirm that amino acid substitutions in LRA-5 do not affect the overall content of the secondary/tertiary structures. Evidence suggests that alternative evolutionary paths could have occurred for β-lactamases like LRA-5, produced by environmental microorganisms: (i) proteins having similar structural features than active β-lactamases may accumulate a small number of mutations (e.g., Y69Q/V166E) to yield active enzymes and (ii) the β-lactamase fold may have lost key residues in the absence of antibiotics.},
}
@article {pmid41312680,
year = {2025},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}
@article {pmid41312645,
year = {2025},
author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC},
title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1283},
pmid = {41312645},
issn = {1362-4962},
support = {DE-AC02-05CH11231//US DOE/ ; FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Hellenic Foundation for Research and Innovation/ ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; },
abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.},
}
@article {pmid41312456,
year = {2025},
author = {Huang, W and Ran, X and Zhang, Z and Yang, L and Yin, J and Lv, S and Liu, G and Pei, Y},
title = {Multiple brain abscesses caused by Nocardia asiatica co-infection with Torque teno virus in an "immunocompetent" patient: a rare case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1661345},
pmid = {41312456},
issn = {2296-858X},
abstract = {Brain abscess is a suppurative infection of brain tissue caused by one or more pathogens under specific susceptible conditions and is associated with a high clinical fatality rate. Beyond surgical intervention, the identification of pathogens is key to clinical antimicrobial therapy, yet this remains a challenge. Nocardia is a ubiquitous bacterium that typically manifests as an opportunistic infection, primarily affecting immunocompromised individuals. Pulmonary involvement, characterized by suppurative inflammation, commonly occurs following inhalation, with subsequent hematogenous dissemination potentially leading to widespread infection. To our knowledge, central nervous system (CNS) infection by Nocardia asiatica (N. asiatica) resulting in brain abscess has hitherto rarely been reported. We present a rare case of multiple brain abscesses caused by N. asiatica co-infection with Torque teno virus (TTV) in an immunocompetent patient with suspected multiple organ involvement. The patient was admitted to our hospital, presenting with a headache, and imaging revealed brain abscess-like lesions. A robot-assisted stereotactic puncture and drainage were used for abscess removal. N. asiatica and TTV were identified by metagenomic next-generation sequencing (mNGS) of the brain abscess aspirate, with N. asiatica subsequently confirmed by mass spectrometry of the cultured organism. A disseminated Nocardia infection was suspected based on the patient's skin trauma history, pulmonary inflammatory changes, and imaging findings (liver cysts, subcutaneous nodules). However, etiological confirmation was not obtained prior to his death. While this is not the first reported instance of Nocardia and TTV co-infection in brain abscesses, our case is notable for its occurrence in an immunocompetent patient. This report highlights the significance and value of TTV in the context of brain abscesses and warrants a re-evaluation of Nocardia and TTV co-infection. Given that the diagnosis of intracranial infection depends on the detection of pathogens, we advocate for the routine and early implementation of mNGS testing in patients with brain abscesses. Moreover, systemic nutritional support and immunomodulatory therapies should be considered in the early stage of treatment for complex cases. Earlier diagnosis and treatment in this case might have altered the patient's outcome.},
}
@article {pmid41312302,
year = {2025},
author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {450},
pmid = {41312302},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).},
}
@article {pmid41312195,
year = {2025},
author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W},
title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5191656},
pmid = {41312195},
issn = {1865-1682},
mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; },
abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.},
}
@article {pmid41312164,
year = {2025},
author = {Onohuean, H and Nnolum-Orji, NF and Naik Bukke, SP and Abass, KS and Alagbonsi, AI and Choonara, YE},
title = {Non-alcoholic fatty pancreas disease (NAFPD) as a pre-neoplastic niche: Metabolic and inflammatory Gateways to pancreatic ductal adenocarcinoma.},
journal = {Journal of clinical &amp; translational endocrinology},
volume = {42},
number = {},
pages = {100424},
pmid = {41312164},
issn = {2214-6237},
abstract = {Non-alcoholic fatty pancreas disease (NAFPD), marked by ectopic triglyceride accumulation in the exocrine pancreas, is increasingly observed yet its recognition as a cancer-predisposing condition remains limited. We synthesize evidence supporting NAFPD as an early and modifiable niche for pancreatic ductal adenocarcinoma (PDAC), using a PRISMA-ScR-guided framework. The findings were synthesized into three domains: epidemiological risk, metabolic-inflammatory signaling, and immune-stromal remodeling. Mechanisms include palmitate-induced ER stress, ROS-driven NLRP3-IL-1β and STAT5 signaling, and KRAS^G12D-mediated lipotoxicity. Lipid-laden stellate cells promote fibrosis, immunosuppression, and epithelial-mesenchymal transition. NAFPD may represent an early, modifiable PDAC niche, warranting further imaging-omic studies and targeted prevention trials.},
}
@article {pmid41311850,
year = {2025},
author = {Aditya, C and Bukke, SPN and Anitha, K and Meeraraje, P and Goruntla, N and Yadesa, TM and Onohuean, H},
title = {A comprehensive review on diabetic foot ulcer addressing vascular insufficiency, impaired immune response, and delayed wound healing mechanisms.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1622055},
pmid = {41311850},
issn = {1663-9812},
abstract = {Diabetic foot ulcers (DFUs) continue to represent one of the most significant and costly complications related to diabetes mellitus, posing serious challenges to healthcare systems and resulting in considerable morbidity rates. This narrative review explores the complex pathophysiology of DFUs, focusing on the interplay between peripheral neuropathy, vascular insufficiency, and a weakened immune response, all of which contribute to delayed wound healing. Neuropathy leads to a loss of protective sensation, causing unnoticed repetitive injuries, while both microvascular and macrovascular complications reduce tissue perfusion and hinder angiogenesis. Additionally, immune dysfunction and exaggerated inflammatory responses raise the occurrence of infection and negatively affect the healing process. The clinical manifestation, progression, and key risk factors of DFUs were discussed in this review, emphasizing the importance of early detection, careful foot care, and routine screening in individuals who are at risk. Numerous therapeutic approaches are reviewed, including wound debridement, sophisticated wound dressings, offloading techniques, glycemic control, and adjuvant therapies such as growth factor administration, hyperbaric oxygen therapy, and negative pressure wound therapy. For optimal results, a multidisciplinary team combining of vascular surgeons, podiatrists, endocrinologists, and wound care specialists was included. The analysis also points out that promising advancements in bioengineered skin substitutes, intelligent dressings, and regenerative medicine hold promise for the treatment of DFU in the future. Self-monitoring, appropriate footwear, and patient education are all important components of prevention, which remains a fundamental strategy. In the clinical management of DFUs, this narrative review incorporates the most recent research and highlights the value of proactive, customized, and multidisciplinary approaches.},
}
@article {pmid41311501,
year = {2025},
author = {Wu, Q and Hu, S and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Liu, Y and Chen, Y and Gan, M and Zhu, L},
title = {Age-related gut microbiota succession in Neijiang pigs: insights for precision feeding and productivity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698169},
pmid = {41311501},
issn = {1664-302X},
abstract = {OBJECTIVE: To characterize age-related gut microbiota succession in Neijiang pigs and translate these dynamics into actionable insights for precision feeding and productivity improvement.<br><br>METHODS: Growth data from 0 to 180&#x202f;days (n&#x202f;=&#x202f;16, 780 weight records) were fitted with three non-linear models to determine the optimal growth curve and partition physiological stages. Fresh feces were collected at 25, 70, 110, and 150&#x202f;days (n&#x202f;=&#x202f;6/stage). 16S rRNA V3-V4 amplicon sequencing was used to profile microbiota composition and diversity; PICRUSt2 was employed to predict metagenome functions against the KEGG database.<br><br>RESULTS: The Gompertz model best described growth (R [2]&#x202f;=&#x202f;0.996) with an inflection point at 84.2&#x202f;days (25.9&#x202f;kg). Microbial alpha-diversity (Shannon, Chao1) increased with age and plateaued after 110&#x202f;days. Firmicutes and Bacteroidota dominated (>90% relative abundance), whereas Spirochaetota and Euryarchaeota expanded significantly in finishing pigs. LEfSe identified 45 stage-specific biomarkers: Prevotella_9, Collinsella and Blautia characterized suckling-weaning stages; Faecalibacterium and Clostridium_sensu_stricto_1 peaked at 70&#x202f;days; Lactobacillus was dominant at 110&#x202f;days; Treponema, Streptococcus and Bacteroides defined the 150-day microbiome. Functional prediction revealed a metabolic shift from basal biosynthesis and DNA repair in early life toward enhanced ABC transporters, bacterial motility proteins, oxidative phosphorylation and methane metabolism in finishing pigs.<br><br>CONCLUSION: Our data provide a temporal blueprint of gut microbiota maturation that mirrors host nutrient requirements across growth phases. These microbial indicators and functional signatures can guide stage-specific dietary formulations and microbiota-targeted interventions to improve feed efficiency, reduce environmental emissions and enhance the productivity of indigenous pig breeds.},
}
@article {pmid41311499,
year = {2025},
author = {Wang, J and Su, W and Chen, Q and Zhou, J and Wang, X and Jiang, R and Li, J and Xing, P},
title = {Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669172},
pmid = {41311499},
issn = {1664-302X},
abstract = {BACKGROUND: Recent studies indicate that microorganisms significantly influence lung cancer pathogenesis. This research explores the variations in microbiota and metabolites in the lower respiratory tract between lung cancer patients and individuals with benign pulmonary lesions to identify potential diagnostic biomarkers.<br><br>METHODS: Two hundred eight patients undergoing bronchoscopy at Tianjin Cancer Institute &amp; Hospital and Tianjin Chest Hospital from October 2022 to October 2023 were screened. Ninety-five bronchoalveolar lavage fluid (BALF) was collected for metagenomic sequencing and untargeted metabolomic analysis. Comparisons of microbial diversity, taxonomic composition, and metabolite profiles were conducted between groups with lung cancer and benign lung conditions.<br><br>RESULTS: The cohort comprised 70 patients with lung cancer and 25 with benign lung lesions. Patients with lung cancer showed significantly reduced &#x3b2;-diversity (p =&#x202f;0.005). Predominant microbes in lung cancer cases included Streptococcus, Haemophilus influenzae, and Veillonella parvula. A microbial-based diagnostic model differentiated lung cancer from benign lesions with an AUC of 0.931 (95%CI: 0.916-0.946). Metabolites increased in lung cancer were Citric acid, N-Acetylneuraminic acid, Oxoglutaric acid, and Neopterin, whereas L-Tryptophan, Uridine, 3-Hydroxybutyric acid decreased. The KEGG pathways suggest a significant link between microbial presence and both tumorigenesis and progression.<br><br>CONCLUSION: Specific microbial patterns in the lower respiratory tract of lung cancer patients could assist in the auxiliary diagnosis of the disease. The notably altered microorganisms and metabolites in the BALF from lung cancer patients, as opposed to those with benign conditions, correlate with cancer initiation and advancement.},
}
@article {pmid41311484,
year = {2025},
author = {Xu, J and Yao, Y and Pan, L and Zhang, N and Li, D and Chen, X},
title = {Pea-cucumber crop rotation suppresses Fusarium pathogens by reshaping soil microbial communities and enhancing nutrient availability.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1697343},
pmid = {41311484},
issn = {1664-302X},
abstract = {INTRODUCTION: Pea-cucumber rotation combined with straw return as green manure is an environmentally friendly management strategy to suppress cucumber (Cucumis sativus L.) Fusarium wilt (FW) and alleviate continuous cropping obstacles.<br><br>METHODS: We evaluated the variations in soil microbial compositions and nutrient levels between long-term cucumber monocropping and pea-cucumber rotation patterns via metagenomic sequencing and determination of soil properties.<br><br>RESULTS: The study found that the bacterial communities exhibited marked diversity, whereas the &#x3b1;-diversity of fungal communities was significantly reduced. Based on the relative abundance of differential fungi and bacteria at the genus level, the genus Bacillus showed the highest abundance, with a two-fold increase, whereas Fusarium species exhibited a 4.9-fold reduction following the pea-cucumber rotation. Additionally, the contents of available nitrogen, potassium, and phosphorus in the soil increased by more than 1.3-fold after the rotation. Correlation analysis revealed that the genus Bacillus and available potassium were significantly and negatively correlated with Fusarium pathogens. Notably, the isolated B. pumilus and B. safensis strains significantly suppressed the growth of cucumber FW pathogens.<br><br>DISCUSSION: These findings provide valuable insights for optimizing the combination of soil Bacillus populations and nutrient availability to maintain soil ecosystem health and improve cucumber growth and yield.},
}
@article {pmid41311478,
year = {2025},
author = {Zhong, Y and Li, R and E, J and Chi, H and Cao, N and Bai, Z and Du, X and Wang, L},
title = {Effects of maize straw and corncob return on the soil quality and on the soil microbial structures and functions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675172},
pmid = {41311478},
issn = {1664-302X},
abstract = {Straw return is an effective agricultural strategy for incorporating organic carbon into soil organic matter pools through microbial decomposition. This process modifies soil physicochemical properties, thereby altering microbial habitats and resource availability, which can influence the structure and function of soil microbial communities. However, the changes of soil physicochemical properties and microbial communities under different straw incorporation forms remain poorly understood. And how these straw return materials alter soil physicochemical properties and microbial communities within a single cycle. In this study, we conducted straw returning experiments in a maize-producing region of Jilin Province, China, comparing the impact of two distinct maize-derived residues (crushed maize straw and crushed corncob) on soil quality and microbial communities. Our results demonstrated that corncob return more effectively improved key soil physicochemical properties compared to maize straw return. While neither residue significantly alters microbial alpha diversity, both induced shifts in beta diversity. We identified distinct correlations between dominant microbial taxa and key soil physicochemical parameters. Furthermore, KEGG and GO analyses revealed that both of the residues altered microbial functional hierarchies, with corncob return inducing more pronounced changes than maize straw return. These findings provide a mechanistic basis for optimizing straw management strategies to enhance microbial-mediated soil fertility.},
}
@article {pmid41311042,
year = {2025},
author = {Choi, JH and Oh, S and Yi, MH and Kang, D and Choi, DY and Chavarria, X and Shatta, A and Cho, YH and Choe, S and Lee, SH and Kim, JY},
title = {Detection of intestinal parasites in leopard cat fecal samples using shotgun metagenomics.},
journal = {Parasites, hosts and diseases},
volume = {63},
number = {4},
pages = {349-353},
doi = {10.3347/PHD.25032},
pmid = {41311042},
issn = {2982-6799},
support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; RS-2023-KH139971//Ministry of Health and Welfare/ ; },
mesh = {Animals ; *Feces/parasitology ; *Metagenomics/methods ; *Intestinal Diseases, Parasitic/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 18S/genetics ; *Panthera/parasitology ; *Parasites/isolation &amp; purification/genetics/classification ; *Felidae/parasitology ; Cats ; },
abstract = {The leopard cat (Prionailurus bengalensis) is a wild felid species that serves as a reservoir of zoonotic parasites. In this study, we investigated intestinal parasite taxa by reanalyzing previously published shotgun metagenomic sequencing data from fecal samples of wild leopard cats using a custom 18S rRNA gene reference database constructed from the NCBI nucleotide database. Among 11 metagenomic samples, 5 parasite species were identified: Toxoplasma gondii, Clonorchis sinensis, Strongyloides planiceps, Cylicospirura petrowi, and Pharyngostomum cordatum. These findings demonstrate that shotgun metagenomic analysis of fecal samples can be a useful tool for monitoring zoonotic parasite infections in this species and for investigating parasite life cycles. However, this approach is limited by its dependence on existing reference databases and requires experimental validation of the findings.},
}
@article {pmid41310806,
year = {2025},
author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J},
title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {248},
pmid = {41310806},
issn = {2049-2618},
support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.<br><br>RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.<br><br>CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.},
}
@article {pmid41310797,
year = {2025},
author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.},
journal = {Radiation oncology (London, England)},
volume = {20},
number = {1},
pages = {179},
pmid = {41310797},
issn = {1748-717X},
support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; },
mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; },
abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.<br><br>METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72&#xa0;h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.<br><br>RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p&#x2009;<&#x2009;0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4&#x2009;+&#x2009;T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5&#x207a; intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.<br><br>CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.},
}
@article {pmid41310780,
year = {2025},
author = {Liu, Y and Brinkhoff, T and Simon, M},
title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {247},
pmid = {41310780},
issn = {2049-2618},
support = {TRR51//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Roseobacter/genetics/classification/isolation &amp; purification ; Phylogeny ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; Phylogeography ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA ; Genome, Bacterial ; },
abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.<br><br>RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for&#x2009;~&#x2009;70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of&#x2009;<&#x2009;2.9 Mbp and G&#x2009;+&#x2009;C contents of&#x2009;<&#x2009;40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.<br><br>CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.},
}
@article {pmid41310694,
year = {2025},
author = {Liu, P and Deng, Z and Wang, Y and Wu, F and Peng, J and Huang, P and Wang, Y and Lao, J},
title = {Application of Probe-Capture metagenomics in rabies diagnosis.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-025-03029-6},
pmid = {41310694},
issn = {1743-422X},
support = {82460480//National Natural Science Foundation of China/ ; 20223638//Qinzhou Scientific Research and Technology Development Program/ ; 2024GXNSFAA010067//Guangxi Natural Science Foundation/ ; },
abstract = {BACKGROUND: Rabies, a lethal viral encephalitis caused by Rabies virus (RabV), is transmitted via bites, scratches, or mucosal contact with infected animals, as well as through inhalation of aerosolized particles, ingestion of contaminated raw animal products, or transplantation of infected organs. It's near-universal fatality, diverse transmission routes, and marked clinical variability significantly impede timely diagnosis, highlighting the demand for a rapid and precise diagnostic approach.<br><br>METHODS: Single-center retrospective case series.<br><br>RESULTS: This series reported three rabies cases admitted to the First People's Hospital of Qinzhou: one without identifiable exposure and two with confirmed exposure histories. Clinical presentations were highly variable and diagnostically misleading. Application of Probe-Capture Metagenomics (pc-mNGS) to cerebrospinal fluid and blood samples enabled direct identification of RabV and concurrent detection of coexisting pathogens.<br><br>CONCLUSION: pc-mNGS demonstrates potential as a rapid, economical diagnostic tool capable of detecting RabV in specimens with low viral loads-such as blood and cerebrospinal fluid-from both exposed and unexposed individuals. Simultaneous identification of additional pathogens further supports its diagnostic utility.},
}
@article {pmid41310465,
year = {2025},
author = {Bae, J and Han, JW and Song, JY and Nam, SH and Sung, JS and Ko, HC and Kim, SH and Lee, YJ},
title = {Targeted elimination of latent endophytes improves cryopreservation success in in vitro grapevine (Vitis vinifera) cultures.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07821-y},
pmid = {41310465},
issn = {1471-2229},
support = {PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; },
abstract = {BACKGROUND: Latent endophytic bacteria are common in grapevine in vitro cultures and, while not always causing visible culture decline, can negatively affect downstream applications such as cryopreservation by reducing post-thaw recovery. While antibiotic treatments are widely used for microbial control, their efficacy varies with bacterial species, plant genotype, and application conditions. Few studies have directly linked targeted elimination of identified endophytes with improved post-cryopreservation recovery.<br><br>RESULTS: In this study, we identified Leifsonia poae in 'Ruby Seedless' and Curtobacterium oceanosedimentum in 'Merlot' using 16&#xa0;S rRNA sequencing. Species-specific antibiotic susceptibility testing revealed rifampicin (minimum bactericidal concentration, MBC&#x2009;=&#x2009;31&#xa0;&#xb5;g mL&#x207b;&#xb9;) as effective against L. poae, and cefotaxime (MBC&#x2009;=&#x2009;1000&#xa0;&#xb5;g mL&#x207b;&#xb9;) as effective against C. oceanosedimentum. In vitro application of these antibiotics eliminated the respective endophytes without significant phytotoxic effects at optimal concentrations. Amplicon-based 16&#xa0;S metagenomic profiling confirmed complete removal of the target bacteria and revealed substantial shifts in community composition, with reduced abundance of dominant taxa but maintenance of overall endophytic diversity. Cryopreservation experiments in 'Ruby Seedless' showed that removal of endophytes increased post-thaw survival from 31.8 to 70.9% and eliminated variability in regrowth across replicates.<br><br>CONCLUSIONS: This study demonstrates that targeted antibiotic elimination of dominant endophytes can restructure the in vitro microbial community and substantially improve cryopreservation outcomes in grapevine. The approach offers a reproducible sanitation strategy for clonal crops vulnerable to endophyte-related culture failures and can be readily adapted for germplasm conservation programs.},
}
@article {pmid41310455,
year = {2025},
author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X},
title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04562-8},
pmid = {41310455},
issn = {1471-2180},
support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; },
abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.},
}
@article {pmid41310063,
year = {2025},
author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM},
title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29138-4},
pmid = {41310063},
issn = {2045-2322},
support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; },
abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.},
}
@article {pmid41309890,
year = {2025},
author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E},
title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42423},
pmid = {41309890},
issn = {2045-2322},
support = {100217/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; },
abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.},
}
@article {pmid41309644,
year = {2025},
author = {Qiu, D and Wang, Y and Xu, N and Chen, B and Zhu, Y and Zhang, Z and Zhang, Q and Lu, T and Dong, H and Shou, J and Qian, H},
title = {Global variation in plant-beneficial bacteria in soil under pesticide stress.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10685},
pmid = {41309644},
issn = {2041-1723},
support = {42377107//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22376187//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Soil/chemistry ; *Soil Pollutants/toxicity ; Agriculture ; Metagenomics ; Crops, Agricultural/microbiology/growth &amp; development ; },
abstract = {The presence of plant-beneficial bacteria (PBB) in soil significantly affects crop production. Excessive agrochemical use in intensive agriculture causes substantial soil residue accumulation, compromising soil health, crop quality, and human health. Understanding changes in beneficial bacteria under pesticide pollution is crucial for guiding sustainable agricultural practices and promoting soil health. We analyze metagenomic data from 1919 soil samples to identify 364 PBBs. We find higher PBB diversity in agricultural soils than in non-agricultural soils; however, pesticide pollution negatively affects the abundance of PBB, particularly those with plant growth-promoting traits. Pesticides not only reduce PBB diversity as individual factors, but they also exert synergistic negative effects with other anthropogenic factors, as determined by Hedges'd effect size and 95% confidence intervals, further accelerating the decline in PBB diversity. Increased pesticide risk also leads to a loss of functional gene diversity in PBB about carbon and nitrogen cycling within essential nutrient cycles, and a reduction in specific amino acid and vitamin synthesis. Artificial application of specific amino acids and vitamins could be an effective strategy to restore PBB in high-pesticide-risk soils. This study provides guidance for regulating pesticide use to mitigate their negative effects on soil PBB and suggests potential remedial measures.},
}
@article {pmid41309591,
year = {2025},
author = {Zhou, N and Li, Q and Liang, Z and Yu, K and Zhang, C and Wang, H and Li, P and He, Z and Wang, S},
title = {Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10670},
pmid = {41309591},
issn = {2041-1723},
mesh = {*Halogenation ; Oceans and Seas ; *Seawater/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Phylogeny ; Archaea/genetics/metabolism/classification ; Molecular Docking Simulation ; *Hydrocarbons, Halogenated/metabolism ; },
abstract = {Microbially mediated organohalide cycling in the ocean has profound implications for global biogeochemical cycles and climate, but the geographic distribution and diversity of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we constructed an organohalide-cycling gene database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling microorganisms and genes from 1473 marine metagenomes. Strikingly, 6204 out of 15,252 metagenome-assembled genomes (MAGs) carry organohalide-cycling genes, of which 84.30% are dehalogenating populations. Microorganisms of Pseudomonadota with even spatial distribution dominate both halogenation and dehalogenation potentials in the ocean, in contrast to lineages of Asgardarchaeota and Thermoproteota solely mediating dehalogenation in the Northern hemisphere. Notably, 80.91% of reductive dehalogenase (RDase) genes and 91.35% of RDase-containing prokaryotes represent uncharacterized lineages, substantially expanding known dehalogenation diversity. Further integration of microbial cultivation, protein structure prediction, and molecular docking revealed four unique "microorganism-RDase-organohalide" patterns for marine dehalogenation and its coupling with carbon/sulfur cycles, being distinctively different from their terrestrial patterns. These results advance our understanding of microbial organohalide cycling by providing insights into the halogenation-dehalogenation microbiomes in the ocean.},
}
@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
doi = {10.4014/jmb.2506.06014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}
@article {pmid41309042,
year = {2025},
author = {Lin, QB and Xiao, S and Sheng, YZ and Shen, YX and He, Y and Liu, HY and Ye, YW and Chen, SD},
title = {Case report: Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma with eosinophilia diagnosed via exclusion using metagenomic next-generation sequencing.},
journal = {The Journal of international medical research},
volume = {53},
number = {11},
pages = {3000605251399037},
doi = {10.1177/03000605251399037},
pmid = {41309042},
issn = {1473-2300},
mesh = {Humans ; Male ; *Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology ; *High-Throughput Nucleotide Sequencing ; *Lung Neoplasms/diagnosis/genetics/pathology/complications ; Adult ; *Eosinophilia/diagnosis/genetics/complications/pathology ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Bronchoscopy ; Bronchoalveolar Lavage Fluid ; },
abstract = {Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma (MALToma) is a slow-growing lymphoma often misdiagnosed or undiagnosed due to its nonspecific clinical symptoms. A man in his late 30s initially presented with cough, sputum production, and chest pain, which improved after antibiotic treatment. A definitive diagnosis of pulmonary MALToma was established via bronchoscopic biopsy. Following the exclusion of alternative diagnoses through metagenomic next-generation sequencing of bronchoalveolar lavage fluid, the marked eosinophilia and diverse chest computed tomography findings highlight the need for clinical awareness of this disease.},
}
@article {pmid41308933,
year = {2025},
author = {Yue, J and Han, X and Yu, J},
title = {Multi-omics insights into ultra-rapid formation of aerobic granular sludge in 9 % salinity wastewater by filling of halotolerant loose mycelial pellets.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133705},
doi = {10.1016/j.biortech.2025.133705},
pmid = {41308933},
issn = {1873-2976},
abstract = {Salt-tolerant aerobic granular sludge (SAGS) had great potential in ultra-hypersaline wastewater treatment while slow and unstable formation hindered its application. Mycelial pellets (MPs) inoculation strategy could accelerate SAGS formation but collapse or peeling commonly occurred due to dense hyphal structures hindering microbial colonization in the connection layer between the shell and core. Besides, no MPs were reported to maintain structure under ultra-hypersaline environment. Herein, a novel strategy using newly-isolated ultra-high salt tolerant fungi Penicillium steckii NCSL-JXA6 with a loose MPs structure was applied for AGS start-up in 9 % salinity wastewater. Granulation completed on Day 1 and maintained stable for 97 days (D10 &amp; D50 > 200 μm, SVI30/SVI5 = 1), which was the fastest under similar salinity. SEM and stained cross-sectional slides showed the loose MPs structure allowed early inner microbial colonization and dense connection layer and core formed before hyphae collapsed, enabling stable transition within 27 days without fragmentation or peeling. Extracellular polymeric substances (EPS) and acyl-homoserine lactone signals (AHLs) (mainly PN, C8-HSL, C12-HSL) increased during transition period, supporting rapid microbial colonization. High TOC and TN removal (∼93 % and ∼ 82 %, respectively) was obtained within only 5 days. Metaproteomic analysis identified Penicillium as module hub of community. Integrative metagenomics and metaproteomics revealed upregulated colonization-related pathways and further confirmed that Penicillium steckii NCSL-JXA6 probably facilitated microbial colonization through metabolic complementarity, adhesion sites, and a loose hyphal structure easily enabling bacterial sensing, motility, adhesion, and biofilm construction. This study proposed a novel loose MPs inoculation theory and achieved the fastest SAGS formation in ultra-hypersaline wastewater.},
}
@article {pmid41308930,
year = {2025},
author = {Wang, S and Dai, B and Wang, Z and Yang, S and Xia, S and Rittmann, BE},
title = {S[0] powder as biofilm carrier and electron donor enhances autotrophic nitrogen removal in sulfur-driven partial denitrification coupled with anammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133707},
doi = {10.1016/j.biortech.2025.133707},
pmid = {41308930},
issn = {1873-2976},
abstract = {Sulfur-driven partial denitrification coupled with anammox (SPD/A) has been proposed as an innovative strategy for nitrogen removal from wastewater. This study proposes a novel strategy that integrates 20-μm S[0] powders with anammox granules to establish S[0]-driven partial denitrification coupled with anammox (i.e., S[0]PD/A) for the simultaneous removal of NH4[+] and NO3[-] from wastewater. When the influent concentrations of NH4[+] and NO3[-] were maintained at 31 and 52 mg-N/L, respectively, the efficiency of total-nitrogen removal reached 92 %, with anammox, S[0]-driven denitrification, and sulfammox accounting for 71 %, 27.4 %, and 1.6 %, respectively. Microbial community analysis revealed that anammox bacteria and sulfur-oxidizing bacteria were dominant functional genera involved in the S[0]PD/A. Anammox bacteria were enriched in anammox granules, and sulfur-oxidizing bacteria were enriched in microgranules of S[0] powders and Candidatus Brocadia. These findings highlight distinct microbial niche differentiation, elucidate nitrogen-sulfur metabolic interactions, and offer insights into an autotrophic process for total-nitrogen removal.},
}
@article {pmid41308739,
year = {2025},
author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S},
title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.056},
pmid = {41308739},
issn = {2090-1224},
abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.<br><br>OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.<br><br>METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography&#x2012;mass spectrometry (LC&#x2012;MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.<br><br>RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.<br><br>CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway and inhibiting acinar cell inflammation.},
}
@article {pmid41308447,
year = {2025},
author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H},
title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140613},
doi = {10.1016/j.jhazmat.2025.140613},
pmid = {41308447},
issn = {1873-3336},
abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.},
}
@article {pmid41308344,
year = {2025},
author = {Mao, YL and Hu, Y and Wu, ZP and Sun, YP and Hou, J and Cui, HL},
title = {Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126680},
doi = {10.1016/j.syapm.2025.126680},
pmid = {41308344},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains, DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T], were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus Natronorubrum judged by 16S rRNA gene and rpoB' gene sequence similarities, and formed tight clusters with current Natronorubrum species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and rpoB' genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus Natronorubrum were 76.8-92.7 %, 22.8-52.7 %, and 73.4-94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7-3.1 M NaCl, 37 °C, and pH 7.0-9.5. Strain WLHS9[T] was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9[T] was identical to that of the current neutrophilic species of Natronorubrum. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T] represent four novel species within the genus, namely, Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., respectively.},
}
@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02595-0},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}
@article {pmid41307551,
year = {2025},
author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H},
title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf212},
pmid = {41307551},
issn = {1745-1701},
support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.<br><br>STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.<br><br>STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.<br><br>CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.},
}
@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}
@article {pmid41306993,
year = {2025},
author = {Cai, X and Yi, H and Chen, K and Dai, J and Yi, J and Tu, B and Wang, Y and Li, J and Zhuang, J},
title = {Meta-Analysis of the Application Value of Metagenomic Next-Generation Sequencing Technology in the Diagnosis of Infectious Diseases of the Spine.},
journal = {JOR spine},
volume = {8},
number = {4},
pages = {e70134},
pmid = {41306993},
issn = {2572-1143},
abstract = {OBJECTIVE: To evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in infectious diseases of the spine (IDS).<br><br>METHODS: Systematic literature on the application of mNGS in the diagnosis of IDS was retrieved by two independent researchers from databases including Pubmed, China National Knowledge Infrastructure (CNKI), Wanfang, and VIP from the inception to 30 November 2024. Meta-analysis was conducted using Meta-Disc 1.4 and Stata 18.0 software.<br><br>RESULTS: The initial search identified 314 articles. After applying predefined inclusion and exclusion criteria, 15 studies were included, encompassing 1236 patients, of which 835 had confirmed IDS. Meta-analysis revealed that the pooled sensitivity and specificity of mNGS for IDS diagnosis were 0.95 (95% CI: 0.88-0.98) and 0.60 (95% CI: 0.48-0.71), respectively. The positive likelihood ratio was 2.3 (95% CI: 1.7-3.2), and the negative likelihood ratio was 0.09 (95% CI: 0.04-0.22). The pooled diagnostic odds ratio was 26 (95% CI: 9-75), with an area under the summary receiver operating characteristic curve of 0.85 (95% CI: 0.82-0.88).<br><br>CONCLUSION: The primary diagnostic value of mNGS lies in its ability to serve as a rapid screening tool for disease exclusion. However, for diagnosing IDS, it is essential to integrate other clinical indicators for a comprehensive assessment to confirm the diagnosis.},
}
@article {pmid41306730,
year = {2025},
author = {Nielsen, AB and Kvist-Hansen, A and Todberg, T and Zachariae, C and Pedersen, O and Skov, L},
title = {Dysbiosis of the Saliva Microbiota in Patients with Psoriasis: A Case-Control Study.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16315-16330},
pmid = {41306730},
issn = {1178-7031},
abstract = {PURPOSE: Accumulating evidence supports the association between altered salivary microbiota and inflammatory diseases. The existing literature on the salivary microbiota in patients with psoriasis is limited. However, differences in the prevalence of Candida species and abundance of several bacterial taxa in saliva have been found between patients and controls. This study aimed to investigate the differences in the composition and functional potential of salivary microbiota in patients with psoriasis compared to their cohabiting partners and healthy controls.<br><br>PATIENTS AND METHODS: Samples from 115 of 123 individuals qualified for statistical analysis: patients with psoriasis who did not receive systemic anti-psoriatic treatment (n=47); cohabiting partners (n=21); and age-, sex-, and BMI-matched healthy controls (n=47). One saliva sample was collected from each participant and analysed by shotgun metagenomic sequencing.<br><br>RESULTS: A difference in the &#x3b1;-diversity of bacterial species was observed exclusively between patients and controls, with a lower diversity in patients (p=0.041). Variation in bacterial composition (&#x3b2;-diversity) was influenced by smoking (p=0.001) and diet (p=0.025) but not by group status. Using a linear regression model adjusted for smoking and diet, we identified four bacterial classes and five species that were significantly different between the patient, partner, and control groups. One Kyoto Encyclopedia of Genes and Genomes module differed significantly between patients with psoriasis and their partners. No differences in Candida species or abundance were found among the three groups.<br><br>CONCLUSION: Comparison of salivary microbiota at the levels of bacterial diversity, composition, and predicted function indicated that psoriasis cases are characterised by dysbiosis.},
}
@article {pmid41306593,
year = {2025},
author = {Xu, H and Xu, Y and Gu, J and Wang, X and Liao, B and Zhou, P and Wu, S and Tao, R and Fu, Y},
title = {Clinical characteristics of Treponema denticola-associated lung abscess diagnosed by metagenomic next-generation sequencing: a case series analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688498},
pmid = {41306593},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Treponema denticola/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *Lung Abscess/microbiology/diagnosis/drug therapy ; Retrospective Studies ; Female ; Aged ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; *Treponemal Infections/diagnosis/microbiology/drug therapy ; Adult ; },
abstract = {INTRODUCTION: Treponema denticola is an oral anaerobic bacterium commonly associated with periodontitis, but its role in lower respiratory tract infections (e.g., lung abscess) has long been overlooked. For bacteria that grow anaerobically, traditional culture methods exhibit low detection rates, which directly lead to the mis-diagnosis of anaerobic infection. With the ultilization of metagenomic next-generation sequencing (mNGS) in clinical practice, we studied the clinical features and treatment strategies of T. denticola-associated lung abscess.<br><br>METHODS: A retrospective analysis was conducted on patients confirmed with T. denticola lung abscess by mNGS from October 2023 to October 2024. Routine aerobic bacterial culture and stains were used. Histopathological analysis and Warthin-Starry silver staining was completed on samples from lung tissue. A literature review was performed using PubMed and CNKI (up to June 2025).<br><br>RESULTS: Seven patients were diagnosed with T. denticola lung abscess under mNGS. The cohort predominantly comprised elderly males (mean age 62.3 years), all of whom had underlying oral diseases. Clinical manifestations featured chronic cough (mean symptom duration 3.6 months) and frequent hemoptysis (85.7%), with notably mild systemic inflammation (only one febrile case). Characteristic CT findings included mass-like lesions with necrosis (100%) and cavitation (71.4%), without air-fluid levels. Conventional cultures were overwhelmingly negative, whereas mNGS detected T. denticola in all seven cases. Among the seven patients, one showed clinical improvement after two months of amoxicillin-clavulanate therapy, and another responded well to seven months of doxycycline treatment. The remaining five patients initially treated with levofloxacin or moxifloxacin demonstrated poor responses, with three cases ultimately requiring surgical resection of the lesions.<br><br>DISCUSSION: T. denticola lung abscess is most commonly seen in individuals with poor oral hygiene. It presents as an indolent, chronic course and a high incidence of hemoptysis. Typical CT findings include a mass-like lesion with cavitation but no air-fluid level. Traditional microbiological detection often yield false negative results, making mNGS a critical diagnostic tool. First-line therapy should include &#x3b2;-lactams or tetracyclines, and surgery is warranted for refractory cases or massive hemoptysis.},
}
@article {pmid41306589,
year = {2025},
author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H},
title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1708266},
pmid = {41306589},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation &amp; purification ; *Murinae/microbiology ; },
abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.<br><br>METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.<br><br>RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.<br><br>CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.},
}
@article {pmid41306406,
year = {2025},
author = {Hongbin, W and Jing, X and Xianwei, W and Hui, G and Xutao, F},
title = {Successful Treatment of Escherichia coli-Related Spondylitis With an Extended Meropenem Infusion Time for a 72-Year-Old Woman: A Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71531},
pmid = {41306406},
issn = {2050-0904},
abstract = {Escherichia coli (E. coli) causes spinal infections relatively rarely and is often closely associated with parenteral infections. E. coli spondylitis can cause fever and local pain and, in severe cases, can lead to bone destruction, abscess formation, and even the risk of high paraplegia. Therefore, timely and precise diagnosis and effective treatment are crucial. We report successful conservative management of E. coli spondylitis in a 72-year-old female using metagenomic sequencing-guided prolonged meropenem infusion. Extending the infusion time of meropenem achieved clinical resolution without surgery, demonstrating this strategy's efficacy for carbapenem-sensitive spinal infections.},
}
@article {pmid41306274,
year = {2025},
author = {Xue, N and Xia, M and Hu, B and Gong, X and Wang, Z and Zhao, X},
title = {Factors influencing the spatial distributions of river microbial communities at the watershed scale: a case study involving the Wuding River Basin.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667966},
pmid = {41306274},
issn = {1664-302X},
abstract = {Microbial communities regulate water quality and biogeochemical cycling in rivers, but their responses to geomorphological factors remain unclear. Water samples were collected in August 2024 (summer wet season) from the Wuding River, and metagenomic sequencing was used to investigate microbial community changes and the influences of geomorphological factors. Environment (nutrients, etc.,) exhibited significant spatial heterogeneity with temperature (p < 0.01), total organic carbon (TOC, p < 0.001), dissolved organic carbon (DOC, p < 0.001), chemical oxygen demand (COD, p < 0.05), total phosphorus (TP, p < 0.001) and suspended solids (SS, p < 0.001), which were significantly higher downstream than upstream. Pseudomonadota, Cyanobacteriota, and Actinomycetota were the most important microbial phyla, and Cyanobacteriota (p = 0.016) was significantly more abundant upstream than downstream. The linear discriminant analysis effect size (LEfSe) revealed 8 and 10 biomarkers upstream and downstream, respectively. Upstream microbial communities were adapted to oligotrophic and high-light environments, whereas heterotrophic, carbon-metabolizing communities occurred downstream. Significantly higher ACE (p < 0.05), Chao1 (p < 0.05), Shannon (p < 0.001), and Pielou's evenness (p < 0.001) indices were observed downstream than upstream. The relative abundance of genes associated with carbon cycling (the methane metabolism pathway, TCA cycle, and rTCA cycle) was greater downstream than upstream, as was the relative abundance of nitrogen functional genes. Elevation affected the upstream microbial communities, whereas temperature, TP, TOC, and nitrate nitrogen (NO3-N) affected the downstream communities. The results improve our understanding of how geomorphology drives the environmental factors and then governs the microbial community and their carbon and nitrogen cycling pathways.},
}
@article {pmid41306264,
year = {2025},
author = {Shi, Y and Wang, X and Mao, X and Mi, L and Liu, W and Wang, N},
title = {Severe mitral valve papillary muscle rupture of isolated Whipple's endocarditis: a case report and review of the literature.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1669997},
pmid = {41306264},
issn = {2297-055X},
abstract = {BACKGROUND: Tropheryma whipplei endocarditis (TWE) is rarely reported. Diagnosis is particularly challenging when it occurs as isolated TWE without classical manifestations of Whipple's disease.<br><br>CASE PRESENTATION: A 35-year-old Asian female with systemic lupus erythematosus presented with acute heart failure secondary to mitral valve papillary muscle rupture as her sole symptom, requiring emergent veno-arterial extracorporeal membrane oxygenation support and urgent valve replacement. Intraoperative absence of vegetations and negative conventional microbiological examination preliminarily ruled out infective endocarditis. However, on postoperative day (POD) 3, her condition rapidly deteriorated into septic shock. Follow-up chest CT revealed bilateral asymmetric pulmonary infiltrates inconsistent with cardiogenic pulmonary edema alone. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected T. whipplei, providing a crucial diagnostic breakthrough. Subsequent periodic acid-Schiff staining of the resected valve confirmed the definitive diagnosis of isolated TWE. Targeted meropenem therapy for 5 days resulted in significant improvement in both pneumonia and septic shock, permitting ECMO discontinuation. The patient was successfully extubated by POD 12 and discharged on POD 22 with oral co-trimoxazole and doxycycline in a stable condition.<br><br>CONCLUSION: We present the first case of isolated TWE in a young Asian female, notable for its atypical clinical presentation, fulminant progression, and profound diagnostic challenges. Clinicians should maintain a high vigilance for blood culture-negative endocarditis. Timely diagnosis and appropriate treatment are crucial for improving prognosis. mNGS analysis of samples from suspected disseminated sites may yield crucial diagnostic breakthrough.},
}
@article {pmid41305954,
year = {2025},
author = {Osei Sekyere, J},
title = {Next-Generation Sequencing in Infectious-Disease Diagnostics: Economic, Regulatory, and Clinical Pathways to Adoption.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70104},
doi = {10.1002/mbo3.70104},
pmid = {41305954},
issn = {2045-8827},
support = {//The author received no specific funding for this study./ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/economics/methods ; *Communicable Diseases/diagnosis ; *Molecular Diagnostic Techniques/economics/methods ; Whole Genome Sequencing/economics/methods ; Polymerase Chain Reaction/economics/methods ; },
abstract = {Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well-established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS-based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole-genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent-only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130-600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near-term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious-disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype-phenotype limits while leveraging multiplexing and centralized reference workflows.},
}
@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}
@article {pmid41305529,
year = {2025},
author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W},
title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111508},
pmid = {41305529},
issn = {1999-4915},
support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; },
abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.},
}
@article {pmid41305512,
year = {2025},
author = {Storms, S and Lim, A and Savard, C and Olivera, YR and Kayastha, S and Wang, L},
title = {Identification of Hunnivirus in Bovine and Caprine Samples in North America.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111491},
pmid = {41305512},
issn = {1999-4915},
support = {1U18FD006673//Food and Drug Administration Veterinary Laboratory Investigation and Response Network/ ; },
mesh = {Animals ; Cattle ; Goats/virology ; Phylogeny ; Feces/virology ; Genome, Viral ; *Cattle Diseases/virology ; North America/epidemiology ; *Goat Diseases/virology ; High-Throughput Nucleotide Sequencing ; *Diarrhea/veterinary/virology ; Sheep ; Metagenomics ; },
abstract = {Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D[pol] RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D[po] region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants.},
}
@article {pmid41305373,
year = {2025},
author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH},
title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111136},
pmid = {41305373},
issn = {2076-0817},
support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; },
abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.},
}
@article {pmid41304932,
year = {2025},
author = {Hasan, GM and Mohammad, T and Shamsi, A and Sohal, SS and Hassan, MI},
title = {Applications of Genome Sequencing in Infectious Diseases: From Pathogen Identification to Precision Medicine.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/ph18111687},
pmid = {41304932},
issn = {1424-8247},
support = {PSAU/2025/RV/7//Prince Sattam Bin Abdulaziz University/ ; },
abstract = {Background: Genome sequencing is transforming infectious-disease diagnostics, surveillance, and precision therapy by enabling rapid, high-resolution pathogen identification, transmission tracking, and genomic-informed antimicrobial stewardship. Methods: We review contemporary sequencing platforms (short- and long-read), targeted and metagenomic approaches, and operational workflows that connect laboratory outputs to clinical and public health decision-making. We highlight strengths and limitations of genomic AMR prediction, the role of plasmids and mobile elements in resistance and virulence, and practical steps for clinical translation, including validation, reporting standards, and integration with electronic health records. Results: Comparative and population genomics reveal virulence determinants and host-pathogen interactions that correlate with clinical outcomes, improving risk stratification for high-risk infections. Integrating sequencing with epidemiological and clinical metadata enhances surveillance, uncovers cryptic transmission pathways, and supports infection control policies. Despite these advances, clinical implementation faces technical and interpretative barriers, as well as challenges related to turnaround time, data quality, bioinformatic complexity, cost, and ethical considerations. These issues must be addressed to realize routine, point-of-care sequencing. Conclusions: Emerging solutions, including portable sequencing devices, standardized pipelines, and machine-learning models, promise faster, more actionable results and tighter integration with electronic health records. The widespread adoption of sequencing in clinical workflows has the potential to shift infectious disease management toward precision medicine, thereby improving diagnostics, treatment selection, and public health responses.},
}
@article {pmid41304632,
year = {2025},
author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z},
title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223480},
pmid = {41304632},
issn = {2223-7747},
support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; },
abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.},
}
@article {pmid41304493,
year = {2025},
author = {Sun, H and Li, J and Zhuang, L and Zhang, Y and Zhou, Z and Sun, J and Wang, D and Ren, Y and Xu, X and He, J and Xue, Y},
title = {Ultrasonic Cavitation Transforms Organic Matter to Achieve Reduction of Excess Sludge and Recycling of Carbon Sources.},
journal = {Toxics},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/toxics13110941},
pmid = {41304493},
issn = {2305-6304},
support = {BK20240983//Natural Science Foundation of Jiangsu Province/ ; 52500021//National Natural Science Foundation of China/ ; SJCX24_1645//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Reducing the generation of excess sludge and achieving resource recovery are crucial for enhancing the economic efficiency and environmental sustainability of wastewater treatment plants (WWTPs). This study utilizes ultrasonic cavitation technology to transform organic matter into excess sludge to achieve sludge reduction and carbon source recovery. To this end, we systematically investigated the effects of various ultrasonic cavitation conditions on sludge reduction, organic matter conversion, and denitrification efficiency. The results showed that the optimal sludge reduction effect occurs at an original mixed liquid suspended solids (MLSS) of 10 g/L, under neutral and non-aerated conditions, reaching 15.07%. Ultrasonic cavitation treatment significantly enhanced the conversion efficiency of organic matter in the sludge, greatly increasing the concentration of organic matter in the supernatant, with soluble chemical oxygen demand (SCOD) maintained around 900 mg/L, thereby significantly improving the denitrification process. Furthermore, through magnetic-nanoparticle mediated isolation (MMI) and metagenomic sequencing analysis, the dominant denitrifying bacteria and their functional genes that utilize organic matter in the supernatant of ultrasonically treated sludge as a carbon source were identified. Finally, long-term pilot-scale operations further validated the practical application potential of ultrasonic cavitation technology for excess sludge reduction and resource utilization.},
}
@article {pmid41304327,
year = {2025},
author = {Li, X and Ma, X and Wu, L and Mo, Z and Chen, Z and Zhang, R and Xing, M},
title = {Metagenomic Analysis of Gut Microbiota Structure and Function in Adults with Subclinical Hypothyroidism: A Cross-Sectional Study in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112643},
pmid = {41304327},
issn = {2076-2607},
support = {2025JK158//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK151//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025KY758//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 2024KY910//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 25TJYX05//Research Project of Zhejiang Provincial Bureau of Statistics/ ; 2025ZL254//Zhejiang Province Traditional Chinese Medicine Science and Technology Plan Project/ ; 2023-B-04//Zhejiang CDC Science and Technology Talent Incubation Project/ ; },
abstract = {Subclinical hypothyroidism (SCH) is a condition characterized by thyroid hormone dysregulation, often associated with subtle clinical symptoms and metabolic disturbances. Emerging evidence suggests that the gut microbiota plays a crucial role in modulating thyroid function, but the microbiota-thyroid axis in SCH remains poorly understood. This study systematically investigates the gut microbiota composition, functional characteristics, and their correlation with thyroid hormone profiles in SCH patients. Using metagenomic sequencing and thyroid function assessments, we identified significant alterations in the gut microbiota of SCH patients, including a depletion of beneficial microbes such as Blautia and Bifidobacterium, and an enrichment of opportunistic pathogens like Bacteroides and Escherichia. Notably, Blautia depletion was negatively correlated with TSH levels, while Bacteroides abundance positively correlated with TSH levels, further highlighting the role of gut microbiota in thyroid dysfunction. Moreover, functional gene analysis revealed significant alterations in microbial metabolic pathways, with key pathways demonstrating correlations with thyroid hormone levels (free triiodothyronine (FT3) and triiodothyronine (T3)). Our findings suggest that gut microbial dysbiosis is closely associated with SCH. The study provides novel insights into the gut-thyroid axis and its role in SCH, offering new targets for early diagnosis, risk stratification, and intervention strategies in thyroid diseases.},
}
@article {pmid41304325,
year = {2025},
author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV},
title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112641},
pmid = {41304325},
issn = {2076-2607},
support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.},
}
@article {pmid41304316,
year = {2025},
author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG},
title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112632},
pmid = {41304316},
issn = {2076-2607},
abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.},
}
@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}
@article {pmid41304302,
year = {2025},
author = {Xiao, H and Jing, Y and Ma, K and Wang, Y and Xu, C and Yu, X},
title = {Spring Rest-Grazing Time Influenced Soil Phosphorus Fractions by Altering the Abundance of Genes Involved in Phosphorus Cycling in a Subalpine Meadow.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112618},
pmid = {41304302},
issn = {2076-2607},
support = {GAU-KYQD-2021-01//Scientific Research Start-up Funds for Openly-recruited Doctors, China/ ; GSAU-DKZY-2025-004//China Agricultural University Collaborative Research Support Fund, China/ ; 32460356, 32301509//National Natural Science Foundation of China/ ; },
abstract = {Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but its effects on soil P availability and the microbial processes driving P transformation remain poorly understood. To address this, a long-term field experiment was conducted with five different spring rest-grazing periods, where soil P fractions were examined and metagenomic sequencing was employed to assess the functional profiles of microbial genes involved in P cycling. Early spring rest-grazing led to higher concentrations of labile P fractions (Resin-P and NaHCO3-Pi), indicating improved soil P availability. Moreover, rest-grazing in early spring significantly reduced HCl-Pi concentration while increased the concentration of conc. HCl-Po. Metagenomic analysis revealed that early spring rest-grazing may have contributed to a higher relative abundance of the organic P mineralization gene phnA but decreasing the relative abundance of inorganic P solubilization genes ppa, and P-uptake and transport gene pstB. The dominant microbial genera involved in P cycling were Rhodopseudomonas and Mesorhizobium. Soil temperature and water infiltration rate, both affected by early rest-grazing, were identified as the main environmental variables correlated with P-cycling functional gene composition. These influenced taxa with functional genes involving organic P mineralization, inorganic P solubilization, and P-uptake and transport, which may associate with enhancing soil labile P. This study provides insights into potential microbial processes under grazing management in grassland ecosystems.},
}
@article {pmid41304301,
year = {2025},
author = {Martinez, A and St-Pierre, B},
title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112617},
pmid = {41304301},
issn = {2076-2607},
support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; },
abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.},
}
@article {pmid41304286,
year = {2025},
author = {Wu, Y and Liu, C and Qiu, Q and Zhao, X},
title = {Xylo-Oligosaccharide Production from Wheat Straw Xylan Catalyzed by a Thermotolerant Xylanase from Rumen Metagenome and Assessment of Their Probiotic Properties.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112602},
pmid = {41304286},
issn = {2076-2607},
support = {20224ACB205007, 20242BAB20309, 20252BAC240121//Natural Science Foundation of Jiangxi Province/ ; 20252ZDF030003//Central Leading Local Science and Technology Development Special Project/ ; 2024H-100160//Ji'an Municipal Science and Technology Plan Project/ ; },
abstract = {A novel xylanase gene (RuXyn854) was identified from the rumen metagenome and was heterologously expressed in Escherichia coli to produce xylo-oligosaccharides (XOSs) as a prebiotic in this study. RuXyn854, a member of glycosyl hydrolase family 10, demonstrated peak enzymatic activity at pH 7.0 and 50 °C. RuXyn854 retains more than 50% of its activity after treatment at 100 °C for 10 min, highlighting the enzyme's excellent heat resistance. RuXyn854 showed a preferential hydrolyzation of xylan, especially rice straw xylan. RuXyn854 activity was significantly increased in the presence of 15 mM Mn[2+], 0.25% Tween-20, and 0.25% Triton X-100 (125%, 20%, and 26%, respectively). The reaction temperature (30, 40, and 50 °C), dosage (0.20, 0.27, and 0.34 U), and time (90, 120, and 150 min) of RuXyn854 affected the XOS yield and composition, with a higher yield at 0.27 U, 50 °C, and 120-150 min. Xylobiose, xylotriose, and xylotetraose were characterized as the predominant XOS products resulting from the enzymatic hydrolysis of wheat straw xylan by RuXyn854, with xylose present at a mere 0.49% of the total yield. The prebiotic potential of XOSs was assessed through in vitro fermentation with established probiotic strains of Bifidobacterium bifidum and Lactobacillus brevis. The results showed that, regardless of incubation time, XOSs stimulated the growth and xylanolytic enzyme secretion of the two probiotics compared to the controls. These results demonstrate that the feature of RuXyn854 to withstand temperatures up to 100 °C is impressive, and its ability to hydrolyze wheat xylan into XOSs promotes the growth of probiotics.},
}
@article {pmid41304279,
year = {2025},
author = {Zhou, M and Li, Q and Han, Y and Wang, Q and Yang, H and Li, H and Hu, C},
title = {Sulfur Cycling and Life Strategies in Successional Biocrusts Link to Biomass Carbon in Dryland Ecosystems.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112594},
pmid = {41304279},
issn = {2076-2607},
support = {32370125//National Natural Science Foundation of China/ ; 41877419//National Natural Science Foundation of China/ ; 41877339//National Natural Science Foundation of China/ ; XDA17010502//Strategic Priority Research Program at the Chinese Academy of Science/ ; },
abstract = {Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin-Benson-Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks.},
}
@article {pmid41304278,
year = {2025},
author = {Qiao, T and Zhu, Z},
title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112595},
pmid = {41304278},
issn = {2076-2607},
support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.},
}
@article {pmid41304274,
year = {2025},
author = {Li, J and Hou, L and Liu, Y and Sun, Y and Li, Y and He, B and Tu, C and Zhou, X},
title = {Metagenomic Sequencing Reveals the Viral Diversity of Bactrian Camels in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112589},
pmid = {41304274},
issn = {2076-2607},
support = {32130104//National Natural Science Foundation of China/ ; 32460902//National Natural Science Foundation of China/ ; 2021GKLRLX10//Ningxia Hui Autonomous Region Science and Technology Innovation Leading Talents Cultivation Project/ ; Ning Ren She Han [2024] No. 106//Ningxia Hui Autonomous Region Young Top-notch Talents Cultivation Project/ ; },
abstract = {The Bactrian camel is a key economic livestock species in China and around the world. It yields meat and milk (high-quality functional foods), and the milk reports health benefits. Dromedary camels, as intermediate hosts of MERS-CoV, have garnered significant public health attention. In contrast, viral surveillance in Bactrian camels from the same genus as dromedaries has received limited attention, with only sporadic or regionally confined reports available. Systematic investigations into the virome of viral species, viral diversity, and novel viruses in Bactrian camels are lacking. In this study, swabs were collected from 701 Bactrian camels in China. Through metagenomics, 3262 viral contigs were classified into 16 viral phyla, 29 viral families, and an unclassified group. The different landforms were found to influence viral diversity and composition in Bactrian camels, with mountainous area exerting the greatest impact. The viral composition significantly differed between captive and free-ranging camels. The study identified at least 12 viruses with zoonotic potential, and phylogenetic analysis indicated cross-species transmission in some of them. Additionally, picornavirus, circular Rep-encoding single-stranded (CRESS) DNA virus, and polyomavirus from Bactrian camels may represent novel species or genotypes. To summarize, in this study, we described the baseline virome profile of Chinese Bactrian camels, investigated the ecological factors influencing the viral distribution of Bactrian camels, identified key potential viral risks, and provided a scientific basis for the prevention, control, and early warning of critical viral diseases in Bactrian camels from China.},
}
@article {pmid41304268,
year = {2025},
author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK},
title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112582},
pmid = {41304268},
issn = {2076-2607},
abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.},
}
@article {pmid41304199,
year = {2025},
author = {Zhang, J and Jiang, F and Li, X and Song, P and Zhang, T},
title = {Metagenome-Based Functional Differentiation of Gut Microbiota and Ecological Adaptation Among Geographically Distinct Populations of Przewalski's Gazelle (Procapra przewalskii).},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112513},
pmid = {41304199},
issn = {2076-2607},
support = {QHEG-2024-04//the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Univer-sity/ ; 2024T170992//the China Postdoctoral Science Foundation/ ; },
abstract = {Przewalski's gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai-Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski's gazelle exhibits a complex spatially structured functional differentiation, reflecting host-microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.},
}
@article {pmid41304195,
year = {2025},
author = {Wen, L and Luo, H and Li, C and Cheng, K and Shi, L and Liu, L and Wang, K and Tang, H},
title = {Substituting Chemical by Organic Fertilizer Improves Soil Quality, Regulates the Soil Microbiota and Increases Yields in Camellia oleifera.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112509},
pmid = {41304195},
issn = {2076-2607},
support = {U21A20187//National Natural Science Foundation of China/ ; 2022tfs201//Director Fund of Hunan Soil and Fertilizer Institute/ ; XDA0440404//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
abstract = {The partial substitution of chemical fertilizer with organic fertilizer has been regarded as an effective strategy for enhancing crop yield and soil quality. Nevertheless, its effects on soil properties and microbes remain contentious. In this study, we examined the effects of four different fertilization strategies (including without fertilizer (CK), 100% chemical fertilizer (NPK), 30% organic fertilizer + 70% chemical fertilizer (LOM) and 60% organic fertilizer + 40% chemical fertilizer (HOM)) on soil nutrients and microbial communities through metagenomic sequencing in a Camellia oleifera field experiment. Compared to CK and NPK, HOM significantly increased SOC, TN, TP, AK and AN contents. The substitution of organic fertilizer notably increased Camellia oleifera yield, with the highest increase of 93.35% observed in HOM relative to NPK. Soil bacterial and fungal communities responded inconsistently to fertilization patterns. Bacteria predominated as the main soil microorganisms, and higher rates of organic fertilizer substitution facilitated a shift from bacterial to fungal communities. Organic fertilizer substitution significantly increased soil bacteria diversity and fungal richness, particularly in the HOM. Soil bacterial community structure was more sensitive to fertilization regimes than soil fungi. High rates of organic fertilizer substitution substantially suppressed oligotrophic and increased copiotrophic bacterial communities. Mucoromycota emerged as the dominant fungal group, with a considerable increment in HOM soils. SOC and TN were the main factors affecting Camellia oleifera yield and shaping soil bacteria and fungal diversity and composition. This study provided crucial insights into the ecological implications of organic fertilizer application and the potential of managing soil microorganisms for sustainable Camellia oleifera productivity.},
}
@article {pmid41304167,
year = {2025},
author = {Vitezić, BM and Franović, B and Renko, I and Kuiš, D and Begić, G and Blašković, M and Gabrić, D and Nikolić, M and Vranić, T&#x160; and Veljanovska, D and Cvijanović Peloza, O},
title = {Microbiome Profiling of Biofilms Formed on d-PTFE Membranes Used in Guided Bone Regeneration.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112478},
pmid = {41304167},
issn = {2076-2607},
support = {2170-137-08-24-19//UNIRI-biomed/ ; IP-2020-02-7875//the Croatian Science Foundation/ ; },
abstract = {In guided bone regeneration (GBR) procedures, d-PTFE membranes are often used as a barrier to promote alveolar ridge regeneration. The aim of this randomized clinical trial was to examine the microbial diversity and structure of biofilms on two types of d-PTFE membranes, Permamem[®] and Cytoplast™, over four-week oral cavity exposure periods. Bacterial biofilm analysis was performed using 16S rRNA next-generation sequencing (NGS) on 36 samples (20 Permamem[®] and 16 Cytoplast™). The results showed significant differences in the microbial profiles: Cytoplast™ membranes showed reduced microbial diversity and an enhanced proportion of pathobionts like Selenomonas, Segatella, Fusobacterium and Parvimonas, which are associated with periodontal and peri-implant diseases and alveolar bone loss. Permamem[®] membranes promoted colonization by bacteria associated with healthy oral conditions, such as the genera Streptococcus, Kingella and Corynebacterium. Overall, our results showed that Cytoplast™ membranes generate a specific type of biofilm, leading to reduction in health-related bacterial species and facilitating growth conditions for dysbiosis shift. Further research and patient follow-ups are essential to thoroughly evaluate the clinical implications of different d-PTFE membranes used in guided bone regeneration.},
}
@article {pmid41304165,
year = {2025},
author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P},
title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112480},
pmid = {41304165},
issn = {2076-2607},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; },
abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.},
}
@article {pmid41304105,
year = {2025},
author = {Zhong, Y and Wu, C and Yao, Z and Li, X and Chi, H and Wu, T and Du, X},
title = {Metagenomic Analysis of Distribution Characteristics and Driving Mechanisms of Antibiotic Resistance Genes, Virulence Factors, and Microbial Communities in Rice Seedling Cultivation Soils.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112419},
pmid = {41304105},
issn = {2076-2607},
abstract = {The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil's pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks.},
}
@article {pmid41302874,
year = {2025},
author = {Berlanga, M and Miñana-Galbis, D and Guerrero, R},
title = {Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111128},
pmid = {41302874},
issn = {2075-4450},
support = {project PID2021-123735OB-C22.//MCIN/ ; },
abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.},
}
@article {pmid41301629,
year = {2025},
author = {Wang, Y and Li, L and Liang, Y and Xu, K and Ye, Y and He, M},
title = {Phage Therapy for Acinetobacter baumannii Infections: A Review on Advances in Classification, Applications, and Translational Roadblocks.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111134},
pmid = {41301629},
issn = {2079-6382},
support = {82302568//National Natural Science Foundation of China/ ; 2308085QH283//Anhui Provincial National Science Foundation/ ; 2022xkjT012//Basic and Clinical Collaboration Enhancement Program Foundation of Anhui Medical University/ ; },
abstract = {The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe public health threat, driving growing interest in phage-based precision antibacterial strategies. This systematic review synthesizes recent advances in the field of A. baumannii phage. Modern taxonomy, based on whole-genome phylogeny, has reclassified the majority of A. baumannii phages into the class Caudoviricetes, revealing distinct evolutionary clades that correlate with host tropism and biological properties, superseding the traditional morphological families (Myoviridae, Siphoviridae, Podoviridae). To overcome limitations of natural phage therapy, such as narrow host range, cocktail therapies (ex vivo resistance mutation rates < 5%) and phage-antibiotic synergism (enabling antibiotic efficacy at 1/4 minimum inhibitory concentration) have significantly enhanced antibacterial efficacy. Preclinical models demonstrate that phage therapy efficiently clears pathogens in pneumonia models and promotes the healing of burn wounds and diabetic ulcers via immunomodulatory mechanisms. Technical optimizations include nebulized inhalation delivery achieving 42% alveolar deposition, and thermosensitive hydrogels enabling sustained release over 72 h. Genetic engineering approaches, such as host range expansion through tail fiber recombination and CRISPR/Cas-mediated elimination of lysogeny, show promise. However, the genetic stability of engineered phages requires further validation. Current challenges remain, including limited host spectrum, the absence of clinical translation standards, and lagging regulatory frameworks. Future efforts must integrate metagenomic mining and synthetic biology strategies to establish a precision medicine framework encompassing resistance monitoring and personalized phage formulation, offering innovative solutions against CRAB infections.},
}
@article {pmid41301609,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Otto, SJG and Chai, Z and Lacoste, S and McCarthy, EL and Links, MG and Herman, EK and Stothard, P and Gow, SP and Campbell, JR and Waldner, CL},
title = {Evaluating the Diagnostic Performance of Long-Read Metagenomic Sequencing Compared to Culture and Antimicrobial Susceptibility Testing for Detection of Bovine Respiratory Bacteria and Indicators of Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111114},
pmid = {41301609},
issn = {2079-6382},
support = {Not applicable//Genome Prairie/ ; Not applicable//Genome Canada/ ; Not applicable//Genome Alberta/ ; Not applicable//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can detect bacteria and antimicrobial resistance genes (ARGs) from bovine respiratory samples, providing an alternative to culture and antimicrobial susceptibility testing (C/S). This study applied Bayesian latent class models (BLCMs) to estimate the sensitivity (Se) and specificity (Sp) of long-read metagenomic sequencing compared to C/S for detecting Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, as well as associated macrolide and tetracycline resistance potential. Methods: Deep nasopharyngeal swabs were collected from fall-placed feedlot calves at arrival, 13, and 36 days on feed across two years and two metaphylaxis protocols. Samples underwent C/S and long-read metagenomic sequencing. BLCMs were used to estimate Se and Sp for the detection of bacteria and potential for antimicrobial resistance (AMR). Results: Se and Sp for detecting respiratory bacteria by metagenomics were not significantly different than culture, with four exceptions. For the 2020 samples, Se for M. haemolytica was lower than culture, and Sp for H. somni was lower, while in both 2020 and 2021 samples, Se for P. multocida was higher for metagenomics than culture. The estimated Se and Sp of metagenomics for the detection of msrE-mphE, EstT, and tet(H) within bacterial reads were either not significantly different or were lower than AST, with Sp > 95% with one exception. Conclusions: This study provided BLCM-based estimates of clinical Se and Sp of metagenomics and C/S without assuming a gold standard in a large pen research setting. These findings demonstrate the potential of long-read metagenomics to support bovine respiratory disease diagnostics, AMR surveillance, and antimicrobial stewardship in feedlot cattle.},
}
@article {pmid41301606,
year = {2025},
author = {Aguilar-Rangel, EJ and Paredes-Cárcamo, F and Andrade, MD and Contreras-Sánchez, D and Rain-Medina, V and Campanini-Salinas, J and Medina, DA},
title = {Hospital Wastewater as a Reservoir of Contaminants of Emerging Concern: A Study Report from South America, Chile.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111111},
pmid = {41301606},
issn = {2079-6382},
support = {Proyectos Colaborativos 2024 #3557//San Sebasti&#xe1;n University/ ; Fondecyt Iniciaci&#xf3;n #11230295//Agencia Nacional de Investigaci&#xf3;n y Desarrollo de Chile/ ; },
abstract = {Background/Objectives: Hospital wastewater is a complex effluent containing a wide range of biological and chemical contaminants, including pharmaceuticals, pathogens, and antimicrobial resistance determinants. These discharges pose a growing threat to aquatic ecosystems and public health, particularly in regions where wastewater treatment is insufficient. This study aimed to characterize the chemical and microbiological composition of untreated effluent from a tertiary care hospital in southern Chile, focusing on contaminants of emerging concern. Methods: Wastewater samples were collected at the hospital outlet before any treatment. The presence of two commonly used pharmaceutical compounds, paracetamol and amoxicillin, was quantified using high-performance liquid chromatography (HPLC). Bacterial isolation was performed using selective media, and antibiotic susceptibility testing was conducted via the disk diffusion method following CLSI guidelines. In addition, metagenomic DNA was extracted and sequenced to assess microbial community composition and functional gene content, focusing on the identification of resistance genes and potential pathogens. Results: A total of 42 bacterial isolates were recovered, including genera with known pathogenic potential such as Aeromonas, Klebsiella, and Enterococcus. Antibiotic susceptibility tests revealed a high prevalence of multidrug-resistant strains. Metagenomic analysis identified the dominance of Bacillota and Bacteroidota, together with 56 antimicrobial-resistance gene (ARG) families and 38 virulence-factor families. Functional gene analysis indicated the presence of efflux-pump systems, β-lactamases, and mobile genetic elements, suggesting that untreated hospital effluents serve as potential sources of resistance and virulence determinants entering the environment. Paracetamol was detected in all samples, with an average concentration of 277.4 ± 10.7 µg/L; amoxicillin was not detected, likely due to its instability and rapid degradation in the wastewater matrix. Conclusions: These findings highlight the complex microbiological and chemical burden of untreated hospital wastewater and reinforce the need for continuous monitoring and improved treatment strategies to mitigate environmental dissemination of antibiotic resistance.},
}
@article {pmid41301593,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Lacoste, SR and Chai, Z and Herman, EK and McCarthy, EL and Campbell, JR and Gow, SP and Stothard, P and Links, MG and Otto, SJG and Waldner, CL},
title = {Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111098},
pmid = {41301593},
issn = {2079-6382},
support = {NA//Genome Canada/ ; NA//Genome Prairie/ ; NA//Genome Alberta/ ; NA//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves sampled in the early feeding period were associated with subsequent bovine respiratory disease (BRD) treatment and phenotypic antimicrobial resistance (AMR) at treatment. Methods: Deep nasopharyngeal swabs (DNPSs) obtained at arrival processing (1 day on feed; DOF), 13 DOF, and the time of BRD treatment were cultured and subjected to antimicrobial susceptibility testing (AST) and long-read metagenomic sequencing. Analyses focused on macrolide (mphE-msrE, EstT) and tetracycline (tet(H)) ARGs within reads assigned to Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Bibersteinia trehalosi. Generalized estimating equations assessed associations between metagenomic results from 1 and 13 DOF and subsequent BRD treatment risk and AST outcomes at treatment, at both the individual animal (calf) and pen levels. Results: Calf-level detection of H. somni at 13 DOF was associated with a greater BRD treatment risk between 14 and 45 DOF. An increased pen prevalence of either M. haemolytica or P. multocida at 13 DOF was associated with a greater BRD treatment risk from 14 to 45 DOF. At 13 DOF, detections of mphE-msrE, EstT, or tet(H) in target bacteria were associated with corresponding phenotypic AMR at BRD treatment. Similarly, a higher pen-level prevalence of mphE-msrE or EstT at 13 DOF was also associated with increased macrolide resistance at BRD treatment. Conclusions: The results from long-read metagenomic sequencing of DNPSs collected at 13 DOF were associated with both BRD risk and AMR at treatment. These findings align with prior culture-based results and support the potential utility of pen-level metagenomic testing for AMR surveillance and informing antimicrobial selection in feedlots.},
}
@article {pmid41301447,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining Thermophile Photosynthesis Genes: A Synthetic Operon Expressing Chloroflexota Species Reaction Center Genes in Rhodobacter sphaeroides.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111529},
pmid = {41301447},
issn = {2218-273X},
support = {DE-AC02-05CH11231//United States Department of Energy/ ; DE-AC02-05CH11231//United States Department of Energy/ ; RGPIN 2018-03898//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 2025-04928//Natural Sciences and Engineering Research Council of Canada/ ; 3-1/PDFP/HEC/2022(B-3)/2339/02//Higher Education Commission/ ; },
mesh = {*Rhodobacter sphaeroides/genetics/metabolism ; *Operon ; *Photosynthesis/genetics ; *Photosynthetic Reaction Center Complex Proteins/genetics/metabolism ; *Chloroflexi/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and is therefore the most important bioenergetic process on earth. The greatest diversity of photosynthetic systems is found in microorganisms. However, our understanding of the biophysical and biochemical processes that transduce light into chemical energy is derived from a relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of predicted proteins that catalyze the initial photochemical reactions deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for the expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90 °C) springs available through the JGI IMG database, to generate a resource of diverse sequences that are potentially adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}
@article {pmid41301445,
year = {2025},
author = {Zhang, J and Xu, G and Yi, Z and Tang, X},
title = {Efficient Mining and Characterization of Two Novel Keratinases from Metagenomic Database.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111527},
pmid = {41301445},
issn = {2218-273X},
support = {2024YFC2815900//National Key R\&amp;D Program of China/ ; SOA: 2017002//Scientific Research Foundation of Third Institute of Oceanography/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; 2021J02015//Fujian Provincial Natural Science Foundation of China/ ; },
mesh = {*Peptide Hydrolases/genetics/metabolism/chemistry ; Phylogeny ; Keratins/metabolism ; Animals ; Enzyme Stability ; *Metagenomics ; Data Mining ; *Metagenome ; Feathers ; Kinetics ; Substrate Specificity ; Amino Acid Sequence ; Databases, Genetic ; },
abstract = {Keratin is a fibrous structural protein found in various natural materials such as hair, feathers, and nails. Its high stability and cross-linked structure make it resistant to degradation by common proteases, leading to the accumulation of keratinous waste in various industries. In this study, we developed and validated an effective bioinformatics-driven strategy for mining novel keratinase genes from the Esmatlas (ESM Metagenomic Atlas) macrogenomic database. Two candidate genes, ker820 and ker907, were identified through sequence alignment, structural modeling, and phylogenetic analysis, and were subsequently heterologously expressed in Escherichia coli Rosetta (DE3) with the assistance of a solubility-enhancing chaperone system. Both enzymes belong to the Peptidase S8 family. Enzymatic characterization revealed that GST-tagged ker820 and ker907 exhibited strong keratinolytic activity, with optimal conditions at pH 9.0 and temperatures of 60 °C and 50 °C, respectively. Both enzymes showed significant degradation of feather and cat-hair keratin. Kinetic analysis showed favorable catalytic parameters, including Km values of 9.81 mg/mL (ker820) and 5.25 mg/mL (ker907), and Vmax values of 120.99 U/mg (ker820) and 89.52 U/mg (ker907). Stability tests indicated that GST-ker820 retained 70% activity at 60 °C for 120 min, while both enzymes remained stable at 4 °C for up to 10 days. These results demonstrate the high catalytic capacity, thermal stability, and substrate specificity of the enzymes, supporting their classification as active keratinases. This study introduces a promising strategy for efficiently discovering novel functional enzymes using an integrated computational and experimental approach. Beyond keratinases, this methodology could be extended to screen for enzymes with potential applications in environmental remediation.},
}
@article {pmid41301179,
year = {2025},
author = {Liu, D and Kuo, J and Lin, CH},
title = {Computational Investigation of Smooth Muscle Cell Plasticity in Atherosclerosis and Vascular Calcification: Insights from Differential Gene Expression Analysis of Microarray Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111223},
pmid = {41301179},
issn = {2306-5354},
abstract = {The dedifferentiation of smooth muscle cells (SMCs) is the main cause of atherosclerosis and vascular calcification. This study integrated the gene expression data of multiple microarrays to identify relevant marker molecules. A total of 72 Gene Expression Omnibus (GEO) samples (GSM) were collected from 10 gene expression data series (GSE) and divided into five groups: non-SMC, SMC, atherosclerotic SMC (SMC-ath), calcified SMC (SMC-calc), and treated SMC (SMC-t). The SMC-t group included synthetic SMCs that had undergone treatment to inhibit proliferation, migration, or inflammation. The gene expression data were merged, normalized, and batch effects were removed before differential gene expression (DGE) analysis was performed via linear models for microarray data (limma) and statistical analysis of metagenomic profiles (STAMPs). The genes with expressions that significantly differed were subsequently subjected to protein-protein interaction (PPI) and functional prediction analyses. In addition, the random forest method was used for classification. Twelve proteins that may be marker molecules for SMC differentiation and dedifferentiation were identified, namely, Proprotein convertase subtilisin/kexin type 1 (PCSK1), Transforming growth factor beta-induced (TGFBI), Complement C1s (C1S), Phosphomannomutase 1 (PMM1), Claudin 7 (CLDN7), Calcium binding and coiled-coil domain 2 (CALCOCO2), SAC3 domain-containing protein 1 (SAC3D1), Natriuretic peptide B (NPPB), Monoamine oxidase A (MAOA), Regulator of the Cell Cycle (RGCC), Alpha-crystallin B Chain (CRYAB), and Alcohol dehydrogenase 1B (ADH1B). Finally, their possible roles in SMCs are discussed. This study highlights the feasibility of bioinformatics analysis for studying SMC dedifferentiation.},
}
@article {pmid41301089,
year = {2025},
author = {Ostos, I and Ruiz, I and Cruz, D and Flórez-Pardo, LM},
title = {Methane Concentration Prediction in Anaerobic Codigestion Using Multiple Linear Regression with Integrated Microbial and Operational Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111133},
pmid = {41301089},
issn = {2306-5354},
support = {No. DGI-01-2025//Direcci&#xf3;n General de Investigaciones of Universidad Santiago de Cali/ ; },
abstract = {Anaerobic codigestion of organic residues is a proven strategy for enhancing methane recovery. However, the complexity of microbial interactions and variability in operational conditions make it difficult to estimate methane concentration in real time, particularly in rural contexts. This study developed a multiple linear regression model to predict methane concentration using operational data and microbial community profiles derived from 16S rRNA gene sequencing. The system involved the codigestion of cassava by-product and pig manure in a two-phase anaerobic reactor. Predictor variables were selected through a hybrid approach combining statistical correlation with microbial functional relevance. The final model, trained on 70% of the dataset, demonstrated satisfactory generalization capability on the other 30 test set, achieving a coefficient of determination (R[2]) of 0.92 and a mean relative error (MRE) of 6.50%. Requiring only a limited set of inputs and minimal computational resources, the model offers a practical and accessible solution for estimating methane levels in decentralized systems. The integration of microbial community data represents a meaningful innovation, improving prediction by capturing biological variation not reflected in operational parameters alone. This approach can support local decision making and contribute to Sustainable Development Goal 7 by promoting reliable and affordable technologies for clean energy generation in rural and resource-constrained settings.},
}
@article {pmid41300910,
year = {2025},
author = {Jin, X and Shen, H and Zhou, P and Yang, J and Yang, S and Ni, H and Yu, Y and Zhang, Z},
title = {Research Progress on Sepsis Diagnosis and Monitoring Based on Omics Technologies: A Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/diagnostics15222887},
pmid = {41300910},
issn = {2075-4418},
support = {2023YFC3603104//China National Key Research and Development Program/ ; Nos. 82472243 and 82272180//National Natural Science Foundation of China/ ; LHDMD24H150001//Huadong Medicine Joint Funds of the Zhejiang Provincial Natural Science Foundation of China/ ; 2024C03240//the Key Research &amp; Development Project of Zhejiang Province/ ; No. GZY-ZJ-KJ-24082//a collaborative scientific project co-established by the Science and Technology Department of the National Administration of Traditional Chinese Medicine and the Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; No. 2024KY1099//the General Health Science and Technology Program of Zhejiang Province/ ; No. ZJDXLQCXZCJBGS2024016//the Project of Zhejiang University Longquan Innovation Center/ ; 320.6750.2024-23-07//Wu Jieping Medical Foundation Special Research Grant/ ; },
abstract = {Sepsis poses a significant global health burden, with millions of cases and high mortality rates annually, largely due to challenges in early diagnosis and monitoring. Traditional methods, reliant on nonspecific clinical manifestations and limited biomarkers like C-reactive protein and procalcitonin, often fail to distinguish infection from non-infectious inflammation or capture disease heterogeneity. This review synthesizes recent progress in omics technologies-genomics, transcriptomics, proteomics, and metabolomics-for advancing sepsis management. Genomics, via metagenomic next-generation sequencing, enables rapid pathogen identification and genetic variant analysis for susceptibility and prognosis. Transcriptomics reveals molecular subtypes and immune dynamics through RNA sequencing and single-cell approaches. Proteomics and metabolomics uncover protein and metabolite profiles linked to immune imbalance, organ damage, and metabolic disorders. Multi-omics integration, enhanced by artificial intelligence and machine learning, facilitates biomarker discovery, patient stratification, and predictive modeling, bridging laboratory findings to bedside applications like rapid diagnostic tools and clinical decision support systems. Despite advancements, challenges including data heterogeneity, high costs, and ethical concerns persist. Future directions emphasize single-cell and spatial omics, AI-driven personalization, and ethical frameworks to transform sepsis care from reactive to proactive, ultimately improving outcomes.},
}
@article {pmid41300336,
year = {2025},
author = {Liu, Y and Xie, J and He, Y and Shi, Q and Gong, Q and Zhao, W and Qin, C and Zhou, C},
title = {Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection.},
journal = {Biology},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biology14111546},
pmid = {41300336},
issn = {2079-7737},
support = {2023M732476//China Postdoctoral Science Foundation/ ; NJTCSC24-3//Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; 2023YFH0046//Sichuan Science and Technology Program/ ; },
abstract = {Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in P. pingi associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in P. pingi, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to I. multifiliis of P. pingi. Concurrently, skin microbiome analysis showed that P. pingi hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, P. pingi skin was significantly depleted of the parasitic bacteria Candidatus_Megaira and Candidatus_Midichloria, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that P. pingi's microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of P. pingi to I. multifiliis is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish.},
}
@article {pmid41300008,
year = {2025},
author = {Rajah Kumar, M and Amankwaa, AO and Razali, NS and Mohamad, NE and Khalid, M and Abdullah, JO and Masarudin, MJ and Osman, MA and Abd Rahman, NMAN and Alitheen, NB},
title = {Preliminary Evaluation of the Gut Microbiota Modulatory Potential of Malaysian Kefir Water in Ageing Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223851},
pmid = {41300008},
issn = {2304-8158},
support = {FRGS-777 MRSA/1/2018/SKK10/UPM/02/1//Fundamental Research Grant Scheme (FRGS) by the Malaysian Ministry of Higher Education (MoHE)/ ; },
abstract = {Ageing is often accompanied by gut microbiota alterations that contribute to dysbiosis-a recognised hallmark of ageing and a risk factor for neurodegenerative diseases. Probiotic interventions offer a promising approach to restore microbial homeostasis. This preliminary study explored the potential modulatory effects of Malaysian kefir water, a Lactobacillus-enriched fermented beverage with previously reported antioxidant and neuroprotective properties in D-galactose-induced ageing mice. Kefir water was administered as both a pre-treatment and co-treatment, and gut microbiota changes were assessed using 16S rRNA metagenomic sequencing of faecal samples. Alpha and beta diversity analyses showed a stable microbial diversity across treatments. However, preliminary descriptive trends suggested that kefir water may influence specific bacterial populations. Increases were observed in Muribaculaceae and Lactobacillaceae, along with apparent decreases in Lachnospiraceae and Prevotellaceae. Both kefir treatments tended to increase the abundance of Ligilactobacillus, with the co-treatment group appearing to restore the Firmicutes/Bacteroidota ratio toward control levels, while the pre-treatment group showed a tendency to further reduce this ratio. Collectively, these findings provide preliminary indications that kefir water may hold potential as a dietary approach to modulate gut microbial changes associated with ageing. However, confirmation through studies with larger sample sizes and broader analytical coverage is necessary to substantiate these initial observations.},
}
@article {pmid41299763,
year = {2025},
author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N},
title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02262-z},
pmid = {41299763},
issn = {2049-2618},
support = {Fondecyt 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; },
abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.<br><br>RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.<br><br>CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.},
}
@article {pmid41299634,
year = {2025},
author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V},
title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {241},
pmid = {41299634},
issn = {2049-2618},
support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; },
abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.<br><br>RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.<br><br>CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.},
}
@article {pmid41299624,
year = {2025},
author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W},
title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {242},
pmid = {41299624},
issn = {2049-2618},
support = {81825019//National Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.<br><br>RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.<br><br>CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.},
}
@article {pmid41299512,
year = {2025},
author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B},
title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.},
journal = {Reproductive biology and endocrinology : RB&amp;E},
volume = {23},
number = {1},
pages = {154},
pmid = {41299512},
issn = {1477-7827},
mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation &amp; purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.<br><br>METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n&#x2009;=&#x2009;15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n&#x2009;=&#x2009;13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.<br><br>RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p&#x2009;=&#x2009;0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.<br><br>CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.},
}
@article {pmid41299356,
year = {2025},
author = {Shen, A and Xu, X and Xu, L and Nie, X and Ai, J and Chen, W},
title = {Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-11814-5},
pmid = {41299356},
issn = {1471-2334},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) and multiple point-of-care testing (POCT) techniques have demonstrated significant potential in pathogen detection. However, neither technology fully meets all clinical diagnostic needs for pulmonary infections. This study aimed to evaluate the complementary detection performance and clinical applicability of POCT and mNGS in pulmonary infections, using conventional culture as a reference.<br><br>METHODS: This study enrolled forty-five patients with suspected lower respiratory tract infections for concurrent evaluation using POCT and mNGS. The detection performance of traditional culture methods, POCT, and mNGS was subsequently analyzed and compared.<br><br>RESULTS: Both molecular methods showed high positive detection rates, surpassing that of the culture method. When conventional culture was used as the gold standard, the sensitivity and positive predictive value (PPV) within the detection range of the PM Easy Lab Respiratory Panel (RP) were 97.1% and 80.5%, respectively, whereas for mNGS, these values were 90.2% and 92.5%, respectively. A comparison of the PM Easy Lab RP and mNGS results revealed that the PM Easy Lab was faster (100&#xa0;min vs. 24&#xa0;h) and more sensitive (88 vs. 63 pathogens) within its detection range, whereas mNGS offered a broader spectrum of pathogen detection. The overall consistency between PM Easy Lab RP and mNGS was 88.9%. Klebsiella pneumoniae and Acinetobacter baumannii were identified as the most prevalent bacterial infections by all three detection methods. Moreover, both PM Easy Lab RP and mNGS demonstrated enhanced capability over culture in detecting mixed infections (57.8%, 84.4% vs. 15.6%, all P&#x2009;<&#x2009;0.01), uncovering a substantial number of viral and bacterial-viral co-infections that are undetectable by conventional culture methods. The most common combination of mixed infections in the PM Easy Lab RP was mixed bacterial infections (76.9%, 20/26), whereas in mNGS, it was bacterial-fungal-viral mixed infections (36.8%, 14/38).<br><br>CONCLUSIONS: The findings indicate that PM Easy Lab RP and mNGS offer distinct yet complementary value. PM Easy Lab has potential advantages in speed, sensitivity, and efficiency in detecting pathogens within its panel, and it could be considered for rapid, frontline testing, while mNGS provides a broad-spectrum detection capability, making it more suitable for comprehensive investigation of complex cases, though careful clinical interpretation is required to distinguish pathogenic from colonizing or contaminating organisms. Understanding their respective strengths can guide the development of optimized, hierarchical diagnostic pathways.},
}
@article {pmid41299229,
year = {2025},
author = {Thurimella, K and Mohamed, AMT and Li, C and Vatanen, T and Graham, DB and Owens, RM and La Rosa, SL and Plichta, DR and Bacallado, S and Xavier, RJ},
title = {Protein language models uncover carbohydrate-active enzyme function in metagenomics.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {285},
pmid = {41299229},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; Humans ; *Enzymes/metabolism/chemistry/genetics ; Carbohydrate Metabolism ; Molecular Sequence Annotation ; },
abstract = {BACKGROUND: The functional annotation of uncharacterized microbial enzymes from metagenomic data remains a significant challenge, limiting our understanding of microbial metabolic dynamics. Traditional annotation methods often rely on sequence homology, which can fail to identify remote homologs or enzymes with structural rather than sequence conservation. To address this gap, we developed CAZyLingua, the first annotation tool to use protein language models (pLMs) for the accurate classification of carbohydrate-active enzyme (CAZyme) families and subfamilies.<br><br>RESULTS: CAZyLingua demonstrated high performance, maintaining precision and recall comparable to state-of-the-art hidden Markov model-based methods while outperforming purely sequence-based approaches. When applied to a metagenomic gene catalog from mother/infant pairs, CAZyLingua identified over 27,000 putative CAZymes missed by other tools, including horizontally-transferred enzymes implicated in infant microbiome development. In datasets from patients with Crohn's disease and IgG4-related disease, CAZyLinuga uncovered disease-associated CAZymes, highlighting an expansion of carbohydrate esterases (CEs) in IgG4-related disease. A CE17 enzyme predicted to be overabundant in Crohn's disease was functionally validated, confirming its catalytic activity on acetylated manno-oligosaccharides.<br><br>CONCLUSIONS: CAZyLingua is a powerful tool that effectively augments existing functional annotation pipelines for CAZymes. By leveraging the deep contextual information captured by pLMs, our method can uncover novel CAZyme diversity and reveal enzymatic functions relevant to health and disease, contributing to a further understanding of biological processes related to host health and nutrition.},
}
@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}
@article {pmid41299116,
year = {2025},
author = {Akhtar, S and Malik, A},
title = {Integrated physicochemical and metagenomic analysis of the Ganges River water.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41299116},
issn = {1614-7499},
abstract = {The perennial River Ganges, one of India's most vital freshwater resources, is increasingly threatened by growing human activities. The present study provides an integrated assessment of water quality, heavy metal pollution, antibiotic resistance, and microbial community dynamics along a culturally important section of the river. Physicochemical parameters showed seasonal variations, with higher pH, TDS, nitrate, and sulfate levels, indicating significant human activities. ICP-AES analysis of heavy metals revealed high levels of Cr and Cd, with a contamination degree of 38.25, indicating a very high pollution level. Antibiotic susceptibility testing of 84 bacterial isolates demonstrated 64.28% multidrug resistance, mainly against β-lactam antibiotics. Although the Water Quality Index was 43.43 (classified as good), microbial and metal contamination indicated hidden ecological risks. 16S rRNA gene-based metagenomic profiling showed dominance of pollution-tolerant bacterial groups, especially Pseudomonadota, Bacillota, and Fusobacteriota. Genera like Brevundimonas, Methylobacterium, Pseudomonas, and Acinetobacter were most common, indicating microbial shifts due to ongoing human activities. Functional predictions (KEGG) suggested enrichment in pathways for xenobiotic degradation, energy production, and environmental information processing. These findings highlight the importance of comprehensive monitoring that combines chemical, microbiological, and genomic tools to better assess the river pollution and efforts to reduce public health risks.},
}
@article {pmid41298564,
year = {2025},
author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP},
title = {Laser-assisted microbial culturomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10614},
pmid = {41298564},
issn = {2041-1723},
support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Biofilms/growth &amp; development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/growth &amp; development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; },
abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.},
}
@article {pmid41298464,
year = {2025},
author = {Ricci, F and Bay, SK and Nauer, PA and Wong, WW and Ni, G and Jimenez, L and Jirapanjawat, T and Leung, PM and Bradley, JA and Eate, VM and Hall, M and Stubbusch, AKM and Fernández-Marín, B and de Los Ríos, A and Cook, PLM and Schroth, MH and Chiri, E and Greening, C},
title = {Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66734-4},
pmid = {41298464},
issn = {2041-1723},
support = {APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE230101346//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; 101115755//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PID2019-105469RB-C22//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; },
abstract = {An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonise both forelands and persist across soil decadal chronosequences serving as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using organic and inorganic compounds, including atmospheric trace gases and sulphur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable environment for subsequent colonisation.},
}
@article {pmid41298409,
year = {2025},
author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS},
title = {National-scale biogeography and function of river and stream bacterial biofilm communities.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10571},
pmid = {41298409},
issn = {2041-1723},
support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; },
abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.},
}
@article {pmid41298355,
year = {2025},
author = {Holcik, L and von Haeseler, A and Pflug, FG},
title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10523},
pmid = {41298355},
issn = {2041-1723},
mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; },
abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.},
}
@article {pmid41298327,
year = {2025},
author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70229},
doi = {10.1111/1758-2229.70229},
pmid = {41298327},
issn = {1758-2229},
support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; },
mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; },
abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.},
}
@article {pmid41298270,
year = {2025},
author = {Zou, J and Xu, H and Qin, B and Lan, C and Li, J and Zhang, B and Zhang, H and Guo, C and Chen, H and Fang, Z and Zhao, Q and Wang, W and Fang, C and Zhang, Z and Lin, W},
title = {Ratoon Season Rice Reduces Methane Emissions by Limiting Acetic Acid Transport to the Rhizosphere and Inhibiting Methanogens.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07916},
doi = {10.1002/advs.202507916},
pmid = {41298270},
issn = {2198-3844},
support = {32001109//Nature Science Foundation of China/ ; 31871542//national Nature Science Foundation of China/ ; 31871556//national Nature Science Foundation of China/ ; 2017YFE0121800//National Key Research and Development Project of China/ ; 2018YFD0301105//National Key Research and Development Project of China/ ; BQW [2024]001//Innovative Talent Team in Rice Crop Science and Technology in Karst Mountainous Areas of Guizhou Province/ ; 2023//Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/ ; (2023) 007//Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions/ ; Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions (//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Qianjiaoji//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (2023)007)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Xiligongmi//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Innovative Talent Workstation of Guizhou Province(Qian-//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Ke//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; -He-Platform-talent KXJZ(2024)038)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (Qian-//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; Ke//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; -He YWZ(2024(004)//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; },
abstract = {Rice paddies are a major, persistent source of atmospheric methane (CH4), emission rates depend on the partitioning of photosynthate carbon between the rice plant and the rhizosphere microbiome. Although ratoon season rice (RR) is shown to emit far less CH4 than main-crop rice (MC), the mechanisms have remained unresolved. This work conducts a 2-year field experiment in which RR is compared with MC and with late rice (LR) synchronized to the RR heading stage. Relative to MC and LR, RR lowers daily CH4 flux by 91%, raises daily grain yield by 34%-57%, and increases net economic return by 90%-136%. Mechanistically, [13]C-labelling reveals that RR diverted more newly fixed carbon to the grain and less to the rhizosphere, thereby restricting acetate availability for methanogens. Rhizosphere metagenomics show reduced abundance of Methanobacteriaceae and down-regulation of methanogenic genes in RR. This carbon-reallocation pattern is underpinned by an abscisic acid (ABA)-mediated interaction between OsCIPK2 and OsSWEET1A, which simultaneously curtailed carbon efflux from roots and enhanced grain filling. This study is the first to establish a comprehensive framework of "ABA regulation-carbon allocation-microbial function-emission reduction and efficiency enhancement." It provides targetable strategies for carbon allocation and microbial management within climate-smart rice farming systems.},
}
@article {pmid41298102,
year = {2025},
author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A},
title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336715},
pmid = {41298102},
issn = {1468-3288},
abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.<br><br>OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.<br><br>DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.<br><br>RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for &#x3b2;-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.<br><br>CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.<br><br>TRIAL REGISTRATION NUMBER: NCT04777812.},
}
@article {pmid41298101,
year = {2025},
author = {Liu, CS and Merrick, B and Taboun, ZS and Mullish, BH and Goldenberg, SD and Terveer, EM and Porcari, S and Bradbury, RS and Ianiro, G and Ng, SC and , and Kao, D and Kuijper, E},
title = {Towards optimising and standardising donor screening for faecal microbiota transplantion.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336532},
pmid = {41298101},
issn = {1468-3288},
abstract = {Rigorous donor screening is fundamental for the safe and effective delivery of faecal microbiota transplantion (FMT) services, whether in the treatment of Clostridioides difficile infection or within microbiome intervention clinical trials. Donor screening is of paramount importance given the potential risk of pathogen transmission-a feared complication. While rare in practice, documented cases of FMT-associated infections have resulted in significant morbidity and even mortality. Despite the importance of screening, evidence-based approaches to developing donor-screening protocols are lacking. Inadequate screening for transmissible pathogens may lead to infections in recipients, while overly cautious screening for pathogens with negligible transmission potential could strain healthcare resources and unnecessarily exclude donors, who are already in limited supply. This review aimed to evaluate the evidence underpinning current FMT donor screening protocols. We began by comparing protocols from major FMT guidelines and manufacturers, highlighting their differences in lists of screened pathogens, laboratory assays and clinical characteristics used for donor selection. We critically appraised the existing literature on transmission dynamics for pathogens. These findings were incorporated into a Delphi process with an expert panel group to develop a rational and streamlined screening approach. We further emphasised the importance of maintaining transparency with regard to donor recruitment, screening, monitoring and traceback record keeping. Finally, we explored future directions in donor screening, including approaches to monitoring emerging pathogens and the potential for integration of new technologies, such as metagenomic assays, to enhance and refine donor selection.},
}
@article {pmid41297753,
year = {2025},
author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S},
title = {Phosphate-Iron Modified Enteromorpha Prolifera Hydrochar Enhances Dry Anaerobic Digestion of Food Waste: Synergistic Mechanisms of Electron Transfer Network, Microbial Consortia Remodeling, and Metagenomic Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123385},
doi = {10.1016/j.envres.2025.123385},
pmid = {41297753},
issn = {1096-0953},
abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6% improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32%. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9%) and hydrogenotrophic methanogens Methanoculleus (+17.7%); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255%), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.},
}
@article {pmid41297621,
year = {2025},
author = {Houmenou, CT and Sokhna, C and Fenollar, F and Mediannikov, O},
title = {Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105859},
doi = {10.1016/j.meegid.2025.105859},
pmid = {41297621},
issn = {1567-7257},
abstract = {Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.},
}
@article {pmid41297516,
year = {2025},
author = {Xu, L and Zhang, J and Xiao, Y and Jin, P and Zhang, J},
title = {High-fat diet promotes colorectal tumorigenesis through gut microbiota-mediated metabolic reprogramming and M2 macrophage polarization.},
journal = {Biochemical and biophysical research communications},
volume = {794},
number = {},
pages = {153014},
doi = {10.1016/j.bbrc.2025.153014},
pmid = {41297516},
issn = {1090-2104},
abstract = {BACKGROUND: High-fat diet (HFD) drives colorectal cancer (CRC) progression through gut microbiota dysbiosis and M2 macrophage polarization, yet the microbiota-immunity crosstalk remains mechanistically unresolved.<br><br>METHODS: APC[min/+] (CRC model, n&#xa0;=&#xa0;8) and wild-type controls (n&#xa0;=&#xa0;7) received 12-weeks HFD. We employed integrated metagenomic sequencing (Illumina NovaSeq) and immunohistochemistry (targeting CD206+ M2 macrophages) to investigate the linkages between the gut microbiota and the host.<br><br>RESULTS: CRC mice exhibited colonic adenocarcinoma with increased M2 macrophages. Gut microbiota in CRC mice showed enrichment of pro-inflammatory taxa (e.g., Bacteroides massiliensis, Vampirovibrion) and upregulated pathways (carbohydrate metabolism, mucin degradation). Strikingly, the relative abundances of Bacteroides massiliensis and Vampirovibrion showed significant positive correlations with CD206+ M2 macrophage infiltration levels.<br><br>CONCLUSION: HFD induces microbiota-directed metabolic reprogramming and M2 polarization, synergistically accelerating CRC. Notably, targeting key pro-inflammatory taxa (e.g., B. massiliensis) or glycan hydrolysis pathways (e.g. GH95 enzyme) may provide mechanism-guided anti-CRC strategies.},
}
@article {pmid41297400,
year = {2025},
author = {Chen, S and Liu, Q and Li, D},
title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128088},
doi = {10.1016/j.jenvman.2025.128088},
pmid = {41297400},
issn = {1095-8630},
abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.},
}
@article {pmid41297255,
year = {2025},
author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y},
title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140566},
doi = {10.1016/j.jhazmat.2025.140566},
pmid = {41297255},
issn = {1873-3336},
abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.},
}
@article {pmid41297254,
year = {2025},
author = {Hatwar, N and Qureshi, A},
title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140589},
doi = {10.1016/j.jhazmat.2025.140589},
pmid = {41297254},
issn = {1873-3336},
abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.},
}
@article {pmid41297084,
year = {2025},
author = {Cameron, CC and Gebbie, W and Bowman, C and Waters, ER and Kalyuzhnaya, MG},
title = {Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126670},
doi = {10.1016/j.syapm.2025.126670},
pmid = {41297084},
issn = {1618-0984},
abstract = {Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N2O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.},
}
@article {pmid41297027,
year = {2025},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deciphering the Interrelation of Gut Microbiota and BMI in Atherosclerosis: A Metagenomic Approach.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0075},
pmid = {41297027},
issn = {1480-3275},
abstract = {Atherosclerotic Cardiovascular Disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modifying the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.},
}
@article {pmid41296543,
year = {2025},
author = {Podlesny, D and Kim, CY and Robbani, SM and Schudoma, C and Fullam, A and Reimer, LC and Koblitz, J and Schober, I and Iyappan, A and Van Rossum, T and Schiller, J and Grekova, A and Kuhn, M and Bork, P},
title = {metaTraits: a large-scale integration of microbial phenotypic trait information.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1241},
pmid = {41296543},
issn = {1362-4962},
support = {460129525//Deutsche Forschungsgemeinschaft/ ; RS-2023-00240807//National Research Foundation of Korea/ ; //Ministry of Science, Research and the Arts Baden-W&#xfc;rttemberg (MWK)/ ; },
abstract = {Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is dispersed across multiple databases and is largely unavailable for taxa that remain uncultured. Here, we present metaTraits, a unified and accessible trait resource that integrates culture-derived trait information from BacDive, BV-BRC, JGI IMG, and GOLD with genome-based predictions for medium and high-quality isolate and metagenome-assembled genomes (MAGs) from proGenomes and SPIRE. metaTraits covers over 2.2 million genomes and >140 harmonized traits mapped to standardized ontologies, spanning cell morphology (e.g. shape, size, and Gram staining), physiology (e.g. motility and sporulation), metabolic and enzymatic activities, environmental preferences (e.g. temperature, salinity, and oxygen tolerance), and lifestyle categories. All records are linked to the original evidence, and species are cross-linked to NCBI and GTDB taxonomies. The interactive metaTraits website provides search and visualization tools, taxonomy-level summaries, and two workflows for annotating user-submitted genomes or community profiles. metaTraits substantially advances accessibility and interoperability of microbial trait data, enabling comprehensive trait-based analyses of microbiomes across diverse environments. metaTraits is accessible via https://metatraits.embl.de.},
}
@article {pmid41296394,
year = {2025},
author = {Albaijan, D and Albaijan, D and Akbar, A},
title = {Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.},
journal = {Current issues in molecular biology},
volume = {47},
number = {11},
pages = {},
doi = {10.3390/cimb47110890},
pmid = {41296394},
issn = {1467-3045},
abstract = {Pampus argenteus (Zobaidy) is an important fish in Kuwait and the Gulf region due to its economic value in the fish industry. Analyzing the gut microbiome of Zobaidy can help determine the health status of the fish and its responses to environmental changes. In this study, we investigated the microbiome composition of the intestinal tract among seven wild-caught silver pomfret specimens sampled in the Arabian gulf. The 16S rRNA was sequenced using the Illumina platform; then, sequences were analyzed using several bioinformatics tools to identify the microbial diversity, taxonomical status, and functional aspects. The results were 5933 operational taxonomic units (OTUs) categorized into 35 phyla. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacterota were most abundant in the Zobaidy and water samples. At the genus level, we found high relative abundances of Acinetobacter. The results indicated that Lactococcus piscium, Enterococcus cecorum, Psychrobacter arenosus, Vagococcus salmoninarum, and Carnobacterium maltaromaticum are the most commonly present species in the analyzed Zobaidy samples. A heatmap analysis indicated notable differences in the functional categories of intestinal microflora within the Zobaidy2 sample compared to other Zobaidy samples. It should be noted that microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention, and increase sustainability in aquaculture production.},
}
@article {pmid41296232,
year = {2025},
author = {Jalal, D and Lotfi, M and Ziad, GA and Mahfouz, S and Madney, Y and Bayoumi, A and Hassanain, O and Tolba, M and Hashem, M and Elanany, M and Sayed, AA and Shalaby, L},
title = {Dual Transmission Dynamics of Carbapenem Resistance in Pediatric Oncology: Plasmid-Mediated and Clonal Spread of blaNDM-5 Enterobacterales.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {41296232},
issn = {2193-8229},
support = {54699605//Pfizer/ ; },
abstract = {INTRODUCTION: Carbapenem-resistant Enterobacterales (CRE) pose a major threat to immunocompromised pediatric oncology patients. However, the routes of resistance spread in this vulnerable population remain poorly understood, despite their importance for guiding infection control.<br><br>METHODS: We analyzed 189 CRE bloodstream isolates (106 Escherichia coli, 72 Klebsiella pneumoniae, and 11 other Enterobacterales) collected at the Children's Cancer Hospital Egypt&#xa0;57357 (August 2021-October 2022). Whole&#xa0;genome sequencing was used to assess sequence types, resistance genes, virulence factors, plasmid content, and transmission dynamics.<br><br>RESULTS: Carbapenem resistance was primarily mediated by blaNDM-5, carried on species-specific plasmids: IncFIA/IncFII in E.&#xa0;coli and IncFIB/IncHIB megaplasmids in K.&#xa0;pneumoniae, frequently co-harboring additional aminoglycoside, sulfonamide, and fluoroquinolone resistance genes. The most common sequence types were ST361, ST167, and ST405 in E.&#xa0;coli, and ST11, ST383, and ST147 in K.&#xa0;pneumoniae. Clonal clustering was observed in 62.5% of K.&#xa0;pneumoniae but only 17% of E.&#xa0;coli. Plasmid phylogenetics and patient movement data indicated extensive horizontal plasmid transfer across unrelated lineages and patients, including ICU cases. A nonfunctional rmpA variant was found in 30 K.&#xa0;pneumoniae isolates, but no hypermucoviscous phenotype was observed.<br><br>CONCLUSION: CRE bloodstream infections in pediatric oncology patients are driven by both clonal expansion and plasmid-mediated dissemination, with plasmids playing a dominant role, especially in E.&#xa0;coli. These findings highlight the limitations of strain-based surveillance and the need for integrated genomic and plasmid-level monitoring to inform infection control in high-risk hospital settings. A Graphical Abstract is available for this article.},
}
@article {pmid41295733,
year = {2025},
author = {O'Donoghue, S and Waters, SM and Morris, DW and Earley, B},
title = {A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111095},
pmid = {41295733},
issn = {2306-7381},
support = {16/RD/US-ROI/11//Department of Agriculture, Food and the Marine (DAFM) US-Ireland R&amp;D partnership call/ ; 2018US-IRL200//the US- Ireland Tri Partite Grant/ ; No. 101000213//European Union Horizons 2020, HoloRuminant project/ ; },
abstract = {Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods-culture, ELISA, and immunohistochemistry-are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host-pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD.},
}
@article {pmid41295660,
year = {2025},
author = {Ren, Q and Lu, W and Zhang, T and Hao, S and Wang, J and Xu, X and Wang, F and Huang, Z and Lei, X and Cao, S and Chen, D and Li, Y},
title = {Comparative Analysis of Bacterial Diversity and Composition in Oral Fluid from Pigs of Different Ages and Water Pipe Wall Biofilms.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111022},
pmid = {41295660},
issn = {2306-7381},
support = {No. 32372957//National Natural Science Foundation of China/ ; },
abstract = {Drinking water pipe biofilms, comprising viable microorganisms, microbial residues, and organic/inorganic particulates, pose significant risks to water safety by promoting the proliferation of opportunistic pathogens, pipe corrosion, and degradation of water quality. Their formation is strongly influenced by environmental conditions within the piping system. However, there is a lack of systematic research investigating the potential correlations between biofilm microbiota and the oral microbiomes of intensively farmed swine, as well as the age-dependent regulatory mechanisms shaping aquatic microbial communities. This pioneering study conducted a comparative analysis of biofilm microbiota from swine house water pipes and oral microbiomes across three growth stages (30-day BBF, 70-day NBF, and 110-day FBF groups), yielding three key findings. First, the biofilm biomass and dominant bacterial genera (e.g., Brevibacterium in BBF vs. Brevundimonas in FBF) exhibited stage-specific variations associated with swine age. Second, while the oral microbiomes showed no significant taxonomic divergence at the phylum or genus level, they shared characteristic phyla, including Actinobacteria and Bacteroidetes, with pipe biofilms, indicating potential cross-habitat microbial interactions. Third, the antibiotic resistance gene (ARG) adeF was consistently detected at high prevalence across all biofilm groups. These findings offer new insights into microbial transmission dynamics and inform risk mitigation strategies for livestock water supply systems.},
}
@article {pmid41295321,
year = {2025},
author = {Liu, X and Fu, C and Gao, Q and Zhang, H and Shi, T and Li, G and Wang, Y and Shang, Y},
title = {Effect of Tryptophan Supplementation Levels on the Cecal Microbial Composition, Growth Performance, Immune Function and Antioxidant Capacity in Broilers.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110736},
pmid = {41295321},
issn = {2218-1989},
support = {ZR2024QC376//Shandong Provincial Natural Science Foundation/ ; CXGC2025F10//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; CXGC2025B03//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; 202228037//Jinan Introductory Innovation Team Project/ ; TSCX202306046//Taishan Industry Experts Program/ ; },
abstract = {BACKGROUND: Tryptophan (Trp) is a limiting amino acid in poultry nutrition. Dietary supplementation of Trp not only enhances production performance, but also supports intestinal barrier integrity, alleviates stress, and boosts immunity, in which the derivatives from gut Trp-metabolizing commensal microbes play crucial roles. However, research on how excessive Trp affects poultry growth, metabolism, and gut microbiota composition remains limited.<br><br>METHODS: In this study, we investigated the effects of varying Trp levels (0.23%, 0.29%, 0.35%) on broiler production performance, immune function, and antioxidant levels through controlled feeding trials. These host responses were further correlated with cecal microbiota metagenomic sequencing data using multivariate analysis.<br><br>RESULTS: Compared with the basal 0.23% Trp level, a 0.35% of Trp addition significantly impaired broiler body weight gain and feed intake, and 0.29% Trp could increase thymus index and serum superoxide dismutase (SOD) level without affecting the growth performance; neither of these two levels affected the feed conversion rate. The cecal microbial metagenomic data further revealed that Trp supplementation reduced the abundance of harmful bacteria, while increasing the abundance of beneficial bacteria and Trp-metabolizing microorganisms. Correlation analysis showed that Trp supplementation was negatively correlated with body weight (BW) but positively correlated with thymus index and SOD level, with similar trends observed between the abundance of specific Trp-utilizing microorganisms and these indicators. Functional analysis revealed an increase in the abundance of KEGG orthology (KO) related to Trp metabolism from the aforementioned microbes.<br><br>CONCLUSIONS: An appropriate addition of Trp (0.29%) can enhance certain metabolic levels without affecting production performance, which might be achieved through relevant metabolic pathways of intestinal microorganisms.},
}
@article {pmid41295300,
year = {2025},
author = {Bai, H and Luo, K and Jin, Y and Sun, X and Zhang, X and Zhao, Y and Muhammad, Y and Huang, A and Yin, P and Zhang, G},
title = {Integrated Metagenomic and Metabolomic Analyses Reveal a Microbiota-Metabolite Axis Associated with Gallstone Pathogenesis.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110714},
pmid = {41295300},
issn = {2218-1989},
support = {82174136//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Gallstone disease is a prevalent digestive disorder worldwide, with incidence increasingly linked to obesity, insulin resistance, and dyslipidemia. Emerging evidence suggests that intestinal microbial communities and their bioactive compounds play a central role in pathogenesis. Here, we aimed to clarify whether diet-related microbial alterations and circulating metabolites contribute to gallstone formation.<br><br>METHODS: We integrated dietary inflammatory index (DII) evaluation, genetic analyses of large-scale cohorts, and a cholesterol gallstone mouse model induced by a lithogenic diet (LD). Serum and fecal samples were subjected to metabolomic and metagenomic profiling, followed by multi-omics integration to identify links between microbial taxa, metabolites, and gallstone risk.<br><br>RESULTS: Higher DII scores were associated with increased gallstone risk. Genetic evidence supported bile acid and amino acid metabolism as potential mediating pathways, with Akkermansia muciniphila linked to decreased N-acetylarginine levels and CAG-448 showing an inverse association with glycodeoxycholate (GDCA). In LD-fed mice, shotgun metagenomics revealed enrichment of lithogenic taxa such as Bacteroides stercorirosoris and Enterocloster, whereas protective taxa, including Akkermansia muciniphila and CAG-448, were markedly depleted. Untargeted metabolomics confirmed elevations of GDCA and N-acetylarginine together with broader bile acid imbalance, amino acid stress, and long-chain acylcarnitine accumulation. Correlation analyses further showed that protective taxa were inversely associated with risk metabolites, whereas gallstone-enriched microbes displayed the opposite pattern.<br><br>CONCLUSIONS: This study provides evidence consistent with a contributory role of gut microbiota-metabolite dysregulation in gallstone pathogenesis. Specific taxa (A. muciniphila, CAG-448) and metabolites (GDCA, N-acetylarginine) may serve as potential biomarkers or targets for microbiota- and diet-based prevention strategies.},
}
@article {pmid41295156,
year = {2025},
author = {Zou, R and Zhang, Y and Zhang, L and Chen, M and Xin, L and Zhang, L},
title = {The Effect of Pseudomonas putida on the Microbial Community in Casing Soil for the Cultivation of Morchella sextelata.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110775},
pmid = {41295156},
issn = {2309-608X},
support = {XJBS-202445; QNYC-202515; Young talent program//Special Fund for Anhui Agricultural Research System; Agricultural Sciences Academy of Anhui Province Talent Project; Science and Technology Innovation Team Project of Anhui Academy of Agricultural Sciences/ ; },
abstract = {Morels are a rare edible and medicinal fungus. A major factor contributing to difficulties with their continuous cropping is alteration in soil microbial communities. Pseudomonas putida is a key microorganism in morel cultivation soils; it has garnered significant attention due to its ability to degrade 1-aminocyclopropane-1-carboxylic acid (ACC), a precursor of ethylene. However, the interaction between Pseudomonas putida and morels remains unclear. This study evaluated the growth-promoting potential of P. putida KT2440 by measuring the casing soil ACC content and assessing its ACC utilization capacity. Metagenomic sequencing was performed to assess the changes in soil microbial composition and function. The results indicated that ACC accumulated in the soil following morel cultivation and that P. putida KT2440 was capable of utilizing ACC as its sole nitrogen source for growth on plates. Inoculation enhanced the depletion of available nitrogen, phosphorus, and potassium; increased bacterial diversity; improved the stability of the soil microbial community; and caused the mycelium of morels to grow earlier. These processes occurred along with a decline in the abundance of the Streptomyces genus. Furthermore, a positive correlation was identified between the abundance of P. putida and ACC deaminase activity in the soil. Overall, this study examined the role of Pseudomonas putida inoculation in modulating the soil microbial community and metabolic processes within casing soil during Morchella sextelata cultivation. The findings indicate that P. putida inoculation promotes Morchella growth through ACC decomposition and microbial restructuring, offering a potential strategy for mitigating ethylene-related suppression in continuous cropping systems.},
}
@article {pmid41294637,
year = {2025},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Dădârlat, DA and Ștef, L},
title = {Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.},
journal = {Clinics and practice},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/clinpract15110206},
pmid = {41294637},
issn = {2039-7275},
abstract = {The oral microbiome may be an indicator of oral pathologies and hormonal fluctuations. Consequently, the proper identification of methods for studying microbial factors is essential. Because more than half of the components of the oral microbiome belong to species that are very difficult or even impossible to cultivate in the laboratory, the assessment of the oral microbiome nowadays is based on genetic sequencing, using techniques such as DNA hybridization, 16S rRNA sequencing, and metagenomics, mainly analyzing saliva and subgingival plaque. Variations in results may be caused by differences in sample type, analysis methods, accuracy in determining cycle phases, and biases introduced by DNA extraction techniques and technical variations. Choosing the right primers for the 16S rRNA gene and reference databases (like HOMD, Greengenes2) is essential for accurately identifying microorganisms. Metagenomic sequencing offers greater taxonomic and functional detail, but it is costlier and presents bioinformatics challenges, including contamination with human DNA. When the patients under study are women, we have to take into consideration the cyclical changes in the menstrual cycle. Studies suggest that estrogen influences local immune and inflammatory responses and can worsen existing gingival inflammation. Certain oral bacteria can even utilize estradiol and progesterone as growth factors. The composition of the oral microbiome is also affected by hormonal contraceptives, carbohydrate intake, smoking, age, body mass index, genetics, and oral hygiene-all factors that need to be controlled for in future studies. Interpreting the biological significance of the reported cyclic changes requires careful examination of the specific methods used in each study.},
}
@article {pmid41294355,
year = {2025},
author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C},
title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118525},
doi = {10.1128/msystems.01185-25},
pmid = {41294355},
issn = {2379-5077},
abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.<br><br>IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.},
}
@article {pmid41294346,
year = {2025},
author = {Bodourian, CS and Imran, M and Georgakis, ND and Papageorgiou, AC and Labrou, NE},
title = {Structural and functional characterization of a metagenomically derived γ-type carbonic anhydrase and its engineering into a hyperthermostable esterase.},
journal = {Protein science : a publication of the Protein Society},
volume = {34},
number = {12},
pages = {e70396},
doi = {10.1002/pro.70396},
pmid = {41294346},
issn = {1469-896X},
mesh = {*Carbonic Anhydrases/chemistry/genetics/metabolism ; *Esterases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Enzyme Stability ; Models, Molecular ; Protein Engineering ; Amino Acid Sequence ; Escherichia coli/genetics ; Molecular Sequence Data ; },
abstract = {The 16S microbial community profiling of a metagenomics library from geothermal spring at Lisvori (Lesvos island, Greece) enabled the identification of a putative sequence exhibiting 95% identity to the γ-type carbonic anhydrase (γ-CA) from Caloramator australicus (γ-CaCA). The sequence of γ-CaCA was amplified by PCR, cloned, and expressed in E. coli. Activity assays showed that γ-CaCA possesses very low, but detectable, anhydrase activity, while exhibiting no measurable esterase activity. Differential scanning fluorimetry (DSF) revealed that the enzyme shows high thermal stability with a melting temperature (Tm) approximately 65-75°C in the pH range between 5.5 and 9.0. The structure of γ-CaCA was determined by X-ray crystallography at 1.11 Å resolution, the highest resolution reported so far for a γ-CA. The enzyme was crystallized as a trimer in the crystallographic asymmetric unit and contains three zinc-binding sites, one at each interface of neighboring subunits of the trimer. Structure-based rational design enabled the design and creation of a mutant enzyme (γ-CaCAmut) which possessed a heptapeptide insertion at the active-site loop and two-point mutations. Kinetic analysis demonstrated that γ-CaCAmut was successfully converted into a catalytically active esterase indicating successful activity gain through structure-guided engineering. The thermostability of γ-CaCAmut was significantly increased, aligning with the thermostability typically observed in hyperthermostable enzymes. X-ray crystallographic analysis of the γ-CaCAmut structure at 2.1 Å resolution, provided detailed structural insights into how the mutations impact the overall enzyme structure, function, and thermostability. These findings provide valuable structural and functional insights into γ-CAs and demonstrate a strategy for converting an inactive enzyme into a catalytically active form through rational design.},
}
@article {pmid41293880,
year = {2025},
author = {Damian, D},
title = {Metagenomic Applications in the Early Detection of Human Viral Threats.},
journal = {Viral immunology},
volume = {},
number = {},
pages = {},
doi = {10.1177/08828245251400169},
pmid = {41293880},
issn = {1557-8976},
abstract = {The rapid evolution of viral pathogens presents significant challenges for global health, as traditional methods for virus detection often fail to identify novel or genetically diverse viruses. The emergence and reemergence of viral pathogens necessitate more advanced and inclusive diagnostic approaches. This review aims to explore the role of metagenomics in overcoming the limitations of traditional viral detection methods and to assess its impact on the discovery, characterization, and surveillance of viral pathogens. A comprehensive review of recent studies employing metagenomic approaches to viral detection was conducted. High-throughput sequencing technologies and bioinformatics tools were highlighted as key components in enabling broad-spectrum viral identification and characterization. Metagenomic approaches have successfully identified novel pathogens, including new arboviruses and reemerging strains of known viruses. These techniques provide a more complete understanding of viral diversity and dynamics, surpassing the limitations of targeted assays and culturing methods. Key findings emphasize the capability of metagenomics to detect viruses previously undetected by conventional methods, improving the scope of surveillance. Metagenomics offers transformative advantages for viral surveillance and outbreak management. It enhances early detection, allows for better-informed responses to viral threats, and contributes to more effective strategies for managing emerging and reemerging viral pathogens. Integration of metagenomic techniques into public health practices is crucial for combating the evolving landscape of viral diseases.},
}
@article {pmid41293547,
year = {2025},
author = {Paul, D and Paasisalo, I and Putkinen, A and Jones, CM and Kohl, L and Hallin, S and Pihlatie, M and Siljanen, HMP},
title = {Microorganisms in the phyllosphere of Norway spruce controlling nitrous oxide dynamics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf196},
pmid = {41293547},
issn = {2730-6151},
abstract = {Current climate change assessments and greenhouse gas flux models often lack information on the microbiological processes that consume atmospheric nitrous oxide (N2O), a potent greenhouse gas. There is limited understanding of phyllospheric microorganisms controlling N2O exchange. In this study, we determined the microbial potential for N2O consumption in aboveground vegetation in boreal forests. For this, we collected shoot samples from upland spruce forests in Finland and used a novel targeted metagenomics approach with a hybridization capture of gene-specific probes. Most of the samples contained nosZ genes, encoding the N2O reductase. Phylogenetic placement showed a significantly higher relative abundance (P < .01) of nosZ Clade I than nosZ Clade II. Bacterial members such as Comamonadaceae, Hydrogenophaga, and Paracoccus, which all harbor nosZ Clade I, were found in high relative abundance in the spruce shoots across the sites, suggesting they play a role in N2O consumption capabilities in the spruce phyllosphere. Anoxic incubations, utilizing gas chromatography for N2O analyses, showed potential N2O consumption activity across the spruce samples. The presence of nirK and nirS suggests potential for denitrification, possibly resulting in N2O production. Our finding provides evidence of microbial communities in spruce canopies with potential for N2O exchange. Given the vast coverage of boreal forests globally, understanding the role of phyllospheric microorganisms in N2O exchange is crucial for improving the accuracy of greenhouse gas models and enhancing climate prediction reliability.},
}
@article {pmid41293456,
year = {2025},
author = {Li, Z and Zhu, P and Zhang, Z and Li, Z and Liu, P and Meng, L and Yang, Q and Yang, Z and Song, J},
title = {Metavirome Identification and Pathogenicity Evaluation of Tibet Orbivirus in Pigs.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {6628384},
pmid = {41293456},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Swine Diseases/virology ; *Reoviridae Infections/veterinary/virology ; Tibet/epidemiology ; *Orbivirus/pathogenicity/genetics/isolation &amp; purification ; Virulence ; Viremia/veterinary/virology ; Phylogeny ; },
abstract = {Tibet orbivirus (TIBOV) is an orbivirus transmitted by mosquitoes and Culicoides, despite specific neutralizing antibodies being detected in pigs, but the molecular genetic characteristics of TIBOV strains in infected pigs are completely uncharted, and their pathogenicity in piglets is poorly elucidated. This study aimed to investigate the genetic characteristics of TIBOV in infected pigs and evaluate the pathogenicity of TIBOV in weaned piglets. Through viral metagenomic sequencing, seven segments (VP1-VP4, VP6, NS1, and NS2) of TIBOV were obtained from swine tissues, and the sequences showed high identity with TIBOVs isolated from Culicoides, mosquitos, and cattle. After infection with TIBOV, the body temperature, appetite, and behavior of the piglets were normal, whereas hemorrhage nodes were observed on the hooves of all piglets and on the abdominal skin of one pig. Viremia was first detected at 2 days postinfection (dpi), peaked at 6 dpi, and remained high until 21 dpi. The virus was distributed in multiple organs, and the highest viral load and strongest viral nucleic acid signals were observed in the spleen. The most severe lesion was observed in the spleen with white pulp atrophy, a decreased number of lymphocytes, and widened septa of the medullary cord, indicating that the spleen was the most important target organ of TIBOV infection. The levels of inflammatory cytokines, including interleukin (IL)-18, tumor necrosis factor-α (TNF-α), interferon (IFN)-α, and IFN-λ3 in peripheral blood lymphocytes decreased significantly from 2 to 6 dpi, and interferon-stimulated gene-15 (ISG-15) and IFN regulatory factor 7 (IRF-7) expression levels declined significantly from 2 to 9 dpi, suggesting that the host immune response was inhibited within 6 dpi. Our findings confirmed that TIBOV elicited long-term viremia with mild clinical symptoms in piglets, the spleen was the target organ of TIBOV proliferation, and the host immune response may be slightly inhibited in the early stage of viral infection.},
}
@article {pmid41293056,
year = {2025},
author = {Lee, JA and Won, D and Lee, EH and Lee, ST and Park, KK and Shin, S and Jeong, SJ},
title = {Utilization of cell-free DNA metagenomic analysis for early detection and microbial identification in prosthetic joint infections: a prospective cohort study in Korea.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663857},
pmid = {41293056},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Prospective Studies ; Synovial Fluid/microbiology/chemistry ; Female ; Male ; Aged ; Middle Aged ; *Cell-Free Nucleic Acids/genetics/analysis ; *Metagenomics/methods ; Republic of Korea ; Early Diagnosis ; *Bacteria/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {BACKGROUND: Prosthetic joint infection (PJI) is a severe complication of hip or knee arthroplasty, often necessitating invasive intervention and posing a high risk of adverse outcomes. Early diagnosis and tailored antibiotic therapy are critical for the effective management of PJI. This study evaluated the utility of cell-free deoxyribonucleic acid (cfDNA) extracted from synovial fluid to diagnose PJI and identify the causative pathogens.<br><br>METHODS: This prospective, single-center study included a PJI group consisting of patients with confirmed infections based on the European Bone and Joint Infection Society criteria and a non-PJI group comprising patients without suspected PJIs who underwent joint surgery or aspiration. Synovial fluid samples were collected from all patients, and various culture methods, including conventional synovial fluid, sonication, and tissue and blood cultures, were applied along with cfDNA analysis.<br><br>RESULTS: A total of 35 patients were included, with 20 diagnosed with PJI and 15 classified as non-PJI. The median cfDNA concentration in synovial fluid was significantly higher in the PJI group (4.560 ng/&#x3bc;l, interquartile range (IQR) [3.320-6.348]) compared with the non-PJI group (0.028 ng/&#x3bc;l, IQR [0.009-0.273]) (p < 0.001). The Youden index identified a cfDNA concentration &#x2265; 1.59 ng/&#x3bc;l as strong likelihood of PJI. Culture positivity rates in the PJI group were as follows: synovial culture (10/20, 50.0%), sonication culture (8/9, 88.9%), tissue culture (2/8, 25.0%), and blood culture (2/12, 16.7%). The bacterial detection rate of cfDNA was 65.0% (13/20).<br><br>CONCLUSION: cfDNA concentration was significantly higher in the PJI group, with synovial cultures showing substantial agreement. Additionally, cfDNA sequencing detected pathogens in patients who had received prior antibiotic therapy and identified multiple pathogens in polymicrobial infections. These findings highlight cfDNA analysis as a valuable diagnostic tool for PJI, with the potential to enhance current diagnostic approaches.},
}
@article {pmid41292684,
year = {2025},
author = {Liu, J and Sha, Y and Dang, R and Zhou, L and Zhou, M and Tan, Y and Wang, J and Ran, G and Xie, W and Xia, D and Wang, L and Zhao, X and Goi, BM and Yu, J and Xiao, L},
title = {Acetate-based syntrophy enhances methane production potential of ruminant feces.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706620},
pmid = {41292684},
issn = {1664-302X},
abstract = {Livestock feces contribute to approximately 32% of global methane emissions. Although ruminants are generally believed to have a higher methane production potential than non-ruminants, the dominant pathways and key regulatory processes underlying methane generation in ruminants remain poorly understood, impeding effective manure management and accurate livestock emission assessments. In this study, metagenomic and carbon isotope techniques were employed to investigate methane production potential and key pathways in sheep, pig, chicken, and duck feces. Methane production potential of ruminant sheep feces was significantly higher (approximately threefold) compared to that of non-ruminants. Isotopic analysis of methane sources revealed that sheep feces primarily produce methane through the acetoclastic pathway, whereas the other three likely rely on CO2 reduction. Metagenomic analysis of methanogenic pathways further indicated that the abundance of functional genes associated with acetoclastic methanogenesis is significantly higher in sheep feces compared to the other three. Moreover, the co-occurrence network analysis highlighted a tightly coordinated, cross-species partnership between fermentative acetogenic bacteria and methanogenic archaea in the sheep fecal microbiome. Together, our findings provide insights into some key methanogenic pathways, such as acetoclastic methanogenesis, contributing to high methane production from ruminant feces.},
}
@article {pmid41292560,
year = {2025},
author = {Li, X and Wang, Y and Ma, F and Zhao, C and Zhang, Y and Zhu, Y and Zhang, Y and Hou, S and Li, B and Yang, F and Hao, L and Zhu, T},
title = {Chaperone-mediated thermotolerance in hyperthermophilic composting: Molecular-Level protein remodeling of microbial communities.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100630},
pmid = {41292560},
issn = {2666-4984},
abstract = {Hyperthermophilic composting (HC) represents a promising approach for converting organic solid waste into valuable resources by leveraging extreme temperatures to enhance microbial degradation and detoxification processes. In this high-temperature environment, microbial communities undergo dynamic succession, where thermophilic bacteria dominate and drive efficient organic matter transformation through adapted metabolic pathways and stress responses. These adaptations include the stabilization of cellular structures and enzymes, often mediated by heat shock proteins (HSPs) that prevent protein misfolding under thermal stress. However, the integrated mechanisms linking community-level functional shifts to molecular-level protein remodeling in thermophiles during HC remain poorly understood. Here we show a coordinated interaction of functional succession and molecular adaptations within thermophilic bacteria in HC, which collectively achieve heat resistance. This interaction encompasses enhanced metabolic and genetic modules, accounting for 97 % of the variance observed in thermophile abundance. Metagenomic analyses revealed upregulation of translation, transcription, amino acid metabolism, and cell wall biosynthesis, coupled with suppression of mobilome functions to maintain genomic stability, as confirmed by partial least squares path modeling and Boruta analyses. Molecular dynamics simulations of key enzymes from the thermophile Truepera further demonstrated intrinsic structural rigidity, reduced hydrophobic exposure, and hierarchical chaperone activity involving DNAJ, DNAK, and GroEL for protein repair. These findings enhance our comprehension of microbial thermotolerance and establish a foundation for optimizing composting efficiency and advancing heat-resistant microbial applications in biotechnology and waste management. Additionally, they offer insights into the evolution of thermophiles, protein engineering, and stress adaptation across various biological and industrial systems, thereby promoting the integration of environmental engineering and systems biology.},
}
@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.<br><br>AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.<br><br>METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as &#x2265;2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.<br><br>RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.<br><br>CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}
@article {pmid41291846,
year = {2025},
author = {Ding, J and Yang, W and Li, X and Liu, X and Zhao, J and Sun, T and Liu, H},
title = {The microbial community metabolic regime adapts to hydraulic disturbance in river-lake systems with high-frequency regulation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00821-3},
pmid = {41291846},
issn = {2524-6372},
support = {National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; },
abstract = {BACKGROUND: River-lake ecosystems are crucial for the rational allocation of water resources, but frequent water diversion can destabilize water quality due to hydraulic disturbance. Microbial communities can respond rapidly to such external perturbations and influence these systems through the effects on nutrient metabolism. Therefore, understanding how microbial communities respond to hydraulic shocks in aquatic systems and whether they can adapt to such disturbances is essential for maintaining the health of river-lake systems. We used 16S rRNA and metagenomic sequencing technologies to examine the metabolic regimes of microbial communities during water regulation and non-regulation periods in river-lake systems.<br><br>RESULTS: We found that hydraulic disturbance tended to drive the microbial community toward homogenized selection, thereby weakening its stability. Flow velocity (V) and the nitrate (NO3[-]-N) concentration significantly affected microbial community composition and abundance, with clear threshold effects. We established low (V&#x2009;=&#x2009;0.284&#xa0;m/s, NO3[-]-N&#x2009;=&#x2009;0.031&#xa0;mg/L) and high (V&#x2009;=&#x2009;0.461&#xa0;m/s, NO3[-]-N&#x2009;=&#x2009;0.055&#xa0;mg/L) thresholds. These thresholds categorize microbial communities into three distinct regimes: regime1 (R1), regime 2 (R2), and regime 3 (R3). The microbial abundances in R1 and R3 were significantly higher than those in R2 (p&#x2009;<&#x2009;0.01), while the community in R3 exhibited a strong denitrification capacity. In R3, the microbial community enhanced its denitrification metabolism by promoting the growth of denitrifying microbial genera (e.g., Pseudomonas and Flavobacterium) to counterbalance the impact of high V and NO3[-]-N. These strains contributed the denitrification-related genes nasA, narB, nirB, and nirD to the community, thereby promoting the NO3[-]-N metabolism and reducing environmental NO3[-]-N concentrations. In addition, we predicted microbial community abundance using an artificial neural network to validate the thresholds we identified.<br><br>CONCLUSIONS: Our study provides theoretical support for understanding how microbial communities adapt to high-frequency hydraulic disturbances and offer valuable insights for managers to adjust water diversion strategies in a timely manner, thereby safeguarding the integrity of river-lake ecosystems.},
}
@article {pmid41291642,
year = {2025},
author = {Xie, Q and Li, D and Ren, C and Shen, Y and Lin, S and Chen, W},
title = {Metabolomic and metagenomic analyses reveal distinct microenvironmental signatures between clear aligner-associated and tooth surface dental plaque.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07231-4},
pmid = {41291642},
issn = {1472-6831},
support = {No. 2023J01643//the Fujian Provincial Natural Science Foundation of China/ ; },
}
@article {pmid41291413,
year = {2025},
author = {Zhang, J and Zhao, Y and Li, W and Xu, J and Chen, Y and Yang, S and Wu, P and Li, Y and Zhou, C and Zhang, W},
title = {Viromic analysis of cerebrospinal fluid (CSF) samples identified an unclassified RNA virus exhibiting an atypical genomic architecture.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {776},
pmid = {41291413},
issn = {1471-2180},
mesh = {Humans ; *Genome, Viral ; Phylogeny ; Open Reading Frames ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Cerebrospinal Fluid/virology ; *Meningoencephalitis/virology/cerebrospinal fluid ; Metagenomics ; Viral Proteins/genetics ; Male ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {The central nervous system (CNS) is highly susceptible to infections that can lead to severe neurological morbidity and mortality. Despite advances in diagnostic technologies, a significant proportion of encephalitis and meningitis cases remain etiologically undiagnosed, underscoring the need for novel pathogen discovery approaches. Here, we report the identification of a novel unclassified RNA virus, provisionally named hucaurvirus ("human CSF-associated unclassified RNA virus"), in the cerebrospinal fluid (CSF) of a pediatric patient with unexplained meningoencephalitis, using metagenomic next-generation sequencing (mNGS). The hucaurvirus exhibits a monopartite, positive-sense RNA genome of 6.5 kb which contains two overlapping open reading frames (ORFs), which was confirmed by conventional PCR amplification and Sanger sequencing. The large ORF encodes a polyprotein containing a capsid domain, while the small ORF overlaps within the large ORF and encodes the RNA-dependent RNA polymerase (RdRp) protein. BLASTp search based on the amino acid sequence of RdRp showed that hucaurvirus had the highest sequence identity and query coverage of 39.2% and 90%, respectively, to a noda-like virus (GenBank no. MT138110). Phylogenetic analysis showed that hucaurvirus was closely related to four viruses annotated as noda-like viruses, forming a cluster that is adjacent to the cluster of the Carmotetraviridae family and appears to form a new viral family within the order Tolivirales. PCR screening confirmed the presence of hucaurvirus in one of ten CSF samples, validating its detection. Our findings emphasize the utility of mNGS in uncovering novel pathogens and expanding our understanding of viral diversity in CNS infections.},
}
@article {pmid41291216,
year = {2025},
author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F},
title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02628-8},
pmid = {41291216},
issn = {1432-184X},
abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.},
}
@article {pmid41291200,
year = {2025},
author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H},
title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29758-w},
pmid = {41291200},
issn = {2045-2322},
support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; },
abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.},
}
@article {pmid41291020,
year = {2025},
author = {Mwape, I and Silwamba, S and Chibesa, K and Luchen, CC and Musukuma-Chifulo, K and Collins, J and Chauwa, A and Liswaniso, F and Nzangwa, TB and Kuntawala, DH and Chisenga, CC and De Beer, C and Chilengi, R and Lu, XJ and Yingst, S and Wickiser, JK and Simuyandi, M},
title = {Pathogen-focused metagenomic analysis reveals predominance of human rotavirus genotypes G3 and G12 in Zambian pediatric diarrhea cases.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28946-y},
pmid = {41291020},
issn = {2045-2322},
support = {DEL-22-012//DELTAS Africa/ ; },
abstract = {Despite global improvements in water, sanitation, and rotavirus vaccination, rotavirus-associated diarrhea continues to cause significant morbidity and mortality among children in low-to-middle-income countries. Genomic surveillance is essential for evaluating vaccine efficacy and detecting emerging escape variants. In this study, we used VirCapSeq-VERT (VCS) to analyze rotavirus genetic diversity during Zambia's 2023 diarrhea surveillance. Stool samples from under five children with diarrhea were collected from health facilities across nine provinces. Out of 245 samples, 72 were rotavirus qPCR-positive with Ct <33 and underwent targeted viral enrichment and sequencing using VCS on the Illumina NextSeq2000. Bioinformatic analysis showed 70/72 strains had near complete genome constellations being genotyped as 45 Wa-like, 11 DS-like, and 14 reassortant strains. VP7 and VP4 analyses showed diverse genotypes (G1-G3, G8-G9, G12; P[4], P[6], P[8], P[11] clustering with vaccine and wild-type strains. Furthermore, G3 and G12 combined with P[4], P[6], and P[8] were the most predominant genotypes (35/70 and 13/70, respectively). Notably, nine samples had an M5 VP3 genotype with a 91% similarity to a simian rotavirus strain. Antigenic epitope analysis highlighted substitutions in P[6], G2, and G12, associated with immune escape. G3P[8] was the most common in severe cases. Fully vaccinated children showed significantly milder disease (p = 0.033). This study highlights VCS's utility in detecting viral diversity, reassortment, zoonotic transmission, and immune escape variants, providing crucial insights for assessing vaccine performance and public health strategies.},
}
@article {pmid41291018,
year = {2025},
author = {Angwong, C and Pientong, C and Ekalaksananan, T and Burassakarn, A and Tongchai, P and Overgaard, HJ and Aromseree, S},
title = {Systematic review and meta-analysis of virome profiles and quantification of Torque teno virus load in blood of acute febrile illness patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29413-4},
pmid = {41291018},
issn = {2045-2322},
support = {IN66039//Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand/ ; },
abstract = {Acute febrile illness (AFI) is a sudden fever which can be caused by various viruses such as dengue, Zika, and chikungunya viruses. This study aimed to identify viruses present in AFI patients via metagenomic next-generation sequencing (mNGS) through meta-analysis, and to compare the prevalence and viral load of the common viruses between AFI patients and healthy blood donors in northeastern Thailand. Our meta-analysis revealed that human anelloviruses-including torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV)-were the most prevalent viruses detected. We confirmed their presence in peripheral blood mononuclear cells from 203 AFI patients and 100 healthy blood donors using real-time PCR. TTV was the most identified anellovirus, detected in 84% of healthy donors and 61.08% of AFI patients. The mean TTV load was significantly lower in AFI patients compared to healthy donors. In AFI patients, TTV load increased in those with higher total white blood cell and neutrophil counts but decreased in those with higher lymphocyte counts. Our findings demonstrate high prevalence of anelloviruses, particularly TTV, in both AFI patients and healthy donors, and highlight the potential value of the TTV load in blood as an immune status biomarker in AFI patients.},
}
@article {pmid41290854,
year = {2025},
author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R},
title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41955},
pmid = {41290854},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.},
}
@article {pmid41290836,
year = {2025},
author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS},
title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41935},
pmid = {41290836},
issn = {2045-2322},
mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.},
}
@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66678-9},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}
@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}
@article {pmid41290639,
year = {2025},
author = {Fisher, LWS and Thorpe, HA and Sassera, D and Corander, J and Bryant, JM},
title = {High frequency body site translocation of nosocomial Pseudomonas aeruginosa.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9862},
pmid = {41290639},
issn = {2041-1723},
support = {220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/isolation &amp; purification/physiology/pathogenicity ; Humans ; *Cross Infection/microbiology/transmission ; *Pseudomonas Infections/microbiology/transmission ; Female ; Male ; *Bacterial Translocation ; Middle Aged ; Metagenomics ; },
abstract = {Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but the rate and directionality of this process is unknown. Here, we explore within-host diversity as well as the body site translocation dynamics using de-convoluted metagenomic P. aeruginosa reads from 256 hospital patients sampled at both respiratory and gut sites. Of the 84 patients where P. aeruginosa genomes could be recovered, there were 27 cases where the same P. aeruginosa clone was detected across multiple body sites. Using a simulation approach, we find that the majority of body site sharing is likely due to within-patient translocation of clones rather than independent acquisition from the hospital environment. Using ancestral reconstruction, we predict that most clones likely occupied a respiratory niche, and that the probable direction of clone transmission is lung-to-gut. Analysis of within-patient variation highlights strong enrichment of mutations in genes associated with antimicrobial resistance, irrespective of sample type. We report significantly more translocation than has been previously reported and highlight that lower respiratory tract infections can result in persistent gut colonisation of P. aeruginosa, a major risk factor for sepsis in vulnerable patients.},
}
@article {pmid41290112,
year = {2025},
author = {An, Z and Bao, Y and Yang, Y and Su, X and Dong, F and Xiao, X and Chen, C and Fu, H and Lin, H and Sun, F},
title = {Quorum quenching driven enzymatic activity and metabolic pathway modulation in anaerobic reactor for enhanced methane production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133668},
doi = {10.1016/j.biortech.2025.133668},
pmid = {41290112},
issn = {1873-2976},
abstract = {The effect of bioaugmentation with the quorum-quenching bacterium Proteus sp. ZJ5 on methane production during anaerobic process was evaluated at dosages of 0-280 mg·L[-1]. The maximum methane yield was achieved at 140 mg·L[-1]Proteus sp. ZJ5, showing a 17 % increase over the control. Enhanced methane production correlated with elevated activities of key enzymes, including protease, α-glucosidase, acetate kinase, and electron transport system, particularly α-glucosidase, which increased by 178 %. The modified Gompertz model confirmed greater methane potential, shorter lag time, and improved COD removal. Metagenomic analysis revealed notable shifts in microbial community structure, characterized by increased relative abundances of hydrogenotrophic methanogens such as Methanosarcina and Methanoculleus, as well as enrichment of genes involved in glycolysis, amino acid metabolism, and methanogenesis pathways. These results demonstrate that Proteus sp. ZJ5 enhances methane recovery by modulating enzymatic activity and microbial metabolic pathways, providing new insight into improving anaerobic treatment performance.},
}
@article {pmid41289884,
year = {2025},
author = {Liu, C and Yang, Q and Shen, Y and Xu, M},
title = {Multidimensional review of viral infectious ocular diseases: Post-Pandemic epidemiology and future directions for control.},
journal = {Molecular aspects of medicine},
volume = {106},
number = {},
pages = {101428},
doi = {10.1016/j.mam.2025.101428},
pmid = {41289884},
issn = {1872-9452},
abstract = {Viral Infectious Ocular Diseases (VIODs) remain a major global cause of vision loss, ranging from highly transmissible conjunctivitis to blinding keratitis and complex neuro-ophthalmic syndromes. Furthermore, the Coronavirus Disease 2019 (COVID-19) pandemic and subsequent reported ocular diseases have fundamentally changed the landscape of VIOD epidemiology and management. Epidemiological data indicate heterogeneous effects on common infections such as Adenoviral conjunctivitis due to varying compliance with hygiene measures. Concurrently, systemic immunological events, notably those induced by COVID-19 infection or certain vaccinations, have been linked to the reactivation of latent Alphaherpesviruses, including Herpes Simplex Virus (HSV) and Varicella Zoster Virus (VZV). The metagenomic next-generation sequencing (mNGS) offers a significantly improved diagnostic yield (up to 92.7 % in some cohorts) for complex infectious keratitis compared to conventional methods, providing an unbiased tool crucial for timely, targeted treatment. Therapeutic challenges are defined by the persistent threat of antiviral resistance, primarily driven by mutations in the viral Thymidine Kinase (TK) gene. To overcome poor ocular bioavailability, novel drug delivery systems (NDDS), such as Acyclovir-loaded Niosomes and Cubosomes, show promise by enabling sustained drug release and enhanced corneal permeation. Effective future VIOD control requires a multi-pronged strategy integrating robust global surveillance, rapid deployment of advanced molecular diagnostics, and the clinical implementation of resistance-beating therapies delivered via optimized nanocarrier platforms. This review provides the current understanding of VIODs, focusing on the epidemiological shifts observed post-2020, advancements in molecular diagnostics, challenges posed by antiviral resistance, and the emergence of next-generation therapeutic strategies.},
}
@article {pmid41289665,
year = {2025},
author = {Diabil, GHMJ and Jalali, A and Komijani, M},
title = {Metagenomic analysis of antibiotic resistance and pathogens in landfill leachates: Environmental implications.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140365},
doi = {10.1016/j.jhazmat.2025.140365},
pmid = {41289665},
issn = {1873-3336},
abstract = {Landfill leachates, rich in antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs), pose significant risks to human, animal, and environmental health. This study analyzed leachate samples from seven sites in Gilan, Mazandaran, and Golestan provinces, northern Iran, using metagenomic sequencing, Inductively Coupled Plasma analysis (ICP), and Gas Chromatography (GC)-based BTEX (Benzene,Toluene, Ethylbenzene and Xylene) quantification. ShortBRED (Short, Better Representative Extract Dataset) analysis revealed higher ARG abundance in GL2 and GL4 compared to GL1 and GL7 (p = 0.0056-0.0265), with Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae as dominant bacterial families. Statistical analysis revealed that metal contaminants had strong correlations with the microbial community structure. Sb and Zn concentrations were strongly negatively correlated with total ARGs abundance (Sb: r = -0.883, p = 0.013; Zn: r = -0.857, p = 0.024). Moreover, there was obvious intense niche partitioning, and major bacterial families showed highly significant correlations with specific metals; e.g., Enterobacteriaceae abundance was inversely correlated with copper (Cu; r = -0.89, p = 0.007) but positively correlated with zinc, antimony, and tin (r = 0.79-0.85, p < 0.05), suggesting metal-mediated selection and co-selection for resistance mechanisms. A PERMANOVA confirmed that spatial analysis was precluded by the sampling design (R[2] = 1.0, residual df = 0), limiting site comparisons to descriptive trends. A correlation between ARGs and elements was noted at GL7 (r = 0.476, p = 0.0251). BTEX levels varied significantly, with higher concentrations in GL2 vs. GL4 (p = 0.0482), GL5 vs. GL3 (p = 0.0090), GL5 vs. GL4 (p = 0.0044), and GL5 vs. GL7 (p = 0.0251), and benzene/toluene exceeding ethylbenzene (p = 0.0276, p = 0.0093) and xylene (p = 0.0038, p = 0.0012). These findings highlight landfill leachates as reservoirs of pathogenic ARB and ARGs, influenced by environmental and microbial factors. The study suggests leveraging leachate-associated bacteria for biochemical treatment of antibiotics and ARGs, and provides a basis for targeted surveillance and risk management to mitigate ARG dissemination and protect ecological/public health.},
}
@article {pmid41289603,
year = {2025},
author = {Zheng, Z and Zhang, R and Hong, W and Yang, S and Lin, X and Shu, W and Price, GW and Song, L},
title = {Landfills as Hotspots of Multidrug Resistance Genes: Profiles, Drivers, and Hosts.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13743},
pmid = {41289603},
issn = {1520-5851},
abstract = {The United Nations has identified municipal solid waste (MSW) landfills as significant reservoirs of antibiotic resistance genes (ARGs). Although ARG profiles, their primary drivers, and associated hosts have been well characterized in landfill leachate, such information remains limited for MSW landfills, which are the original source of the resistome. This knowledge gap impedes effective ARG monitoring at the source and poses challenges for public health management. Herein, we investigated the profiles of ARGs, their potential drivers, and associated hosts in refuse samples collected from a large-scale landfill using metagenomic sequencing and quantitative polymerase chain reaction analysis. Our findings revealed that landfills harbor diverse ARGs, with multidrug resistance genes (MDRGs) emerging as the dominant class, accounting for 39.78% of all ARGs detected. Notably, MDRGs exhibited high mobility potential (associated with plasmids, phages, and mobile genetic elements (MGEs)) and were frequently colocated with virulence factors. Pseudomonas, Acinetobacter, and Brevundimonas were identified as key MDRG hosts. Partial least-squares path modeling analysis indicated that MDRG variation was driven by multiple factors (i.e., MGEs, metal resistance genes (MRGs), hosts, and environmental factors). Additionally, metagenome-assembled genomes were found to carry multiple MDRGs. Collectively, these results underscore the role of landfills as critical hotspots for MDRGs.},
}
@article {pmid41289391,
year = {2025},
author = {Li, J and Gao, ZY and Chen, C and Liu, Y and Zhang, SY and Xu, J and Zhu, YG and Tang, X},
title = {Microbial necromass carbon enhances arsenic methylation in paddy soils.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2527462122},
doi = {10.1073/pnas.2527462122},
pmid = {41289391},
issn = {1091-6490},
support = {42477003//National Natural Science Fundation of China/ ; LZ25D010002//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Arsenic/metabolism/chemistry ; Methylation ; *Carbon/metabolism ; *Soil/chemistry ; Oryza/growth &amp; development ; Bacteria/metabolism ; Fungi/metabolism ; },
abstract = {Microbial necromass carbon (MNC) constitutes a critical component of soil organic carbon. Yet, how MNC regulates microbial arsenic (As) methylation processes in soil remains unclear. Across major Chinese rice-growing regions, bacterial and fungal necromass carbon showed significant positive correlations (P < 0.05) with the transcribed arsM gene. Soil incubation experiments with seven soils explored how straw and three types of MNC-gram-positive bacterial necromass carbon (G[+]-NC), gram-negative bacterial necromass carbon (G[-]-NC), and fungal necromass carbon (F-NC)-affect As methylation. Our results demonstrated that all types of MNC enhanced As methylation, and G[-]-NC exhibiting the most pronounced effect on methylated As accumulation. The addition of 10 to 60 mg G[-]-NC maximally increased As(III) by 43.0 to 75.9% and enhanced methylated As by 4.4- to 18.0-fold in soil porewater vs. the control. Further, metagenomic and metatranscriptomic analyses demonstrated that G[-]-NC addition upregulated the relative abundance of transcribed arsM and arsC2 genes, which were mostly assigned to Acidobacteriota, Pseudomonadota, Planctomycetota, and Bacteroidota. Notably, the transcriptional activity of arsM-harboring Methanosarcinales and Moorellales was markedly enhanced at the order level. By promoting As reduction process, G[-]-NC provides more substrates for As methylation process in soil. Furthermore, G[-]-NC could be used as a carbon source for As-methylating microorganisms, stimulating the transcriptional activity of arsM, which has been confirmed by the incubation experiment with pure culture of Paraclostridium benzoelyticum TC8. This study highlights the critical role of MNC in regulating As biogeochemistry, establishing a basis for predicting the extent of As methylation and risk of rice straighthead disease in paddy ecosystems.},
}
@article {pmid41289388,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2523178122},
doi = {10.1073/pnas.2523178122},
pmid = {41289388},
issn = {1091-6490},
support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; K01DK134840/GF/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; },
abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.},
}
@article {pmid41289374,
year = {2025},
author = {Nachman, EJ and Ardis, CK and Ardis, AKB and Nieto, J and Bresson, MM and Robertson, CM and Seale, MN and Villafuerte, NM and Lyu, Z and Preisner, EC and Danhof, HA and Di Rienzi, SC and Becker, YT and Britton, RA},
title = {Erratum for Nachman et al., "Increased fungal burden in the gastrointestinal tract of brain-dead organ donors".},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285825},
doi = {10.1128/spectrum.02858-25},
pmid = {41289374},
issn = {2165-0497},
}
@article {pmid41289310,
year = {2025},
author = {Zhao, JX and Zheng, WB and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Yang, MT and Nan, FL and Jiang, J and Elsheikha, HM and Zhang, XX},
title = {Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {11},
pages = {e0013768},
doi = {10.1371/journal.pntd.0013768},
pmid = {41289310},
issn = {1935-2735},
abstract = {Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.},
}
@article {pmid41288577,
year = {2025},
author = {Wu, QL and Lan, T and Deng, L and Jia, JW and Ren, WT and Wang, HZ and Du, JS and Ren, NQ and Guo, WQ},
title = {Aromatic Pollutants Rewire Soil Microbial Carbon Fixation via Chain Elongation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf254},
pmid = {41288577},
issn = {1751-7370},
support = {ZD2024E004//Natural Science Foundation of Heilongjiang Province of China/ ; },
abstract = {Widespread aromatic pollutants such as benzene, toluene, ethylbenzene, and xylene are traditionally considered to drive soil carbon loss through mineralisation and ecotoxicity. Contrary to this view, our study reveals that low concentrations of these pollutants stimulate microbial carbon chain elongation-a previously overlooked carbon conversion pathway producing medium-chain fatty acids, thereby reshaping soil carbon dynamics. Using phased amplicon sequencing, metagenomics, and metaproteomics of soil microcosms amended with these compounds, we demonstrate that aromatic pollutants bidirectionally regulate carbon chain elongation at both taxonomic and molecular levels. These pollutants selectively enrich Clostridium_sensu_stricto_12 and Rummelibacillus while suppressing Acinetobacter, a key elongation taxon in natural soils. Simultaneously, they inhibit Petrimonas, a syntrophic fatty acid degrader, promoting the accumulation of medium-chain fatty acids. Carbon chain-elongating bacteria cooperate with aromatic degraders, redirecting pollutant-derived carbon towards chain elongation rather than complete mineralisation to CO2. Among them, Bacillus occupies a pivotal niche bridging aromatic degradation and carbon elongation. At the molecular level, aromatic pollutants enhance chain elongation by accelerating substrate uptake and channelling the key intermediate acetyl-CoA into the reverse β-oxidation pathway. Additionally, aromatic pollutants restrain fatty acid biosynthesis pathway by upregulating fabR, whereas inhibiting acrR and fadR. They also maintain NADH availability to alleviate Rex-mediated repression of bcd, a critical gene in the β-oxidation pathway. However, high concentrations of aromatic pollutants disrupt metabolic homeostasis and suppress chain elongation activity. Our findings redefine the ecological impact of aromatic hydrocarbon contamination in soil, demonstrating their role in modulating anaerobic carbon fixation and retention within soil microbial communities.},
}
@article {pmid41288390,
year = {2025},
author = {Kimbrel, JA and Thissen, JB and Lisboa, FA and Mabery, S and Jaing, CJ and Elster, EA and Schobel, SA and Be, NA},
title = {High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0187625},
doi = {10.1128/spectrum.01876-25},
pmid = {41288390},
issn = {2165-0497},
abstract = {The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated "high" quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.IMPORTANCEThe ability to comprehensively and accurately characterize microbial pathogens in wound infections is critical to efficacious treatment and is especially important in the context of complex battlefield injuries. Our study shows that high-quality metagenome-assembled genomes can be obtained from shotgun metagenomic sequence data for military-relevant wound pathogens including Acinetobacter baumannii. We demonstrate that these metagenome assemblies are directly comparable to genomes derived from cultured isolates, thereby supporting the ability to generate genome-level data sets from non-culturable biospecimens and perform comparative assessments that inform future approaches for improving diagnostic precision in military and civilian wound care.},
}
@article {pmid41288174,
year = {2025},
author = {Lvov, DK and Akimkin, VG and Zaberezhny, AD and Borisevich, SV and Alkhovsky, SV},
title = {Virus taxonomy and megataxonomy (Vira domain) - current status.},
journal = {Voprosy virusologii},
volume = {70},
number = {5},
pages = {401-416},
doi = {10.36233/0507-4088-344},
pmid = {41288174},
issn = {2411-2097},
mesh = {*Viruses/classification/genetics ; Archaea/virology/genetics ; Animals ; Humans ; Bacteria/virology/genetics ; Eukaryota/virology/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Metagenomics ; },
abstract = {For nearly 80 years since the discovery of the first virus by the Russian scientist D.I. Ivanovsky, it has been recognized that all organisms of Earth's biosphere serve as natural hosts for viruses. Viruses, grouped within the informal domain Vira, infect all three domains of cellular life: archaea - Archaea, bacteria - Bacteria, and eukaryotes - Eucarya (algae, fungi, protozoa, plants, invertebrates, and vertebrates). The formation of viral population gene pools through interactions with the gene pools of their hosts has taken place under changing environmental conditions over 3.5 billion years, giving rise to the vast diversity of the virosphere. The accumulation of data on the Earth's virosphere, facilitated by the advent of high-throughput sequencing technologies (NGS), has necessitated a reassessment of approaches to virus classification and, since 2018, has led to a reform of viral taxonomy through the introduction of higher taxonomic ranks (megataxonomy). As of September 2025, the International Committee on Taxonomy of Viruses (ICTV) recognizes 15 taxonomic ranks for viruses, the most significant being: realm - 7, kingdom - 11, phylum - 23, class - 49, order - 93, family - 368, genus - 3769, and species - 16,215. Ongoing advances in metagenomics, metatranscriptomics, and the global ecology of the virosphere will inevitably drive further changes in viral taxonomy and megataxonomy. These developments are of fundamental importance for understanding the evolution of the biosphere and of practical relevance for developing new strategies to strengthen biological security and to mitigate the consequences of epidemic emergencies associated with emerging and reemerging infections.},
}
@article {pmid41288100,
year = {2025},
author = {van Dam, F and Westmeijer, G and Rezaei Somee, M and Ketzer, M and Kietäväinen, R and Ono, S and Bertilsson, S and McIntosh, JC and Dopson, M and Drake, H},
title = {Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.},
journal = {mBio},
volume = {},
number = {},
pages = {e0301725},
doi = {10.1128/mbio.03017-25},
pmid = {41288100},
issn = {2150-7511},
abstract = {Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a δ[13]Cmethanol-methane isotope enrichment of up to 98.6‰. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.},
}
@article {pmid41287997,
year = {2025},
author = {Brício, DG and Gloria, MBA and Bitencourt, JAP and Argôlo, LA and de Lima Ribeiro, R and da Silva, IA and da Silva Pena, R and Lopes, AS and Chagas Junior, GC and Ferreira, NR},
title = {Metagenomic and biogenic amine changes in cassava fermentation for tucupi production using Pediococcus acidilactici starter culture.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70350},
pmid = {41287997},
issn = {1097-0010},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (D.G. Br&#xed;cio master scholarship, Process number 161678/2021-1)/ ; //Bank of the Amazon (BASA S.A., Brazil; Contract No. 2022-230)/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (ROR: 00x0ma614)/ ; },
abstract = {BACKGROUND: The use of starter cultures is essential for producing fermented foods with desirable standardized characteristics and for preventing pathogens. Pediococcus acidilactici, isolated from cocoa fermentation, was used in the production of tucupi, a widely appreciated sauce made from the juice of cassava root (manipueira) in the Brazilian Amazon. Manipueira was submitted to fermentation with and without Pediococcus acidilactici inoculum at 1 × 10[12] CFU mL[-1] (Pa treatment and control treatment (CT), respectively), over a 24-h period. Samples were collected at 4-h intervals and analyzed for physicochemical characteristics following official methods, bioactive amines by high-performance liquid chromatography with fluorescence detection (HPLC-FLD), and microbial genera identification by metagenomic analysis.<br><br>RESULTS: Physicochemical results indicated that fermentation took its due course, with increased acidity, as well as lower pH and reducing and total sugars (Tukey test, P&#x2009;&#x2264;&#x2009;0.05). Only two biogenic amines were detected (putrescine and histamine), and higher levels were found in Pa treatment compared to CT, probably due to the increased Lactobacillus prevalence. Six genera were identified in CT (Weissella, Lactobacillus, Lactococcus, Leuconostoc, Bacillus, and Enterococcus), whereas seven were in Pa (Weissella, Lactobacillus, Pediococcus, Lactococcus, Leuconostoc, Streptococcus, and Enterococcus). Weissella, which was predominant in manipueira, decreased during fermentation, whereas Lactobacillus became predominant in CT. However, when P. acidilactici was used, Lactobacillus was prevalent throughout fermentation, and there was a reduced prevalence of Bacillus and Enterococcus, bacteria with pathogenic potential.<br><br>CONCLUSION: The starter culture optimized tucupi production by maintaining low levels of biogenic amines, inhibiting the growth of undesirable microorganisms, and enhancing tucupi quality and safety. &#xa9; 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid41287884,
year = {2025},
author = {Wang, W and Chen, F and Ye, L and Chen, O and Qing, H and Zhuang, L and Gan, L and Hu, X and Ma, Q and Jian, X},
title = {Enhanced diagnostic yield and clinical impact of metagenomic next-generation sequencing in infective endocarditis: a continuous and prospective surgical cohort study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000003954},
pmid = {41287884},
issn = {1743-9159},
abstract = {BACKGROUND: Traditional culture-based techniques for diagnosing infective endocarditis (IE) suffer from limited sensitivity, particularly in blood culture-negative endocarditis (BCNE). Metagenomic next-generation sequencing (mNGS) has emerged as a promising alternative to improve pathogen detection and guide treatment. This study aimed to evaluate the diagnostic performance of mNGS in IE, and assess its impact on clinical decision-making.<br><br>METHODS: We conducted a continuous and prospective cohort study of 352 patients undergoing cardiac surgery for suspected IE. Each patient underwent blood culture, tissue culture, and mNGS testing on matched arterial blood, venous blood, and valve tissue.<br><br>RESULTS: Traditional tissue culture had low sensitivity (accuracy 24%, AUC 0.57), while blood culture performed better (accuracy 48%, AUC 0.71). In contrast, clinically adjusted valve tissue mNGS showed higher accuracy (84%) and AUC (0.91), outperforming traditional methods. Streptococcus species were most common, but mNGS also detected fastidious pathogens like Coxiella burnetii, especially in BCNE cases. mNGS results prompted antibiotic adjustments in 30% of all patients and 45% of blood-culture negative patients, enabling targeted or de-escalated therapy. Notably, no IE relapses were observed at 1-year follow-up, supporting the effectiveness of mNGS-guided treatment.<br><br>CONCLUSION: mNGS significantly enhances microbiological diagnosis in IE, especially in BCNE, complements traditional methods, and improves clinical decision-making. However, it requires expert interpretation to mitigate false positives.},
}
@article {pmid41287793,
year = {2025},
author = {Yang, T and Lin, X and Chen, R and Wang, R and Li, T and Shen, F and Zhang, X and Lai, L and Lu, B and Wei, J and Xie, X},
title = {Integrated metagenomics and metabolomics analysis reveals dynamic changes of microbiota and metabolic profile during fermentation of cigar tobacco (Nicotiana tabacum L.) leaves.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1662815},
pmid = {41287793},
issn = {1664-8021},
abstract = {Optimizing fermentation duration is critical for producing high-quality cigar tobacco leaves This study examines changes in microorganisms and metabolites during CTL fermentation at four time points: 0 days (T0), 25 days (T1), 50 days (T2), and 75 days (T3). We observed a decreasing trend in total soluble sugars, starch, total nitrogen, and nicotine levels as fermentation progressed. Notably, chemical components stabilized after T2 stages. The microbial community showed dynamic fluctuations, with alpha diversity indices (Shannon, ACE, Pielou's evenness, and Chao-2) reaching equilibrium at T2 and maintaining stability thereafter. Dominant genera such as Staphylococcus, Aspergillus, Sphingomonas, and Penicillium persisted throughout the fermentation process. A total of 1801 metabolites were identified, with 584 showing differential expression across the fermentation periods. Notably, comparisons between T0 and T1, T2, and T3 revealed 218, 377, and 419 differentially expressed metabolites, respectively. KEGG enrichment analysis identified 28 co-existing metabolic pathways, seven of which are linked to cigar quality formation. Furthermore, 29 out of 47 differential metabolites significantly correlated with the eight dominant microbial genera. These findings indicate that the T2 stage achieves optimal balance between microbial activity and metabolite stabilization, providing a scientific basis for industrial process optimization.},
}
@article {pmid41287120,
year = {2025},
author = {Mungun, T and Ulziibayar, M and Nguyen, CD and Batsaikhan, P and Suuri, B and Luvsantseren, D and Narangerel, D and Tsolmon, B and Do, LAH and Ong, DS and Ortika, BD and Pell, CL and Boelsen, LK and Wee-Hee, AC and Spry, L and Hinds, J and Pride, MW and Dunne, EM and Gessner, BD and Mulholland, EK and Satzke, C and von Mollendorf, C},
title = {Pneumococcal carriage and disease in adults hospitalised with community-acquired pneumonia in Mongolia: prospective pneumonia surveillance program (2019-2022).},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {27},
pmid = {41287120},
issn = {2200-6133},
support = {WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; 1087957//NHMRC Career Development Fellowship/ ; },
abstract = {BACKGROUND: Streptococcus pneumoniae is an important cause of pneumonia in older adults, however, serotyping and indirect impact information from low and middle-income countries is lacking. Mongolia has a childhood 13-valent pneumococcal conjugate vaccine (PCV13) program, but no adult pneumococcal vaccination program. We describe pneumococcal carriage rates, disease and serotype distribution among adults hospitalised with pneumonia, and explore changes over the COVID-19 pandemic period.<br><br>METHODS: Adults (&#x2265;&#x2009;18 years) hospitalised with clinical pneumonia were enrolled over 3 years (March 2019-February 2022) into a prospective pneumonia surveillance program. Nasopharyngeal swabs were tested to detect pneumococci using lytA qPCR and molecular serotyping by DNA microarray and metagenomics. Pneumococcal pneumonia was identified using serotype-specific urinary antigen detection and BinaxNOW[&#xae;] assays. Pneumococcal carriage and pneumonia prevalence were assessed over the COVID-19 period with log-binomial regression used to estimate prevalence and adjusted prevalence ratios (pre- versus early- and late-COVID-19 periods).<br><br>RESULTS: Of 3,178 pneumonia cases, S. pneumoniae was identified in 12.1% (333/2,759) of swabs and 8.6% (253/2,925) of urine samples. PCV13 serotype carriage prevalence was 3.1% (82/2,663) and non-PCV13 serotype carriage prevalence 5.7% (152/2,663). In the late-COVID-19 period, pneumococcal carriage prevalence was reduced by 66% (aPR 0.34, 95%CI 0.25-0.46) and pneumococcal pneumonia by 82% (aPR 0.18, 95%CI 0.12-0.27) compared with the pre-COVID-19 transmission period.<br><br>CONCLUSION: Despite paediatric vaccination with high coverage, we identified some residual PCV13 serotypes with predominance of non-PCV13 serotypes carried and causing disease in adults. Direct adult vaccination which targets these serotypes will potentially reduce disease in adults in Mongolia.},
}
@article {pmid41286929,
year = {2025},
author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM},
title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {401},
pmid = {41286929},
issn = {1474-760X},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; },
abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.},
}
@article {pmid41286813,
year = {2025},
author = {Shen, H and Zhang, X and Hu, B and Wang, Y and Yang, B and Fan, P and Liu, J and Zhang, Z and Chen, W and He, L and Yang, W and Lu, G and Yan, G},
title = {Clinical application and impact of metagenomic next-generation sequencing for the diagnosis of infectious diseases in severely immunocompromised pediatric patients.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {950},
pmid = {41286813},
issn = {1471-2431},
support = {EKQM202406//CHFU Young Talents Program/ ; EKQM202406//CHFU Young Talents Program/ ; EKQM202406//CHFU Young Talents Program/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; },
mesh = {Humans ; Retrospective Studies ; *Immunocompromised Host ; Child ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Infant ; Sensitivity and Specificity ; Critical Illness ; *Communicable Diseases/diagnosis/microbiology ; Intensive Care Units, Pediatric ; Adolescent ; },
abstract = {BACKGROUND: Accurate and rapid microbiological diagnosis is essential for the identification and management of critically ill children experiencing immunocompromised (ICH) conditions. Metagenomic next-generation sequencing (mNGS) has shown promising applications in diagnosing infectious diseases in adults; however, its performance in critically ill pediatric infections remains elusive. We aimed to evaluate the performance of mNGS, compared with that of conventional microbiological tests (CMT) as a front-line diagnostic tool for pediatric intensive care unit (PICU) patients, and assess its clinical impact.<br><br>METHODS: In this retrospectively study, a total of 179 samples including blood, sputum or cerebrospinal fluid etc. from 97 children, categorized as ICH or immunocompetent (ICO), were included. The positive detection rate and diagnostic performance (sensitivity, specificity) of mNGS and CMT were compared. The clinical impact of mNGS was assessed on its influence on diagnosis and treatment decisions.<br><br>RESULTS: mNGS demonstrated a significantly higher positive rate than CMT (72.63% vs. 55.31%, P&#x2009;<&#x2009;0.001), particularly in sputum and cerebrospinal fluid (CSF) samples, among both ICH and ICO samples. Samples from ICH patients exhibited a relatively higher positive rate and yielded more microbes detections than ICO samples with both methods. The sensitivity of mNGS assay was 91.34%, significantly outperforming CMT (73.23%, P&#x2009;<&#x2009;0.001). The specificity of mNGS was 73.08%, relatively lower than that of CMT (88.46%, P&#x2009;<&#x2009;0.05). Specific to ICH and ICO, mNGS showed significantly higher sensitivity than CMT (ICH: 94.94% vs. 81.01%, P&#x2009;<&#x2009;0.01; ICO:85.42% vs. 60.42%, P&#x2009;<&#x2009;0.01). Regarding clinical impact, mNGS had a positive impact on diagnosis in 66.0% patients, with a significantly higher proportion of positive impacts observed in ICH samples compared to ICO samples (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: mNGS exhibited superior diagnostic performance compared to CMT for diagnosing infections in critically ill children. More than half (66.0%) of mNGS tests resulted in a positive clinical impact on diagnosis and treatment, particularly among ICH patients.},
}
@article {pmid41286799,
year = {2025},
author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K},
title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {1117},
pmid = {41286799},
issn = {1471-244X},
mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; },
abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.<br><br>METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13&#x2009;years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.<br><br>RESULTS: Fifty-three participants (mean age&#x2009;=&#x2009;10.2&#x2009;years, SD&#x2009;=&#x2009;1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M&#x2009;=&#x2009;2.03, SE&#x2009;=&#x2009;0.33 vs. 2.86, SE&#x2009;=&#x2009;0.34), p&#x2009;=&#x2009;0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M&#x2009;=&#x2009;70.10, SE&#x2009;=&#x2009;0.09) than the placebo group (M&#x2009;=&#x2009;89.72, SE&#x2009;=&#x2009;0.07), p&#x2009;=&#x2009;0.04. However, the kefir group self-reported more sleep problems post-intervention (M&#x2009;=&#x2009;39.81, SE&#x2009;=&#x2009;0.75 vs. 37.40, SE&#x2009;=&#x2009;0.65), p&#x2009;=&#x2009;0.02. For Go/NoGo RT variance, a non-significant interaction (p&#x2009;=&#x2009;0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.<br><br>CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.<br><br>ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.<br><br>TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.},
}
@article {pmid41286718,
year = {2025},
author = {Wu, C and Sun, X and Zhang, W and Yang, Y and Niu, P and Chen, J and Zhang, X and Lu, R and Wang, W and Chen, Z and Tan, W},
title = {Pathogen profiles in CSF from patients with acute infectious meningitis or encephalitis: a multicenter study based on multiplex PCR and mNGS in China, 2018-2019.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12204-7},
pmid = {41286718},
issn = {1471-2334},
support = {2022YFC2303401//the National Key Research and Development Program of China/ ; },
abstract = {Acute meningitis or encephalitis (AME) is mainly caused by viral and bacterial infections, leading to severe sequelae and even death. However, there is limited systematic research on the spectrum of pathogens causing AME in China. Here, cerebrospinal fluid (CSF) samples from 229 acute meningitis or encephalitis patients (AMEP) excluding Japanese encephalitis virus infections collected from multicenter of China between 2018 and 2019 were analyzed. The pathogen profile was comprehensively characterized using both 43-pathogens multiplex PCR (MPCR) and metagenomic next-generation sequencing (mNGS). MPCR revealed that 73 (31.88%) cases had at least one potential pathogen. mNGS were conducted on 22 randomly selected AMEPs, and the results showed that mNGS reported all the pathogens detected by MPCR. Interestingly, mNGS successfully identified multiple pathogens in cases that were undiagnosed by MPCR. The most frequently detected viruses by MPCR were Human herpesvirus (HHV), Adenovirus, Enterovirus/Rhinovirus (Ev/Rv), and Bocavirus. The most abundant bacteria were Bordetella pertussis, Haemophilus influenzae, and Listeria monocytogenes. Coronavirus and other respiratory viruses could also induce AME. Ev/Rv were significantly enriched in the adolescent cases, and tick-borne encephalitis cases were concentrated in northeastern China. This study systematically characterized the pathogen spectrum and distribution of AME in China. Additionally, it revealed that combining MPCR and mNGS significantly improves the diagnostic rate of pathogens in AME. These findings will provide important support for the diagnosis, treatment, and development of drugs and vaccines for AME.},
}
@article {pmid41286386,
year = {2025},
author = {Sadhukhan, S and Bhattacharya, R and Bhattcharya, D and Sahana, S and Pradhan, B and Pandit, S and Gill, HS and Rajeev, M and Nag, M and Lahiri, D},
title = {Artificial intelligence in protein-based detection and inhibition of AMR pathways.},
journal = {Journal of computer-aided molecular design},
volume = {40},
number = {1},
pages = {4},
pmid = {41286386},
issn = {1573-4951},
mesh = {*Artificial Intelligence ; *Anti-Bacterial Agents/pharmacology/chemistry ; Humans ; Deep Learning ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Drug Resistance, Bacterial/drug effects ; *Proteins/chemistry ; Algorithms ; *Bacterial Proteins/chemistry/antagonists &amp; inhibitors/metabolism ; },
abstract = {Antimicrobial Resistance (AMR) is a global concern demanding high-throughput and precise AMR surveillance strategies. This review provides a comprehensive list of Artificial Intelligence (AI) driven frameworks widely employed in the early detection, structural characterization, and designing of novel inhibitors to block the resistance pathways critical for AMR. Deep learning algorithms including DeepGO, DeepGOPlus, DeepGO-SE, PFresGO, DPFunc, ProtENN and graph-based architectures of GraphSite, GrASP enables precise functional annotation of resistance-associated proteins. AI-guided protein modeling performed by AlphaFold, RoseTTAFold, ProtGPT-2, ESMFold etc. generates high resolution 3D conformations, further utilized in performing molecular docking via tools like AutoDock, DeepDocking and DeepChem and analyzed with tools like DeepDriveMD, TorchMD, and PRITHVI, which can perform real-time molecular dynamics simulations. Identification of relevant resistant biomarkers from mass-spectrometry profiles can also be achieved with the help of DeepNovo, Casanovo, or Prosit. Tools like DeepARG, HMD-ARG, and BacEffluxPred enables identification of unannotated resistance genes from metagenomic samples. Natural Language Processing (NLP) and Large Language-based models (LLM) facilitate identification of resistant determinants via literature mining enabling regulatory network mapping and rational inhibitor design. Furthermore, AI-mediated de-novo inhibitor design is achieved using Variational Autoencoders (VAE), Generative Adversarial Networks (GAN), diffusion and flow-matching based frameworks serve as potential options for enhancing diagnostic interventions against resistant phenotypes. AI-based protein-protein interaction predictors include DeepInteract, Pred_PPI, PLIP, DeepAIPs-Pred, DeepAIPs-SFLA, SBSM-Pro, Deep Stacked-AVPs, and pNPs-CapsNet help in understanding how resistance proteins interact with each other enabling precise identification of AMR-modulating peptides and supports the modeling of novel antibiotics for blocking interactions and disrupting resistance pathways.},
}
@article {pmid41285810,
year = {2025},
author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ},
title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {216},
pmid = {41285810},
issn = {2055-5008},
support = {F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; },
mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; },
abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.},
}
@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}
@article {pmid41285454,
year = {2025},
author = {Safika, S and Nisa, C and , and Cahyadi, DD},
title = {Gut microbiota profiling of Javan pangolin (Manis javanica).},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0036},
pmid = {41285454},
issn = {1347-7439},
abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.},
}
@article {pmid41285255,
year = {2025},
author = {Wang, S and Ma, G and Qi, C and Cheng, S and Lai, H and Zhou, L and Wu, G and Chen, Z and Mao, X and Jing, T and He, Y and Zhou, H},
title = {Trimethylamine-N-oxide disrupts spermatogenesis by inducing mitochondrial oxidative stress injury through Hippo signaling.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.11.052},
pmid = {41285255},
issn = {1873-4596},
abstract = {BACKGROUND: The gut-testis axis is increasingly recognized as a regulator of male reproductive health; however, the key microbial contributors, metabolites, and underlying mechanisms remain unclear.<br><br>METHODS: We performed fecal metagenomic sequencing in 107 participants to identify microbial taxa associated with abnormal semen parameters. Serum trimethylamine-N-oxide (TMAO) levels were measured and correlated with semen quality. In mouse models, including fecal microbiota transplantation, dietary choline supplementation, mono-colonization, and direct TMAO administration, we assessed sperm morphology, testicular androgen synthesis, and testicular histology. Testicular transcriptomics, in vitro Leydig cell assays, and mitochondrial function analyses were conducted to investigate the effects of TMAO on Hippo signaling, oxidative phosphorylation, mitochondrial membrane damage, and steroidogenesis.<br><br>RESULTS: Choline-to-trimethylamine converting bacteria, including Phocaeicola massiliensis, Veillonella spp., and Klebsiella pneumoniae, were enriched in men with abnormal semen parameters. Circulating TMAO levels were inversely associated with semen volume, total sperm count, and motile sperm count. In mouse models, elevated TMAO induced testicular dysfunction characterized by impaired sperm morphology, reduced testicular androgen synthesis, and histological abnormalities. Consistently, gene set enrichment analysis (GSEA) of testicular transcriptomes revealed significant suppression of mitochondrial translation, membrane integrity, oxidative phosphorylation, and adenosine triphosphate (ATP) metabolism. TMAO also suppressed steroidogenesis by reducing the expression of steroidogenic acute regulatory protein (StAR). Mechanistic studies in TM3 Leydig cells further demonstrated that TMAO, by promoting Yap phosphorylation, disrupted mitochondrial structure and morphology, decreased mitochondrial membrane potential, increased mitochondrial reactive oxygen species (ROS) levels, impaired ATP synthesis, and promoted mitochondrial fragmentation with upregulation of the mitochondrial fission molecule (Fis1).<br><br>CONCLUSIONS: In conclusion, our findings demonstrate that TMAO activates Hippo signaling to induce mitochondrial dysfunction and suppress testosterone synthesis, thereby impairing spermatogenesis. These results highlight TMAO biosynthesis and its downstream signaling as potential therapeutic targets for improving male fertility.},
}
@article {pmid41285136,
year = {2025},
author = {Sujith, S and Vasudevan, S and Sajeevan, A and Solomon, AP},
title = {Genomics to function: integrating rapid metagenomics with quorum-sensing biosensing for precision infectious disease management.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101291},
doi = {10.1016/j.lanmic.2025.101291},
pmid = {41285136},
issn = {2666-5247},
}
@article {pmid41283812,
year = {2025},
author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y},
title = {From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf626},
pmid = {41283812},
issn = {1477-4054},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; 9667256//City University of Hong Kong/ ; 9678241//City University of Hong Kong/ ; 217310019//Open Research Fund of Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Genomics/methods ; *Computational Biology/methods ; Benchmarking ; *Host-Pathogen Interactions ; Genome, Viral ; },
abstract = {Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks-link prediction and multi-class classification-and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.},
}
@article {pmid41283667,
year = {2025},
author = {Zhang, J and Meng, F and Sun, Y and Xu, W and Wu, S and Su, X},
title = {Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145325},
doi = {10.1128/msystems.01453-25},
pmid = {41283667},
issn = {2379-5077},
abstract = {The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning (DL) models, which typically focus on microbial distribution patterns, neglecting the underlying relationships between microbes. As a result, model performance can be significantly affected by data sparsity, misclassified features, or incomplete microbial profiles. To overcome these challenges, we introduce Phylo-Spec, a phylogeny-driven deep learning algorithm that integrates multi-aspect microbial information for improved status recognition. Phylo-Spec fuses convolutional features of microbes within a phylogenetic hierarchy via a bottom-up iteration and significantly alleviates the challenges due to sparse data and inaccurate profiling. Additionally, the model dynamically assigns unclassified species to virtual nodes on the phylogenetic tree based on higher-level taxonomy, minimizing interferences from unclassified species. Phylo-Spec also captures the feature importance via an information gain-based mechanism through the phylogenetic structure propagation, enhancing the interpretability of classification decisions. Phylo-Spec demonstrated superior efficacy in microbiome status classification across two in silico synthetic data sets that simulate the aforementioned cases, outperforming existing ML and DL methods. Validation with real-world metagenomic and amplicon data further confirmed the model's performance in multiple status classification, establishing a powerful framework for microbiome-based health state identification and microbe-disease association. The source code is available at https://github.com/qdu-bioinfo/Phylo-Spec.IMPORTANCEThe human microbiome profoundly influences health and disease, but current computational tools often overlook the evolutionary relationships among microbes, leading to incomplete or inaccurate interpretations of complex microbial data. Phylo-Spec provides a new way to understand the microbiome by combining microbial abundance, taxonomy, and phylogeny within a unified deep learning framework. This model not only improves the accuracy of health status classification but also highlights key microbial contributors linked to disease. By capturing both microbial diversity and evolutionary context, Phylo-Spec bridges the gap between bioinformatics and biological insight, offering a powerful and interpretable approach for advancing microbiome-based diagnostics and precision medicine.},
}
@article {pmid41283171,
year = {2025},
author = {Ping, Y and Zhao, X and Lv, L and Meng, W and Meng, Y and Ruan, G and Cheng, Y and Xiao, Z and Tian, Y and Chen, M and Chen, L and Yi, A and Tang, Z and Li, N and Chen, D and Wei, Y},
title = {Gut microbiota and metabolic signatures of anxiety in ulcerative colitis: a cross-sectional study.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251393419},
pmid = {41283171},
issn = {1756-283X},
abstract = {BACKGROUND: Patients with ulcerative colitis (UC) usually experience anxiety symptoms that seriously affect their quality of life, treatment, and prognosis. Dysbiosis of the gut microbiota plays an important role in UC and mental illness. However, little is known about the role of the gut microbiota in UC patients with anxiety.<br><br>OBJECTIVES: To identify the gut-microbiome and fecal metabolome profiles uniquely associated with comorbid anxiety in UC patients and to explore potential biomarkers for diagnosis.<br><br>DESIGN: A cross-sectional, two-group comparative study.<br><br>METHODS: To study the underlying association between them, we recruited 126 UC patients in this study, including 78 with anxiety and 48 without anxiety. A total of 102 fecal samples were collected for metagenomic sequencing and metabolome sequencing. Microbial diversity, differential gut microbiota, functional pathways, and metabolites were analyzed. Multivariable logistic regression was used to identify independent risk factors associated with anxiety in UC patients, while Spearman correlation was employed to explore microbe-metabolite interactions and the performance of potential biomarkers.<br><br>RESULTS: We found that disease severity, steroid usage, and abdominal pain may promote the occurrence of anxiety. Compared to UC patients without anxiety, UC patients with anxiety had low fecal microbial community diversity, with an increase in the species Haemophilus sp. HMSC71H05 and Corynebacterium durum, and a decrease in the species Roseburia intestinalis (RI), Bifidobacterium longum (BL), and Enterococcus hirae. The metabolic pathways driven by the gut microbiota were disrupted. Moreover, the levels of most metabolites (such as L-kynurenine) were increased in the feces, while the levels of a few metabolites decreased, including indole-2-carboxylic acid, N-demethylmirtazapine, and tauroursodeoxycholic acid.<br><br>CONCLUSION: Our research further revealed that these gut microbiota and metabolites are highly correlated. This study provides a new perspective for understanding the occurrence and development of anxiety in UC patients, suggesting that RI and BL may serve as potential candidate biomarkers to diagnose UC patients with anxiety.},
}
@article {pmid41282996,
year = {2025},
author = {Wang, JM and Pan, YY and Hong, JC and Jiang, ZJ and Zhang, SY and Fan, RJ and Yang, BH and Wang, ZQ and Zhu, JT and Yao, XP},
title = {Exploring the Spectrum of Microbiota in Central Nervous System Infections Through Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6019-6033},
pmid = {41282996},
issn = {1178-6973},
abstract = {PURPOSE: This study leveraged CSF metagenomic next-generation sequencing (mNGS) to bridge this knowledge gap and elucidate the microbiota spectrum of CNS infections.<br><br>PATIENTS AND METHODS: We retrospectively analyzed CSF mNGS reports and clinical data from 264 patients with suspected CNS infections, who were enrolled from September 2019 to November 2023.<br><br>RESULTS: According to diagnostic criteria, 145 patients were diagnosed with CNS infections, including bacterial (27 cases, 18.6%), Mycobacterium tuberculosis (30, 20.7%), fungal (23, 15.9%), and viral (65, 44.8%) infections. The mNGS positive detection rate was 46.2% (67/145), with significant differences among groups (p < 0.001). A total of 22 pathogens were identified, most commonly Cryptococcus neoformans (16, 23.9%), Mycobacterium tuberculosis (10, 14.9%), and Epstein-Barr virus (9, 13.4%). The most frequent background microorganisms detected by mNGS were Cutibacterium acnes (58.6%), Moraxella osloensis (29.0%), and Malassezia restricta (26.2%).<br><br>CONCLUSION: High-throughput sequencing using mNGS revealed the microbial compositions in CSF samples from patients with CNS infections. This approach may enhance our understanding of pathogens and assist clinicians in making effective therapeutic decisions.},
}
@article {pmid41282988,
year = {2025},
author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y},
title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20199},
pmid = {41282988},
issn = {2167-8359},
mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; Archaea/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.<br><br>METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.<br><br>RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P&#xa0;=&#xa0;0.038 at the family, P&#xa0;=&#xa0;0.019 at the genus and P&#xa0;=&#xa0;0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P&#xa0;<&#xa0;0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P&#xa0;=&#xa0;0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.<br><br>CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.},
}
@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}
@article {pmid41282900,
year = {2025},
author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, D and Teixeira, M and Earl, AM and Worby, C and Kong, HH and Huang, SS and Segre, J},
title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.25339587},
pmid = {41282900},
abstract = {Antimicrobial resistance (AMR) is a global public health threat that disproportionately affects vulnerable populations, including nursing home (NH) residents. Surveillance and control in NHs are resource-limited and typically restricted to perirectal cultures, overlooking both skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here we show, within the cluster-randomized Project PROTECT trial (NCT03118232), that residents' skin serves as a major reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using shotgun metagenomics, selective culturing, and isolate genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ST131/ST648 in 4 (10.5%) and methicillin-resistant Staphylococcus aureus in 7 (18.4%). In contrast, metagenome-assembled genomes identified broader MDRO colonization, including multidrug-resistant E. coli ST93 in 27 residents (71.1%), methicillin-resistant Staphylococcus epidermidis ST2 in 14 (36.8%), Proteus mirabilis in 16 (42.1%), Providencia stuartii in 7 (18.4%), Enterococcus faecalis in 7 (18.4%), and Pseudomonas aeruginosa in 5 (13.2%). Colonization persisted after bathing. Clonal E. coli ST93 (<=30 SNPs) was shared by 27 residents across 9 facilities, and 5 resident pairs (13.2%) carried clonally related strains of >=2 MDRO species, consistent with polymicrobial transmission. Our findings demonstrated the skin as a persistent reservoir of MDROs and the importance of metagenomic surveillance to uncover hidden colonization and transmission pathways, underscoring the need to expand AMR monitoring in long-term care.},
}
@article {pmid41282695,
year = {2025},
author = {Lande, SJ and Stephney, LM and Ramirez, LGA and Nesbeth, PC and Hartman, TJ and Jones, DP and Valvi, D and Hechenbleikner, EM and Lin, E and McConnell, RS and Chatzi, VL and Alvarez, JA and Ziegler, TR},
title = {Dietary Macronutrient Intake and the Gut Microbiome in Adults Undergoing Bariatric Surgery for Obesity.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.25338397},
pmid = {41282695},
abstract = {Limited information linking dietary intake to gut metagenomic data in bariatric surgery patients is available. We examined whether there were correlations between macronutrient intake and the gut microbiome and related gene pathways prior to and following bariatric surgery. Participants were 29 adults living with obesity undergoing bariatric surgery (93% females). Three-day food records were analyzed prior to and after surgery to estimate mean daily intakes of macronutrients to derive measures of diet quality [glycemic index, added sugar intake, and the Healthy Eating Index 2015 (HEI-2015)]. Pre- and post-operative stool samples were sequenced using whole-genome shotgun sequencing to identify changes in microbial composition. Diversity indices and differential abundance were calculated, and correlations between dietary intake and outcomes were assessed using linear regression and machine learning models. At the phylum level, pre-operative Synergistetes abundance was positively correlated with soluble fiber intake, and Proteobacteria was inversely linked with HEI-2015 scores. Post-operatively, Lentisphaerae was inversely correlated with dietary glycemic index. The change in Verrucomicrobia abundance was inversely correlated with the change in glycemic index, and the change in Fusobacteria abundance was positively correlated with the change in glycemic index. The changes in several functional gene pathways were positively linked to the change in HEI-2015 scores, the change in soluble fiber intake, and the change in insoluble fiber intake. In adults undergoing bariatric surgery, intakes of specific macronutrients pre-operatively and as a function of the change after surgery were correlated with several microbial phyla, genera, and nutrient-related functional gene pathways.},
}
@article {pmid41282688,
year = {2025},
author = {Zhang, H and Dominguez, EG and Junak, M and Murtaza, M and Pepperell, CS and Kisat, MT},
title = {Fragment end motif analysis to distinguish pathogens from contaminants in enriched plasma microbial DNA.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.25339688},
pmid = {41282688},
abstract = {INTRODUCTION: Despite its promise, accuracy of microbial cell-free DNA (mDNA) in plasma as a diagnostic tool is hindered by its low abundance and process contaminants. We have previously shown that combining size selection with single-stranded DNA (ssDNA) library preparation increased mDNA yield by 200-fold but also decreased sensitivity for pathogen detection due to higher background noise. A recent study showed that pathogen-derived DNA was enriched for CC dinucleotide at 5' ends compared to contaminants. Since ssDNA libraries preserve sequence motifs at both ends (5' and 3'), we hypothesized that analysis of nucleotide motifs at microbial fragment ends in size-selected ssDNA libraries could help differentiate pathogen DNA from background noise.<br><br>METHODS: We performed deep sequencing on size-selected ssDNA libraries (<110 bp) generated from longitudinal plasma samples of 11 critically-ill patients (5 with culture-proven infections, 20 samples; 6 without infections, 18 samples) and 6 no-template controls (NTCs). For each 2-mer and 1-mer motif, we calculated the ratio between its frequency observed at 5' and 3' fragment ends in sequencing data and its expected frequency in the corresponding reference genome (O/E ratio). We compared enrichment of motifs in pathogen DNA and contaminant DNA fragments.<br><br>RESULTS: Pathogen-derived mDNA fragments were more biased in O/E end motif ratios compared to contaminants across all 3 groups (NTCs, no-infections and culture-proven infections), at both 5' and 3' fragment ends. Notably, the GG dinucleotide was enriched at the 3' end in pathogens compared to contaminants (P < 0.0001). Combining O/E ratios for C and G nucleotides at the 3' end achieved areas under the receiver operating characteristic curve of >0.98 for distinguishing common contaminants from culture-proven pathogens.<br><br>CONCLUSIONS: Pathogen-derived mDNA in size-selected ssDNA libraries is biased at 5' and 3' fragment end compared to contaminants. Incorporating microbial fragment end motif analysis can enhance signal-to-noise ratio and improve pathogen detection and identification in plasma metagenomic sequencing.},
}
@article {pmid41282530,
year = {2025},
author = {Shoji, F and Kawabata, T and Kosai, K and Fujishita, T and Toyozawa, R and Shimamatsu, S and Ito, K and Taguchi, K and Yamaguchi, M},
title = {Intratumoral microbiome is associated with the response to cancer immunotherapy in lung cancer patients with high PD-L1 expression.},
journal = {Immuno-oncology technology},
volume = {28},
number = {},
pages = {101066},
pmid = {41282530},
issn = {2590-0188},
abstract = {BACKGROUND: High expression of tumoral programmed death-ligand 1 (PD-L1) [high PD-L1 tumor proportion score (TPS)] is a predictive biomarker of response to cancer immunotherapy in lung cancer; however, its predictiveness is insufficient. Recently, resident microbiomes in several organs including the lung have been demonstrated to control host immunity but their role in the response to cancer immunotherapy is still unknown.<br><br>MATERIALS AND METHODS: This single-center, retrospective study analyzed 32 high PD-L1-TPS lung cancer patients treated with immune checkpoint inhibitors (ICI). We carried out shotgun metagenome sequencing using frozen tumor tissues, then analyzed the correlation between the intratumoral microbiota and response to ICI therapy.<br><br>RESULTS: In this study, only 56.3% of patients with high PD-L1-TPS showed response to ICI therapy. Among 11 significant compositional differences in intratumoral microbiota observed in ICI responders, there was significantly longer progression-free survival (PFS) in patients with abundant Tetrasphaera and Mesorhizobium. Of patients with these abundant microbiota, 83.3% showed response to ICI therapy and all patients without these microbiota were ICI nonresponders (P = 0.0050). There were significant differences among three groups classified by the abundance of g_Tetrasphaera and g_Mesorhizobium (PFS, P = 0.0016 and overall survival, P = 0.0013). Twenty pathway modules were enriched in ICI responders and eight were enriched in ICI nonresponders.<br><br>CONCLUSIONS: This study revealed the specific compositions of intratumoral microbiota as demonstrating relevance to response to ICI therapy in high PD-L1-TPS lung cancer patients. The intratumoral microbiota components Tetrasphaera and Mesorhizobium may have a key role in determining the response to cancer immunotherapy for lung cancer.},
}
@article {pmid41282313,
year = {2025},
author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Tahir, M and Zhong, J},
title = {Multi-omics profiling reveals microbial regulation of a key aromatic ester phenethyl acetate formation in fermented alfalfa and its impact on sheep feed preference.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103249},
pmid = {41282313},
issn = {2590-1575},
abstract = {This study utilized headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) to identify the key volatile flavor compounds in fermented alfalfa. The contribution of core microbiota to forming these key flavor compounds was investigated using a combination of absolute quantification of 16S rRNA gene copy number and metagenomic technology. Additionally, the critical roles of core fermentation microorganisms were quantitatively detected and validated through liquid chromatography mass spectrometry (LC-MS). Results revealed that Lactiplantibacillus plantarum B90 treated group achieved superior fermentation quality, with esters and aldehydes being the dominant volatile flavor compounds. Phenethyl acetate was the only aromatic ester that was significantly up-regulated after fermentation. The aryl alcohol dehydrogenase from L. plantarum facilitated the conversion of phenylacetaldehyde into phenylethyl alcohol, which serves as the precursor for phenethyl acetate. Furthermore, fermented alfalfa sprayed with phenethyl acetate was associated with increased feed intake in sheep. These findings propose new insights for microbial modulation of fermented flavor in fermented forage to enhance sheep feed intake.},
}
@article {pmid41282134,
year = {2025},
author = {Zitvogel, L and Carrier, A and Manghi, P and Silva, CAC and Lahmar, I and Birebent, R and Suissa, D and Laheurte, C and Schreibelt, G and Lemant, L and Fahrner, JE and de Sousa, E and Berthier, F and Villemonteix, J and Chevalier, M and Piccinno, G and Hocquet, D and Lebhar, I and Maeurer, M and Caillat-Zucman, S and Kroemer, G and Derosa, L and Launay, O and Golden, E and Bol, K and De Vries, IJM and Adotévi, O and Segata, N and Formenti, S and Kobold, S and Pieper, D and Vital, M and Santos-Peral, A and Zaucha, M and García-Bengoa, M and Thorn-Seshold, J and Stirling, H and Rothenfusser, S and Iebba, V and Almonte, A and Ajami, N and White, M and Sahasrabhojane, P and Hoballah, Y and Losh, J and DePinho, C and Dondossola, E and Wargo, J},
title = {Gut microbiota: a new factor modulating the immunizing potential of viral and cancer vaccines.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4294379/v1},
pmid = {41282134},
issn = {2693-5015},
abstract = {Vaccines represent a major public health intervention against infectious diseases and potentially cancer. Surrogate markers of vaccine efficacy usually rely on neutralizing antibody titers afflicted by high interindividual variabilities. Automated multiplexed T cell assays currently allow to test the clinical relevance of T lymphocyte responses during vaccine rollout. We examined cellular and/or humoral immune responses in five independent cohorts of health care workers, young healthy individuals and patients with cancer (melanoma or lung cancer) receiving various immunizing formulations (non-replicating, viral/tumoral, mRNA/peptides/cellular/viral particles). Here we show that about 20% of vaccinees to non-replicating formulations fail to mount protective antibody and Th1/Tc1 responses while 9% receiving a live vaccine were hyperresponders. Vaccine outliers could at least in part be attributed to gut dysbiosis at baseline, evaluated by shotgun metagenomics-based machine learning or the TOPOSCORE. These findings highlight the requirement of diagnostic tools to identify intestinal dysbiosis, as well as microbiota-centered interventions to optimize the efficiency of mass vaccinations.},
}
@article {pmid41282078,
year = {2025},
author = {Rumi, MA and Nguyen, L and Davis, BC and Brown, CL and Pruden, A and Zhang, L},
title = {Mapping the underlying drivers of resistome risk across diverse environments.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7085902/v1},
pmid = {41282078},
issn = {2693-5015},
abstract = {Background Understanding the drivers of antimicrobial resistance (AMR) across the One Health spectrum is crucial for controlling its spread. The MetaCompare framework, which assesses "resistome risk" based on antibiotic resistance gene (ARG) co-occurrence patterns on metagenomic contigs, has been expanded to distinguish between "ecological resistome risk" (ERR) and "human health resistome risk" (HHRR) scores across anthropogenic gradients. However, comprehensive surveys are still needed to untangle the biological (e.g., ARG relative abundance), ecological (e.g., taxonomic diversity), and technical (e.g., coverage) factors influencing these risk scores. Here, we analyzed 1,326 metagenomes from 12 key environments using the MetaCompare 2.0 pipeline to map global ERR and HHRR landscapes, identifying significant factors modulating risk scores through network analysis, machine learning, and multivariate regression models. Results ERR and HHRR scores varied significantly across environments and were highly correlated (ρ = 0.73, p < 2e-16), indicating shared underlying drivers. Transient environments closely linked to human activity, such as wastewaters and the human gut, produced the highest ERR and HHRR scores, while stable environments like sediments, soils, and activated sludge yielded the lowest. These patterns corresponded directly with taxonomic diversity, where more diverse ecosystems exhibited lower risk scores, supporting the hypothesis that niche occupation may act as an ecological barrier to ARG invasion. In contrast, scores were positively correlated with sul1 and crAssphage, further confirming that transient, low-diversity environments have higher resistome risks, although they did not fully account for risk variability across all environments. ARG relative abundance correlated with risk scores, but only in high-diversity, low-coverage environments due to poor assembly quality and an inability to resolve ARG flanking regions. The ARGs contributing to ERR and HHRR scores were largely aligned with existing ARG risk ranking frameworks. Conclusions This study demonstrated how the MetaCompare 2.0 pipeline can effectively disentangle complex relationships between ARG abundance, composition, and environmental context. Although robust across diverse environments, the framework's ability to detect ARGs and their co-occurrences may be limited in high-diversity, low-coverage samples, such as soils and sediments. Finally, we provide a series of recommendations for appropriate use cases for MetaCompare 2.0.},
}
@article {pmid41282070,
year = {2025},
author = {Bowie, K and Luhung, I and Burke, T and Roberts, S and Martinello, R and Gerstein, M and Peccia, J and Healy, H},
title = {Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7888495/v1},
pmid = {41282070},
issn = {2693-5015},
abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas . Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.},
}
@article {pmid41281954,
year = {2025},
author = {Johnston, PI and Chizani, K and Chirwa, E and Dale, H and Patel, P and Silungwe, N and Mkwangwanya, C and Kachala, T and Mhango, C and Nyirenda, G and Diness, Y and Mpesi, S and Wachepa, R and Shumba, F and Mwakiseghile, F and Rashid, V and Misiri, T and Ashton, PM and Chunga, A and Cocker, D and Cunningham-Oakes, E and Jewell, C and Feasey, N and Gordon, MA and Nyirenda, T},
title = {Transmission dynamics for invasive Non-Typhoidal S almonella serovars (TiNTS): protocol for a household study of transmission and immune response to non-typhoidal Salmonella in Malawi.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {581},
pmid = {41281954},
issn = {2398-502X},
abstract = {BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) disease is a leading cause of community-onset bloodstream infection in Africa, driving high morbidity in young children. The World Health Organization has published preferred product characteristics for an iNTS vaccine, but lack of transmission data is an impediment to vaccine licensure. Enteric NTS (eNTS) is the asymptomatic carriage of NTS in stool that precedes invasive disease. We do not know how long eNTS shedding lasts, how often infection spreads in endemic settings, or how an eNTS episode shapes immunity against later invasion. These gaps make it difficult to define trial sites, select cohorts, refine target product profiles, and build reliable models of vaccine impact. Here we describe TiNTS, a prospective household study in Blantyre, Malawi, which will measure real-time eNTS incidence, transmission, and antibody responses to close these evidence gaps and accelerate rational vaccine deployment.<br><br>METHODS: We will recruit all members of at least 60 households in Ndirande, Blantyre, Malawi. Stool samples will be collected every other day for at least four weeks and tested for NTS using culture and pan- Salmonella PCR on growth media. Environmental samples collected at enrolment will be tested using the same methods. Symptoms and exposure risks will be recorded throughout.We will collect blood samples at enrolment, after four weeks, and four weeks after the first eNTS episode in each household. We will measure serum IgG responses to Salmonella Typhimurium and Enteritidis LPS antigens. We will extend follow-up if participants continue shedding or if the first household case occurs with fewer than 14 days of follow-up remaining.All culture-positive isolates and PCR-positive broths will undergo Illumina sequencing to enable genome and metagenome reconstruction for transmission inference.<br><br>CONCLUSIONS: TiNTS will define the burden, transmission patterns, and immune response to eNTS. Findings will inform vaccine modelling, trial design, and targeted introduction strategies.},
}
@article {pmid41281952,
year = {2025},
author = {Marangon, E and Ramsby, BD and Luter, HM and Bell, SC and Laffy, P and Webster, NS and Hentschel, U and Fiore, C and Oatley, G and Thomas, T and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Cliona cf. orientalis Thiele (1900) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {342},
pmid = {41281952},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Cliona cf. orientalis (Porifera; Demospongiae; Clionaida; Clionaidae). The genome sequence has a total length of 217.17 megabases. Most of the assembly (98.28%) is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,502 protein-coding genes. Furthermore, three prokaryotic binned genomes were generated, including a high-quality metagenome-assembled genome (MAG) of the family Parvibaculaceae. Although Symbiodiniaceae sequences were also identified, a complete genome assembly could not be generated due to low coverage.},
}
@article {pmid41280484,
year = {2025},
author = {Zhu, Y and Pan, R and den Haan, R and Jiang, Y and Xin, F},
title = {Recent progress on the bioconversion of lignocellulose to fuels and chemicals.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {443},
pmid = {41280484},
issn = {2190-572X},
abstract = {With the continuous strengthening of green and sustainable development, chemical production is entering a new era. Lignocellulose, a widely available renewable biomass, offers potential for biofuel and chemical production; however, its complex structure hinders efficient utilization. Accordingly, this review will first summarize the required enzymes for its degradation based on the structural characteristics of lignocellulose. Oriented by bioconversion technology, pretreatment methods of lignocellulose are elaborated in detail. Additionally, we introduce four mainstream process configurations including separate hydrolysis and fermentation, simultaneous saccharification and fermentation, simultaneous saccharification and co-fermentation, consolidated bioprocessing. As is well known, the production of biofuels and bio-based platform chemicals is critically important for ensuring energy security and reducing greenhouse gas emissions. Thus, this review summarizes typical high value-added products synthesized from lignocellulose, including biofuels (bioethanol, biobutanol, biodiesel, biohydrogen), bulk chemicals (lactic acid, succinic acid, malic acid), and fine chemicals (vanillin, xylitol, carotenoids). Finally, we discuss the technological challenges and innovative solutions of lignocellulose bioconversion, while briefly mentioning the life cycle assessment.},
}
@article {pmid41280427,
year = {2025},
author = {Soni, PK and Kala, A and Agarwal, P and Deka, R and Rahman, H and Vijayalakshmy, K and Chaudhary, LC},
title = {Taxonomic and functional shifts in the rumen microbiome of buffalo calves under long-term strategic supplementation of phyto-feed additives.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1647762},
pmid = {41280427},
issn = {2297-1769},
abstract = {INTRODUCTION: The present study aimed to understand the shift in the rumen microbiome of buffaloes fed diets with and without phyto-additives. The rationale was based on the hypothesis that plant-based additives can modulate the microbial population in the rumen, potentially reducing methane production and enhancing fiber degradation. Given the possibility that prolonged use of the same additives may lead to microbial adaptation and diminished efficacy, the study also investigated the effects of periodically switching additives.<br><br>METHODS: Three male buffalo calves were fed a control diet, while another three received additive-supplemented diets. Two additive formulations were used: FAI (a blend of garlic Allium sativum, ajwain Trachyspermum ammi, harad Terminalia chebula, and soapnut Sapindus mukorossi) and FAII (ajwain oil). The additives were alternated every 15 days to prevent microbial adaptation. After 21 days of feeding, rumen liquor samples were collected 2 hours post-feeding for metagenomic analysis. The study included both in vivo and in vitro assessments of rumen fermentation.<br><br>RESULTS: Metagenomic analysis revealed that dominant bacterial phyla included Prevotella, Bacteroides, Succiniclasticum, Fibrobacter, Clostridium, Alistipes, Ruminococcus, and Butyrivibrio, with over 50 bacterial species consistently present across all animals. The main archaeal phylum was Euryarchaeota (>85%), along with notable presence of Candidatus_Bathyarchaeota and Thaumarchaeota. At the genus level, Methanomicrobium and Methanobrevibacter each accounted for approximately 30% of the archaeal community, followed by Methanosphaera, Methanosarcina, and Methanomassiliicoccus. While total abundances of Archaea and Bacteroidota were not significantly different among groups, specific taxa within these phyla showed marked changes.<br><br>DISCUSSION: The inclusion of phyto-additives in the buffalo diet influenced the rumen microbiome composition by reducing methanogen populations, particularly Methanobrevibacter, and enhancing fiber-degrading microbial communities. These microbial shifts were associated with improved fiber utilization and decreased methane emissions. Rotating the additives every 15 days appeared to sustain their efficacy over time, potentially by preventing microbial adaptation. This approach may offer a sustainable strategy to optimize rumen function and reduce enteric methane emissions in ruminants.},
}
@article {pmid41280102,
year = {2025},
author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, L and Yeow, C and Alvarado, LV and Adams, PD and Banfield, J and Siegel, JB and Prywes, N and Shih, PM},
title = {Diversity-driven biochemical survey reveals dimeric structural origin of rubisco.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.686826},
pmid = {41280102},
issn = {2692-8205},
abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sampled and synthesized a library of diverse rubisco sequences with an emphasis on clades that have previously not been characterized. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily -- in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize the largest rubisco described to date, originating from a cryptic, early-branching subclade with novel structural folds that have previously not been observed in the rubisco superfamily. By integrating biochemical data with an updated phylogenetic framework, we propose a revised nomenclature for the rubisco protein family that reflects current insights and will better accommodate future discoveries.},
}
@article {pmid41280077,
year = {2025},
author = {Diaz, L and Kong, AX and Zhang, P and Chi, J and Pham, K and Johnson, M and Eno, A and Douglas, I and Mao, Y and MacDonald, JW and Cui, JY and Bammler, T and Gu, H and Geng, Y},
title = {Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41280077},
issn = {2692-8205},
abstract = {Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPF's contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrate's rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.},
}
@article {pmid41279986,
year = {2025},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and , and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.685084},
pmid = {41279986},
issn = {2692-8205},
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, we used constraint-based metabolic modelling to associate an increased risk of AD with altered production of microbiome-derived metabolites. In this study, we investigated whether these previous results can also be identified in AD patients. Therefore, we created personalised whole-body metabolic models from gut metagenomics samples from 34 AD dementia patients, 51 individuals with mild cognitive impairments, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found an increased capacity of AD host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD dementia patients and patients with mild cognitive impairments. The metabolic predictions were then mechanistically linked to gut microbial changes in AD. This analysis identified that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron were key factors driving the predicted metabolic changes. Furthermore, the predicted altered microbial influences on blood metabolites were also associated with allelic variations in the APOE risk gene in healthy individuals, which confirmed our previous findings. In conclusion, we identified blood metabolites whose perturbations in AD may be influenced by gut microbiota and predicted the key microbial drivers for these metabolic influences. These findings may facilitate the development of microbiome-informed treatments of AD.},
}
@article {pmid41279864,
year = {2025},
author = {Andersen, SE and Kirsch, JM and Singh, N and Garret, SR and Whitney, JC and Hesselberth, JR and Duerkop, BA},
title = {Serine recombinases are conserved genetic markers of antiphage defense systems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.07.681051},
pmid = {41279864},
issn = {2692-8205},
abstract = {Antiphage defense systems confer bacteriophage (phage) resistance in bacteria. Renewed interest in phage therapy indicates a need to understand the breadth and molecular mechanisms of antiphage defenses. Traditionally, strategies to identify antiphage defenses lack throughput or are biased toward model bacteria. Herein, we developed a bioinformatic pipeline that uses a serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our informatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage effector domains and prokaryotic Schlafen proteins support phage defense. Our work shows that serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.},
}
@article {pmid41279814,
year = {2025},
author = {Lucas, A and Reale, M and Wolf, YI and Duong, B and Zhang, Y and Wickramasinghe, J and Behlman, L and Jones, SM and Higgins, S and Moustafa, AM and Elbasir, A and Amaravadi, R and Mitchell, T and Huang, A and Auslander, N},
title = {Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.686285},
pmid = {41279814},
issn = {2692-8205},
abstract = {The gut microbiome has been causally linked to the efficacy of immune-checkpoint inhibitor therapy (ICI), prompting numerous clinical trials of microbiome-targeting strategies. Yet, mechanisms by which gut microbiota shape immune responses remain elusive as taxonomic biomarkers have failed to generalize across multiple cohorts. In this study, we develop a taxonomy-agnostic framework to identify microbial biomarkers of ICI response and immune-related adverse event (irAE) occurrence from metagenomic sequencing. Applying this approach to four independent melanoma cohorts from clinical centers across the United States, we uncover gut microbial proteins produced by diverse bacterial taxa that consistently predict ICI response. Notably, we uncover a previously uncharacterized operon involved in cellular redox homeostasis that is encoded by different bacteria and reliably predicts irAE occurrence. We further validated the predictive power of this operon in a prospectively sequenced melanoma cohort. Our results demonstrate that taxa-agnostic microbial protein biomarkers are robust, generalizable, and provide a path towards pretreatment risk stratification for melanoma patients initiating ICI therapy.},
}
@article {pmid41279647,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.25.645238},
pmid = {41279647},
issn = {2692-8205},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached bacteria and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.},
}
@article {pmid41279399,
year = {2025},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, J and Yin, Y},
title = {Mucinolysome in gut microbiomes of farm animals and humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682383},
pmid = {41279399},
issn = {2692-8205},
abstract = {Mucins are glycoproteins that create a protective barrier protecting host tissues from microbial pathogens and are instrumental for host health. Here, we provide evidence that mucin glycan degradation in the gut can be mediated by mucinolysomes, defined as extracellular multi-enzyme complexes specializing in mucin glycan degradation. We computationally predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of anaerobic Limousia bacteria, including seven MAGs from human samples of six countries. All 65 genomes were found to display core mucinolysome components, consisting of 3∼6 scaffoldins (containing up to 12 cohesin modules) and up to 22 dockerin-containing mucin glycan-degrading CAZymes (carbohydrate active enzymes). The organization of mucinolysomes allows the assembly of up to 24 CAZymes in the same complex. We validated that a cultivated Limousia strain ET540 from chicken cecum can support growth on mucins as its sole carbon source, triggering the expression of most mucinolysome-related genes, including both scaffoldins and CAZymes. We also modeled the assembly of proteins into a multi-enzyme complex by predicting the cohesin-dockerin interactions among most of the mucinolysome proteins using AlphaFold3. While mucinolysosome-encoding Limousia have low abundance in different animal hosts, their abundance and prevalence are higher in farm animals than in humans, highlighting a potentially important role in livestock gut ecosystems. Our findings reveal a novel mechanism of mucin glycan degradation and provide a framework to explore microbial contributions to gut health and host-microbe interactions across species.},
}
@article {pmid41279300,
year = {2025},
author = {Yancey, CE and Brumfield, KD and Buss, J and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.09.681436},
pmid = {41279300},
issn = {2692-8205},
abstract = {Advances in next generation sequencing have made it possible to explore microbial community dynamics and regulation of functionally important genes through metagenomics and metatranscriptomics. However, the use of meta-omics to link enzyme function directly with complex, community-level phenotypes remain largely unexplored. To overcome this gap, we developed a novel framework that integrates ecological concepts by microbial community perturbation with association analysis to a targeted phenotype. Specifically, we introduce a hypothesis-free "bait and switch" strategy demonstrated through salt marsh soil microcosm pulse experiments to detect and characterize novel enzymes responsible for chitin degradation. Soil microbial communities were "baited" with shell compost, a chitin-rich substrate, to trigger community succession toward chitin degraders and gene upregulation of chitinases. A "switch" was then employed, by addition of glucose, inducing rapid downregulation of genes putatively responsible for chitin degradation. Results demonstrate the feasibility of this approach to identify functionally important enzymes, in this example, 48 hours after chitin addition. The bait and switch community perturbation provides a framework for discovery of polymer degrading enzymes present in complex microbial communities and serves as a proof of concept applicable for linking enzyme function with emergent community level phenotypes.},
}
@article {pmid41279291,
year = {2025},
author = {Camargo, AP and Baltoumas, FA and Ndela, EO and Fiamenghi, MB and Merrill, BD and Carter, MM and Pinto, Y and Chakraborty, M and Andreeva, A and Ghiotto, G and Shaw, J and Proal, AD and Sonnenburg, JL and Bhatt, AS and Roux, S and Pavlopoulos, GA and Nayfach, S and Kyrpides, NC},
title = {A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.01.686033},
pmid = {41279291},
issn = {2692-8205},
abstract = {Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic representation, sparse taxonomic classification, and insufficient functional annotation, hindering detailed investigation into phage biology. Here, we present the Unified Human Gastrointestinal Virome (UHGV), a collection of 873,994 viral genomes from globally diverse populations that addresses these limitations. UHGV provides high-quality virome references with extensive host predictions, comprehensive functional annotations, protein structures, a classification framework for comparative analysis, and a web portal to facilitate data access. Using UHGV to profile worldwide metagenomes, we found that host range breadth is strongly associated with phage prevalence. Additionally, we identified diversity-generating retroelements and DNA methyltransferases as key factors enabling phage populations to access diverse hosts, revealing how specific genomic features contribute to global phage distribution patterns. UHGV is available at http://uhgv.jgi.doe.gov.},
}
@article {pmid41279261,
year = {2025},
author = {Schuran, FA and Mishra, N and López-Agudelo, VA and Sommer, N and Bernardes, JP and Walker, A and Hinrichsen, F and Gong, T and Gilbert, F and Schröder, L and Bhardwaj, A and Künzel, S and Weber-Stiehl, S and Ito, G and Tran, F and Groussin, M and Röcken, C and Matute, J and Schreiber, S and Penninger, JM and Blumberg, RS and Schmitt-Kopplin, P and Baines, JF and Sommer, F and Rosenstiel, P},
title = {Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.20.683425},
pmid = {41279261},
issn = {2692-8205},
abstract = {Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and function of the intestinal epithelium and its associated microbiota, we employed a comprehensive multi-omics approach, including (spatial) transcriptomics, DNA methylation analysis, fecal metagenomics, and metabolomics. Our findings show that PEM persistently alters the intestinal epithelium by depleting Paneth cells and suppressing antimicrobial gene expression - changes linked to DNA methylation that persist despite dietary recovery. In germ-free mice, the sustained epithelial phenotype after was absent. We identified the microbial lipid metabolite 9-HODE and epigenetically deregulated PPAR-driven GDF15 expression as key molecular drivers of the persistent PEM-induced Paneth cell dysfunction. Targeting microbial lipid production and its link to the host GDF15 pathway could offer novel therapeutic strategies for long-term consequences of malnutrition and other Paneth cell-associated diseases.},
}
@article {pmid41279255,
year = {2025},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.686673},
pmid = {41279255},
issn = {2692-8205},
abstract = {UNLABELLED: The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgae polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, macroalgae polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens , to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing were employed to distinguish the natural active fraction from transient gut microbiome taxa. Four media combinations were able to propagate between 96% to 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo . Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.<br><br>IMPORTANCE: Seaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes to propagate these active microbial communities in vitro . This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}
@article {pmid41279103,
year = {2025},
author = {Seki, K and Nguyen, MTA and Penev, PI and Banfield, JF and Isaacs, FJ and Jewett, MC},
title = {Engineered orthogonal translation systems from metagenomic libraries expand the genetic code.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.30.685624},
pmid = {41279103},
issn = {2692-8205},
abstract = {Genetic code expansion with non-canonical amino acids (ncAAs) opens new opportunities for the function and design of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation is limited both by a small collection of orthogonal aminoacyl-tRNA synthetases (aaRSs) and tRNAs and by low-throughput methods to discover them. Here, we report the discovery, characterization, and engineering of a UGA suppressing orthogonal translation system mined from metagenomic data. We developed an integrated computational and experimental pipeline to profile the orthogonality of >200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNA [Trp] UCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNA [Trp] UCA is highly active in cell-free and cellular contexts. We then use Ochre , a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion.},
}
@article {pmid41278862,
year = {2025},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole Metagenome Sequencing: not Deep Enough for Complete Microbial Function Recovery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.685665},
pmid = {41278862},
issn = {2692-8205},
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated.We analyzed oral-rinse WMS data from a study cohort including 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data were annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.<br><br>RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in e.g. case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire.<br><br>CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights.},
}
@article {pmid41278782,
year = {2025},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.23.683462},
pmid = {41278782},
issn = {2692-8205},
abstract = {Studies of whole viral populations--the "virome"--are yielding exciting new insights into biological systems, but methods are still being optimized. Here we describe generation and use of a synthetic viral community to assess several technical challenges important in virome analysis. Our mock community was comprised of phages lambda, T4, M13, MS2, and phi6, together with adeno-associated virus (AAV), murine hepatitis virus (MHV), and vaccinia virus (VV). We spiked the mock community into different human sample types, including stool, saliva, oropharyngeal (OP) wash, and bronchoalveolar lavage (BAL), then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared to direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from virus-rich samples such as from stool and saliva. Three VLP enrichment work flows were compared, and each was found to have strengths and weaknesses. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. Bacteriophage DNA can be modified by at least 12 different chemistries, raising the question of whether these modifications might block recovery in virome analytical protocols. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC), and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.},
}
@article {pmid41278757,
year = {2025},
author = {Luo, RS and Kille, B and Vaughan, EE and Clark, JR and Maresso, AW and Nute, MG and Treangen, TJ},
title = {Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.10.681738},
pmid = {41278757},
issn = {2692-8205},
abstract = {MOTIVATION: Strain-level microbiome profiling has revealed key insights into microbial community composition and strain dynamics. However, accurate strain-level analysis remains challenging due to limited linkage information, ambiguous read mapping, and complicating factors such as genome similarity, sequencing depth, and community complexity. These challenges are especially pronounced for short-read metagenomic data when estimating the relative abundances of multiple strains, a task critical for genotype-phenotype association studies.<br><br>RESULTS: To address this gap, we present Strainify, which enables accurate strain-level abundance estimation from short-read metagenomes with as little as 1% genome coverage. Specifically, Strainify combines (1) identification of informative variants via core genome alignment, (2) filtering of confounding variants via a window-based test, and (3) maximum likelihood estimation of strain abundances. A Shannon entropy-weighted version of the model further improves robustness in noisy, low-coverage settings by downweighting sites with low information content. Across simulated communities of varying complexity, Strainify consistently outperformed existing approaches. On mock community sequencing data, Strainify's estimates aligned more closely with reference abundances. When applied to a longitudinal gut microbiome dataset, Strainify successfully recapitulated the reported temporal dynamics of Bacteroides ovatus strain groups, demonstrating its ability to recover biologically meaningful patterns from real-world metagenomes. Together, these results establish Strainify as a robust and versatile solution for accurate strain-level abundance estimation in short-read, low-coverage microbiome studies.<br><br>AVAILABILITY: The Strainify code and results are available at: https://github.com/treangenlab/Strainify.},
}
@article {pmid41278729,
year = {2025},
author = {Lu, R and Lee, N and Drake, AK and Fulton, RP and Abutaleb, NS and Seleem, M and Oakland, DN and Garin-Laflam, MP and Pop, M and Luo, XM},
title = {Discovery of Novel Probiotic Species to Improve Infant Health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.27.684727},
pmid = {41278729},
issn = {2692-8205},
abstract = {UNLABELLED: Selecting an appropriate infant formula can be challenging for parents given the wide range of available options, which may lead to suboptimal choices or frequent switching. Our recent studies in mice demonstrated that the maternal microbiota-particularly Limosilactobacillus reuteri present in breast milk-plays a critical role in shaping neonatal immunity by promoting the production of immunoglobulin A (IgA), a key antibody for defense against enteric pathogens. To extend these findings to humans, we analyzed fecal samples from healthy breastfed infants using shotgun metagenomic sequencing combined with whole-bacterial-cell ELISA to assess associations between specific taxa and pathogen-reactive IgA. We found that members of the Oscillibacter species (including Oscillibacter sp. KLE1728, KLE1745, PC13, PEA192, and O. valericigenes) and Morganella (e.g., M. morganii, Morganella sp. EGD-HP17, and Morganella sp. HMSC11D09) were strongly correlated with IgA responses against Salmonella and Shigella . In contrast, IgA reactive to enterohemorrhagic Escherichia coli (EHEC) was associated with other genera, including Staphylococcus . Notably, Lactobacillus species (L. bombi, L. kefiri, L. equi , and L. rhamnosus) were consistently linked to elevated IgA responses against Salmonella, Shigella , and EHEC. Moreover, levels of anti- Salmonella and anti- Shigella IgA were positively correlated with the use of infant formula containing prebiotic fibers or human milk oligosaccharides (5-HMO). Collectively, these findings highlight novel commensal taxa with potential as probiotic candidates to guide the development of next-generation infant formulas aimed at enhancing mucosal immunity and supporting infant health.<br><br>IMPORTANCE: Early-life nutrition shapes immune maturation, yet the microbial factors driving mucosal antibody responses remain poorly defined. Through integrated metagenomic and IgA profiling, this study identifies commensal taxa, particularly Lactobacillus, Oscillibacter , and Morganella , associated with pathogen-specific IgA in infants. These taxa may enhance mucosal defense against enteric pathogens, revealing key microbial contributors to early immune development. The findings provide a foundation for designing next-generation infant formulas that leverage targeted probiotics or prebiotics to promote protective IgA responses and gut health.},
}
@article {pmid41278541,
year = {2025},
author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T},
title = {MeTAline: enabling reproducible and scalable metagenomic analyses.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf158},
pmid = {41278541},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; },
abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.},
}
@article {pmid41278535,
year = {2025},
author = {Berg, M and Reiter, T and Emerson, J and Brown, CT and Roux, S},
title = {Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf163},
pmid = {41278535},
issn = {2631-9268},
mesh = {*Soil Microbiology ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; },
abstract = {Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome regions and that long-read sequencing can complement short-read metagenomes by improving assembly contiguity and the recovery of variable regions.},
}
@article {pmid41278475,
year = {2025},
author = {An, W and Zhang, Y and Liu, Y and Yang, T and Bai, S and Zhou, P and Si, J and Zhao, Y and He, Y and Pan, Y and Jiang, Y},
title = {Impact of metagenomic sequencing on clinical outcomes in patients with suspected central nervous system infections: a retrospective case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1677092},
pmid = {41278475},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; *Central Nervous System Infections/diagnosis/microbiology/cerebrospinal fluid/mortality ; Female ; Middle Aged ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Adult ; Treatment Outcome ; Hospital Mortality ; },
abstract = {OBJECTIVES: Although the value of metagenomic sequencing (mNGS) in diagnosing pathogens in central nervous system infections (CNSi) has been confirmed, its impact on the clinical outcomes of patients remains to be elucidated. This study intended to investigate the clinical impact of cerebrospinal fluid (CSF) mNGS on the outcomes of patients with suspected CNSi.<br><br>METHODS: Between January 2022 and July 2024, patients who met both the inclusion and exclusion criteria were enrolled in the study and assigned to either the mNGS group (CSF tested by both mNGS and conventional microbiological tests [CMTs]) or the CMT group (CMTs alone). Following this, propensity score matching (PSM) was applied to balance baseline differences. The primary endpoint, time to clinical improvement, was then compared between the two groups and analyzed in stratified subgroups. Secondary endpoints included the rates of clinical improvement at 14 and 30 days, hospital stay, in-hospital mortality, and the proportion of GCS score <15.<br><br>RESULTS: A retrospective analysis of 338 patients was conducted, with 169 cases in each group. In the mNGS group, a comparison of diagnostic performance between the two testing methods demonstrated that mNGS yielded a significantly higher positivity rate in patients with CNSi compared to CMTs (67.5% vs. 18.3%, p < 0.001), identifying 111 pathogens in total, which was substantially more than the 24 detected by CMTs. Subsequent comparison of clinical outcomes between the groups showed that the duration until clinical improvement was significantly reduced in the mNGS group when compared to the CMT group (median: 14 days vs. 17 days; p=0.032). Moreover, a significantly higher percentage of patients in the mNGS group experienced clinical improvement within 14 days compared to those in the CMT group(42.6% vs. 31.4%; p=0.032). Subgroup analysis further revealed that the mNGS group's superiority in clinical improvement over the CMT group was only evident in patients with CNSi, especially when complicated by pneumonia.<br><br>CONCLUSION: The combination of mNGS with CMT significantly improves the clinical outcome of CNSi patients, offering greater clinical utility than traditional methods alone.},
}
@article {pmid41278474,
year = {2025},
author = {Huang, R and Zhang, Y and Dong, C and Chen, J and Zou, H and Liu, Y and Guo, M and Gao, H and Ke, Q and Wu, W},
title = {Clinical application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1661213},
pmid = {41278474},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; *Pneumonia/diagnosis/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Intensive Care Units ; Adult ; Fungi/genetics/isolation &amp; purification/classification ; *Pneumonia, Bacterial/diagnosis/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Severe pneumonia is a significant cause of mortality among ICU patients. Metagenomic next-generation sequencing (mNGS) is an advanced, comprehensive, unbiased diagnostic tool for pathogen identification in infectious diseases. This study aimed to evaluate the clinical efficacy of mNGS for diagnosing severe pneumonia.<br><br>METHODS: This study retrospectively analyzed 323 patients with suspected severe pneumonia admitted to the intensive care unit (ICU) of Wuhan University Renmin Hospital between January 2022 and December 2023. Bronchoalveolar lavage fluid (BALF) samples were collected from all 323 patients, and blood samples were obtained from 80 patients. Both mNGS and conventional microbial testing (CMT) were performed on the collected BALF and blood samples to analyze the pathogen spectrum. The diagnostic performance of mNGS and CMT was systematically evaluated and compared.<br><br>RESULTS: The overall positivity rate of mNGS was significantly greater than that of CMT (93.5% vs. 55.7%, p < 0.001). mNGS demonstrated significantly greater sensitivity than did CMT (94.74% vs. 57.24%, p < 0.001) but lower specificity (26.32% vs. 68.42%, p < 0.01). mNGS identified 36 bacterial species, 14 fungal species, 7 viral species, and 1 Chlamydia species, whereas CMT detected 21 bacterial species and 9 fungal species. According to the pathogen spectrum, Klebsiella pneumoniae, Acinetobacter baumannii, and Candida albicans were the predominant pathogens associated with severe pneumonia. The detection rate of mixed infections was significantly higher with mNGS than with CMT (62.8% vs. 18.3%, p < 0.001).<br><br>CONCLUSIONS: Compared with CMT methods, mNGS has significant advantages in pathogen detection for severe pneumonia. Owing to its broad detection range and high sensitivity, mNGS serves as a valuable complementary approach to traditional culture-based methods.},
}
@article {pmid41278471,
year = {2025},
author = {Wang, Y and Guo, P and Chen, Y and Zhu, H and Yu, X and Deng, J},
title = {Comparison and evaluation of metagenomic next-generation sequencing (mNGS) and real-time PCR for the detection of Mycobacterium tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694179},
pmid = {41278471},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Real-Time Polymerase Chain Reaction/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Metagenomics/methods ; Male ; Female ; Adult ; *Tuberculosis/diagnosis/microbiology ; Middle Aged ; Sputum/microbiology ; Aged ; *Molecular Diagnostic Techniques/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Young Adult ; Adolescent ; },
abstract = {OBJECTIVE: This study aimed to evaluate and compare the performance of metagenomic next-generation sequencing (mNGS) and real-time polymerase chain reaction (RT-PCR) for the detection of Mycobacterium tuberculosis (MTB) in patients with suspected tuberculosis (TB).<br><br>METHODS: Samples from patients undergoing routine clinical testing for MTB using both mNGS and RT-PCR were included. The diagnostic agreement between the two methods was assessed. Discordant results were further validated using the Xpert MTB/RIF assay on cryopreserved aliquots.<br><br>RESULTS: A total of 556 samples from suspected TB patients were analyzed. The majority were lower respiratory tract specimens, including bronchoalveolar lavage fluid (BALF; 94.06%), sputum (3.24%), and extrapulmonary samples (2.70%). Compared with Xpert MTB/RIF and clinical diagnosis as composite reference standard, both mNGS and RT-PCR showed high sensitivity (92.31% and 90.38%, respectively) and perfect specificity (100%). There was a high level of agreement between mNGS and RT-PCR, with a positive agreement of 82.69%, negative agreement of 98.25%, overall agreement of 98.38%, and a kappa value of 0.896 (P < 0.001). Concordance was higher in samples with lower RT-PCR cycle threshold (Ct) values: 100% at Ct &#x2264; 15, 100% at 15<Ct &#x2264; 20, 76.47% at 20<Ct &#x2264; 25. Among concordant positive samples (n=43), mNGS SMRNs showed a strong negative correlation with RT-PCR Ct values (r = -0.668, P < 0.001). Analysis of nine discordant cases identified five mNGS-positive/RT-PCR-negative samples with low SMRNs (median: 7 vs. 1788 in concordant positives), four of which were confirmed by Xpert MTB/RIF to have extremely low bacterial loads. The remaining four mNGS-negative/RT-PCR-positive samples exhibited higher Ct values (median: 22.97 vs. 17.06 in concordant positives), and three of these were also verified by Xpert MTB/RIF to contain extremely low bacterial concentrations.<br><br>CONCLUSION: Both RT-PCR and mNGS demonstrate high overall agreement for MTB detection, with concordance strongly influenced by microbial burden. These findings support the complementary use of these methods in the diagnosis of TB.},
}
@article {pmid41278154,
year = {2025},
author = {Zheng, L and Duan, SL and Wang, K},
title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {31},
number = {42},
pages = {113170},
pmid = {41278154},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; },
abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.},
}
@article {pmid41278038,
year = {2025},
author = {Li, B and Liao, Y and Li, J},
title = {Legionella-induced suppurative cervical lymphadenitis in a child diagnosed by metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1655298},
pmid = {41278038},
issn = {2296-2360},
abstract = {Legionella pneumophila, primarily associated with respiratory infections, rarely causes extrapulmonary disease. Conventional diagnostic methods for Legionella are often limited. Here we report a case of suppurative cervical lymphadenitis caused by L. pneumophila. And we highlight the critical role of mNGS in enabling rapid and accurate pathogen identification, guiding effective targeted therapy for rare and challenging infections.},
}
@article {pmid41278006,
year = {2025},
author = {Minch, B and Moniruzzaman, M},
title = {BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf284},
pmid = {41278006},
issn = {2635-0041},
abstract = {MOTIVATION: Viruses in the kingdom Bamfordvirae, specifically giant viruses (NCLDVs) in the phylum Nucleocytoviricota and smaller members in the Preplasmiviricota phylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom, such as giant viruses, polinton-like viruses, and virophages, have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets.<br><br>RESULTS: Here, we present, BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, and Preplasmiviricota genome identification and annotation. BEREN's performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs and Preplasmiviricota genomes. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis.<br><br>BEREN is available at https://gitlab.com/benminch1/BEREN, and results from testing BEREN on a real-world metagenome are available in the Supplementary Files.},
}
@article {pmid41277975,
year = {2025},
author = {Wang, B and Li, W and Xue, N and Xi, R and Wang, Y and Fang, L and Wang, Q and Liang, X and Xiao, Y and Yang, X and Wu, X},
title = {Co-application of biochar and compost enhanced soil carbon sequestration in urban green space.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1707894},
pmid = {41277975},
issn = {1664-302X},
abstract = {The mechanism of biochar and compost as soil amendments in urban green spaces remains unclear. Using Euonymus kiautschovicus as a model system, this study established eight treatment gradients, 0 (CK), single biochar applications: 4% (BC4), 8% (BC8), 12% (BC12), 7.5% compost (COM), and their combinations BCC4 (BC4 + 7.5% COM), BCC8 (BC8 + 7.5% COM), BCC12 (BC12 + 7.5% COM). Through metagenomic sequencing and metagenome-assembled genomes (MAGs) analysis, we investigated soil microbiome structure, carbon sequestration functional genes, and their interactions in response to amendments. The combined application of medium-low dose biochar (4-8%) with compost significantly optimized the physicochemical properties and microbial functions in soils. Compared to single amendments, hybrid treatments synergistically enhanced soil moisture content. Specifically, BCC8 increased by 27% compared to the CK, organic carbon levels reached 12.8 g/kg with BCC12, and available nutrients showed 45% higher available phosphorus with BCC4. Metagenomic analysis revealed that hybrid treatments reshaped microbial community structure, with BCC8 significantly enriching Acidobacteria (8.72%) and Nitrospira (1.42%), driving an increased abundance of carbon fixation genes. Among key carbon fixation pathways, the reductive tricarboxylic acid cycle (rTCA) exhibited the highest gene abundance (mean 15.03), dominated by MAG176. The Calvin-Benson-Bassham (CBB) cycle displayed broad adaptability, with MAG59 identified as a core carbon-fixing strain. This study has significant implications for the application of biochar-compost combinations in carbon management of urban green spaces.},
}
@article {pmid41277970,
year = {2025},
author = {Chapagain, C and Khezri, A and Ali, J and Smistad, M and Sølverød, LS and Ahmad, R},
title = {Optimizing sample preparation for culture-free nanopore sequencing to enable rapid pathogen and antimicrobial resistance profiling in bovine mastitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680165},
pmid = {41277970},
issn = {1664-302X},
abstract = {Long-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk is challenging due to the complex milk matrix, low bacterial count, and high somatic cell content. This study primarily aimed to further optimize our previously developed culture-free nanopore sequencing protocol for milk samples from mastitis cases. Additional optimizations included combining centrifugation, gradient centrifugation, and fat fraction treatment with Tween 20 and citric acid. Subsequently, four DNA extraction kits (Blood and Tissue, Molysis Complete5, HostZero, and SPINeasy Host depletion) were evaluated for their ability to remove host DNA and enrich bacterial DNA for long-read sequencing with Oxford Nanopore technologies. qPCR was used to quantify bacterial and bovine DNA, allowing comparison of host depletion efficiency among the kits. Our results show that simple centrifugation effectively concentrates bacterial cells, removing the need for chemical treatments. The HostZero kit consistently produced higher DNA yields, improved DNA integrity, and more effective host DNA depletion. Using nanopore sequencing, both Gram-positive and Gram-negative mastitis pathogens, along with their AMR genes, were successfully detected. Overall, this study underscores the importance of an effective DNA extraction method for the direct sequencing of mastitis milk samples. Additionally, our findings support the potential of direct metagenomic sequencing as a rapid, culture-free approach for identifying mastitis pathogens and their resistance profiles.},
}
@article {pmid41277885,
year = {2025},
author = {Solís, VE and Bangratz, M and Brugo Carivali, MF and Comte, A and Luciani, CE and Lacombe, S and Fontana, ML and Filloux, D and Pachecoy, MI and Fernandez, E and Dirchwolf, PM and Ayala, JOA and Julian, C and Kruger, RD and Hébrard, E and Fernandez, FD and Perotto, MC and Roumagnac, P and Gutiérrez, SA and Poulicard, N and Celli, MG},
title = {Near-complete genome sequences of a rice necrosis mosaic virus isolate infecting rice in Argentina.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059825},
doi = {10.1128/mra.00598-25},
pmid = {41277885},
issn = {2576-098X},
abstract = {While rice necrosis mosaic virus (RNMV) has only been described in Asia, we identified this virus on a rice plant from Argentina using a viral metagenomic approach. We further confirmed this result by RT-PCR and small-RNA Illumina sequencing to obtain the near-complete genome and to confirm actual infection by RNMV.},
}
@article {pmid41277537,
year = {2025},
author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH},
title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1190},
pmid = {41277537},
issn = {1362-4962},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; },
abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.},
}
@article {pmid41276871,
year = {2025},
author = {Torres-Beltrán, M and Hernández-Guzman, M and Barcelos, C and Chong-Robles, J and Sidón-Ceseña, K and García-Maldonado, JQ and Aguirre-Macedo, ML and Lago-Lestón, A},
title = {Alternative carbon and energy metabolisms linked to hydrocarbon degradation are widely distributed across the different microbial communities from deep-sea sediments of the Gulf of Mexico.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00823-1},
pmid = {41276871},
issn = {2524-6372},
support = {201441/WT_/Wellcome Trust/United Kingdom ; Postdoctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Master fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Doctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
abstract = {In marine sediments, microorganisms' roles in recycling organic and inorganic molecules, including hydrocarbons, are critical for ecosystem function. Genomic studies in the Gulf of Mexico (GoM) reveal that microbial community composition and function are shaped by environmental gradients, with hydrocarbon degradation relying on consortia dynamics rather than single species, highlighting their collective ecological importance. Our study evaluated the prokaryotic microbial community in deep-sea GoM sediments, under a depth gradient, in Coatzacoalcos and Perdido regions, two areas influenced by crude-oil efflux and petroleum extraction. Findings indicated depth was the primary driver of microbial community structure, with distinct compositional shifts between shallow (< 1000 m) and deep (> 1200 m) sediments, showcasing microbial adaptation to deep-sea nutrient-limited conditions. Furthermore, functional gene analysis revealed depth-specific metabolic partitioning, with Deltaproteobacteria dominating amino acid and energy metabolism in shallow sediments, while Alphaproteobacteria and Thaumarchaeota prevailed in deeper zones. This underlines the importance of microbial community shifts in composition and structure in ensuring environmental resilience. In addition, relatively low-abundance but critical hydrocarbon degradation genes were detected, primarily in shallow/transition zones, indicating niche-specific potential for bioremediation despite their apparent limited representation. This research contributes to advancing our understanding of alternative carbon and energy metabolisms linked to hydrocarbon degradation that are widely distributed across different microbial communities inhabiting deep-sea marine sediments.},
}
@article {pmid41275986,
year = {2025},
author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , },
title = {Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism.},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jrn.2025.10.015},
pmid = {41275986},
issn = {1532-8503},
abstract = {BACKGROUND AND HYPOTHESIS: Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.<br><br>METHODS: We conducted a non-randomized, open-label, three-phase pilot trial, to investigate the effect of daily oral oligofructose-enriched inulin (p-inulin) on stool functional metagenome and changes in plasma, urine and stool metabolites in 13 CKD patients. The study comprised a pre-treatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).<br><br>RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In the plasma metabolic biosynthetic pathways for valine, leucine and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and non-polar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.<br><br>CONCLUSION: P-inulin administration to CKD patients resulted a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.},
}
@article {pmid41275762,
year = {2025},
author = {Stevenson, EM and Buckling, A and Cole, M and Hayes, A and Lindeque, PK and Murray, AK},
title = {Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments.},
journal = {Environment international},
volume = {206},
number = {},
pages = {109944},
doi = {10.1016/j.envint.2025.109944},
pmid = {41275762},
issn = {1873-6750},
abstract = {Microplastic particles are extremely prevalent environmental pollutants which support microbial biofilms known as the 'plastisphere'. Antimicrobial resistant (AMR) and pathogenic bacteria have been detected in these communities, but it is currently unknown whether microplastics pose a unique risk in terms of AMR or pathogen enrichment. In addition, previous work has been largely lab-based, so it is difficult to understand the role of different substrates in supporting AMR pathogens within the environment, and how this varies as a function of levels of pollution from wastewater. This study investigated in situ bacterial colonisation dynamics on microplastics alongside natural, inert and free-living controls. Samples were incubated along a transect predicted to decrease in anthropogenic pollution, and taxonomy, AMR gene and pathogen presence were assessed using whole metagenome sequencing. Several AMR gene (e.g. aminoglycosides, oxazolidinones and tetracyclines) and pathogen classes (e.g. Flavobacteriia, Chlamydiia and Sphingobacteriia) of concern were detected, and increased in relative abundance in biofilms moving downstream, with polystyrene and HDPE nurdle communities posing a particular risk by supporting AMR bacteria. This work contributes to our understanding of how microplastics may support AMR development, persistence and dispersal in natural systems. In addition, these findings highlight the importance of considering the combined impacts of co-contaminants in wastewater settings, especially following spills into surface water.},
}
@article {pmid41275684,
year = {2025},
author = {Liu, Q and Chen, J and Xu, R and Huang, C and Ren, N and Gao, S and Li, W and Xin, X and Lv, S and Yang, S and Ben, W and Wang, AJ},
title = {Bacterial, viral and environmental interactions shape antibiotic resistance genes in China's anaerobic-anoxic-oxic wastewater treatment systems.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124911},
doi = {10.1016/j.watres.2025.124911},
pmid = {41275684},
issn = {1879-2448},
abstract = {The dissemination of antibiotic resistance genes (ARGs) threatens global public health. Urban wastewater treatment plants (WWTPs), serving as critical reservoirs and dissemination hubs for ARGs, are driven by complex bacteria-virus interactions and environmental factors in activated sludge. This study employed metagenomics and 16S rRNA gene sequencing of activated sludge from 28 A[2]O WWTPs across China to decipher the national distribution of ARGs and their associations with bacterium-phage systems and environmental factors. Research outcomes: fluoroquinolone resistance genes (adeF) and sulfonamide resistance genes (sul1, sul2) dominated ARG abundance (mean 41.7 %, 11.51 %), with significant regional differentiation (PERMANOVA, R[2] = 0.153, p = 0.043). The involvement of bacteria and viruses was significantly associated with ARG dissemination. Among these, Proteobacteria and Actinobacteria were identified as pivotal putative bacterial vectors. Additionally, Myoviridae was predicted to be the predominant viral host for ARGs, while Siphoviridae and Demerecviridae were preferentially associated with specific ARG types. Correlation analysis indicated that ions, such as cobalt, zinc and cadmium, were positively correlated with specific ARG subtypes, whereas arsenic was consistently negatively correlated with most ARG subtypes. Additionally, the oxidation-reduction potential was significantly linked to ARG abundance. This study reveals complex ARG association patterns from the perspective of bacteria-virus interactions and environmental factors, providing insights and a valuable reference for future phage-based control strategies and regional antibiotic resistance pollution policies.},
}
@article {pmid41275679,
year = {2025},
author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J},
title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124956},
doi = {10.1016/j.watres.2025.124956},
pmid = {41275679},
issn = {1879-2448},
abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.},
}
@article {pmid41275070,
year = {2025},
author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G},
title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66733-5},
pmid = {41275070},
issn = {2041-1723},
support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.},
}
@article {pmid41274992,
year = {2025},
author = {Becsei, &#xc1; and Stéger, J and Visontai, D and Munk, P and Aarestrup, FM and Csabai, I and Papp, K},
title = {A case study using sewage metagenomic data for assessment of text-to-SQL capabilities in large language models.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28341-7},
pmid = {41274992},
issn = {2045-2322},
support = {No. 874735 (VEO)//European Union's Horizon 2020 research and innovation programme/ ; U24AI183840//National Institute Of Allergy And Infectious Diseases of the National Institutes of Health/ ; RRF-2.3.1-21-2022-00004//National Research, Development, and Innovation Office of Hungary within the framework of the MILAB Artificial Intelligence National Laboratory/ ; },
abstract = {Relational databases offer an efficient solution for storing and retrieving complex data sets, yet the requirement for SQL programming expertise presents a significant challenge for many life science users. We explore whether a cutting-edge large language model can effectively translate plain English queries into SQL scripts (Text-to-SQL), thereby simplifying database interaction and eliminating the typical usage barriers. A complex database comprising 19 interconnected tables of metagenomic analyses from 239 sewage samples across five European cities was available. A large language model was provided with details of the database's structure and background information on its contents. We evaluated the functionalities of this "SewageGPT" tool and assessed the accuracy of its responses to complex questions and visualisation of results. Providing a detailed description of the database enabled SewageGPT to accurately respond to complex inquiries, accelerating the database querying process. Knowledge of the database content proved beneficial, as it minimized the risk of ambiguities in queries; however, ambiguities can lead to incorrect responses. Therefore, human oversight remains crucial, particularly for questions that lack detail or involve ambiguities. The integration of state-of-the-art large language models with direct database connectivity substantially enhances the efficiency of query generation, statistical analysis and visualization of the results.},
}
@article {pmid41274878,
year = {2025},
author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R},
title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66497-y},
pmid = {41274878},
issn = {2041-1723},
support = {R01HD109830//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32HD105364//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD080444//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.},
}
@article {pmid41274873,
year = {2025},
author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J},
title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66612-z},
pmid = {41274873},
issn = {2041-1723},
abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.},
}
@article {pmid41274479,
year = {2025},
author = {Xu, X and Hong, X and Zeng, W and Yan, R and Li, F and Meng, C and Shi, X and Luo, J and Wang, G},
title = {Stereoselective synthesis of (S)-3-Hydroxy-3-phenylpropionate with a novel carbonyl reductase identified from a soda lake metagenome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149193},
doi = {10.1016/j.ijbiomac.2025.149193},
pmid = {41274479},
issn = {1879-0003},
abstract = {This study aimed to discover novel carbonyl reductases from a soda lake metagenome for the efficient synthesis of the chiral drug intermediate (S)-ethyl 3-hydroxy-3-phenylpropionate ((S)-EHPP). A carbonyl reductase (denoted as SLCR1) was identified and found to share less than 30 % sequence identity with known functionally characterized NAD(P)-dependent oxidoreductases, suggesting its novelty. The recombinant enzyme demonstrated optimal activity at 50 °C and pH 7.0, along with excellent stability at 45 °C and within a pH range of 6.0-7.5. Semi-rational design was applied to enhance the catalytic efficiency of SLCR1 toward ethyl benzoylacetate (EBA). After three rounds of mutagenesis and screening, a triple mutant (I212F/I176L/R216L) was obtained, which exhibited a ~ 29-fold improvement in catalytic efficiency compared to the wild-type. Molecular docking indicated that the triple mutant achieves superior catalytic efficiency and binding affinity at the expense of reduced structural stability. In whole-cell biocatalysis co-expressing the mutant enzyme and Bacillus subtilis glucose dehydrogenase (GDH), 150 mM EBA was fully consumed within 1 h, affording (S)-EHPP with 95 % conversion yield and > 99 % enantiomeric excess (e.e.). To the best of our knowledge, this biocatalytic system sets a new benchmark by enabling unprecedented single-batch substrate loading (150 mM) coupled with a remarkably short completion time of 1 h. This study demonstrates an efficient one-step synthesis of (S)-EHPP through the discovery of a novel carbonyl reductase, engineered enhancement, and optimized biocatalysis, providing a promising basis for the industrial production of chiral intermediates.},
}
@article {pmid41274194,
year = {2025},
author = {Jin, L and Xinting, L and Shuaiyang, Z and Qiaoyun, R and Obaid, MK and Peiwen, D and Guiquan, G and Guangyuan, L and Hong, Y},
title = {Comparative metagenomic profiling of microbial pathogen diversity in Haemaphysalis longicornis and Hyalomma dromedarii ticks.},
journal = {Veterinary parasitology},
volume = {341},
number = {},
pages = {110656},
doi = {10.1016/j.vetpar.2025.110656},
pmid = {41274194},
issn = {1873-2550},
abstract = {Ticks are globally important vectors of human and animal pathogens. This study characterized microbial communities in Haemaphysalis longicornis (from humid Zhangjiachuan County) and Hyalomma dromedarii (from arid Minqin County, Gansu Province, China) using metagenomic sequencing. We identified diverse bacteria and viruses including known pathogens (Anaplasma phagocytophilum, Totivirus spp., Escherichia spp.) and potentially novel agents (Totivirus-like and Trachysalambria curvirostris-associated sequences). These results highlight the role of these tick species in pathogen transmission across different environments and emphasize the need for region-specific surveillance. Our findings contribute to the understanding of tick-borne disease risks and inform strategies for targeted control.},
}
@article {pmid41273975,
year = {2025},
author = {Yuan, C and Zhao, X and Qing, C and Li, P},
title = {Phylogenetic diversity and divergent arsenite oxidation of photoarsenotrophs in geothermal springs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140531},
doi = {10.1016/j.jhazmat.2025.140531},
pmid = {41273975},
issn = {1873-3336},
abstract = {A unique metabolic process coupling anoxygenic photosynthesis with arsenite oxidation plays a critical role in arsenic (As) biogeochemical cycling within terrestrial thermal springs. While previous studies have identified restricted ranges of photoarsenotrophic bacteria, their phylogenetic diversity and physiological characteristics remain poorly understood. In this study, we obtain 12 putative metagenome-assembled genomes (MAGs) of photoarsenotrophs from global geothermal springs using metagenomics. These MAGs belong to five thermophilic taxa: Chloroflexales, Burkholderiales, Rhizobiales, Steroidobacterales, Rhodobacterales, significantly expanding the photoarsenotrophic bacteria diversity beyond the previously recognized Gammaproteobacteria. We identified the first Betaproteobacteria lineage supported by integrated physiological characterization, phylogenomics and genomic analysis, which belonging to Calidifontimicrobium sediminis of the order Burkholderiales. Comparative genomic analysis revealed their divergent arsenite oxidase systems: strains G02091 and YIM 73032 employ the arx gene cluster (ARX system), whereas strain SYSU G00088 have evolved the aio gene cluster (AIO system). Our finding extends the known phylogenetic range of photoarsenotrophy, and reveals metabolic versatility of among these bacteria, offering insights into their ecological roles in As cycling, as well as a potential biological resource for its remediation in environments.},
}
@article {pmid41273973,
year = {2025},
author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z},
title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140564},
doi = {10.1016/j.jhazmat.2025.140564},
pmid = {41273973},
issn = {1873-3336},
abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.},
}
@article {pmid41273932,
year = {2025},
author = {Tang, J and Kang, Z and Cui, S and Xu, H and Ren, H and Li, P and Han, J and Zou, Y},
title = {Exploration of molecular diagnosis for HHV-6 encephalitis in immunocompetent individuals: A study combining mNGS and PCR.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117196},
doi = {10.1016/j.diagmicrobio.2025.117196},
pmid = {41273932},
issn = {1879-0070},
abstract = {PURPOSE: To evaluate clinical features, diagnosis, treatment, and prognosis of HHV-6 encephalitis in immunocompetent adults, a rare and challenging condition.<br><br>METHODS: In this retrospective, single-centre study, we enrolled six immunocompetent adults (mean age 60.67 &#xb1; 15.57 years) diagnosed with HHV-6 encephalitis at Hengshui People's Hospital between January 2022 and December 2024. Clinical data, laboratory variables, cerebrospinal fluid (CSF) parameters, brain magnetic resonance imaging (MRI) findings, and electroencephalography (EEG) recordings were systematically collected. CSF samples underwent metagenomic next-generation sequencing (mNGS) for unbiased pathogen detection. All HHV-6-positive findings were subsequently confirmed by quantitative real-time polymerase chain reaction (PCR).<br><br>RESULTS: HHV-6 encephalitis presented with fever, unconsciousness, convulsions, headache, and cognitive dysfunction. CSF analysis showed mild intracranial pressure elevation(median 186.67 mmH2O, IQR 157.50-217.50mmH2O), lymphocytic pleocytosis(58.6 &#xb1; 31.70 %), and normal or mildly elevated protein(0.234&#xb1;0.99 g/L) and glucose(median 4.03 mmol/L, IQR 3.42-4.50 mmol/L) levels. MRI revealed high-FLAIR signals in the right temporal lobe in three patients and chronic foci in the frontal lobe and basal ganglia in three others. EEG abnormalities were noted in two patients. mNGS revealed an average of 578&#xb1;512.09 unique HHV-6 reads, with HHV-6A identified in five patients and HHV-6B in one. All findings were confirmed by quantitative PCR. Prompt ganciclovir therapy led to complete recovery without sequelae in all six cases.<br><br>CONCLUSIONS: mNGS enables rapid detection of the rare but treatable HHV-6 meningitis in immunocompetent adults that conventional tests miss, prompting early antiviral therapy and better outcomes.},
}
@article {pmid41273911,
year = {2025},
author = {Zhang, Z and Wang, R and An, Z and Liu, Y and Zhao, J and Zhang, T and Ye, X and Liu, P and Jia, H},
title = {Polystyrene and its dissolved organic matter accelerate antibiotic resistance gene dissemination in anaerobic digestion by posing resistance pressure on functional microorganisms.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124997},
doi = {10.1016/j.watres.2025.124997},
pmid = {41273911},
issn = {1879-2448},
abstract = {Microplastics (MPs) in sludge can release dissolved organic matter (MP-DOM) and affects the dissemination of co-existing antibiotic resistance genes (ARGs). However, the contributions and mechanisms of MPs themselves and released MP-DOM on ARGs dissemination during anaerobic digestion (AD) remain unclear. This study investigated the dissemination potential of ARGs under MP and MP-DOM treatment by combining metagenomic sequencing with partial least squares structural equation modeling (PLS-SEM). Results showed that both treatments increased the abundances of ARGs, virulence factor genes and mobile genetic elements, with 1.25-1.79 fold enhancement relative to control, highlighting ARGs dissemination in AD. Notably, MP-DOM exhibited a stronger enhancement than MPs. The enhancement was mainly ascribed to the resistance pressure on functional microbial communities becoming ARGs hosts by increasing membrane permeability and type IV secretion system activation through reactive oxygen species generation, as evidenced by the 108.2 % and 120.5 % increases in VirD4 expression under MPs and MP-DOM, respectively. Different from the induced selection pressure of MPs on ARGs dissemination, MP-DOM mainly exerted a strongly biological effect by stimulating stress-adaptive carbohydrate metabolism (glycolysis and pentose phosphate) within hydrolytic microorganisms (Clostridium and Defluviicoccus) in the microbially-driven AD environment. This study identifies a dominant factor yet previously overlooked driver of MP-DOM that amplifies ARGs dissemination in sludge AD, providing new insights into the risks of plastic-derived contaminants.},
}
@article {pmid41273495,
year = {2025},
author = {Liu, Z and Shao, X and Jin, Y and Shan, X and Zhang, H and Liang, Q and Lu, W and Zhou, G and Lan, H and Zhang, Y},
title = {GO/iron series enhance performance of anaerobic system for treatment of sulfate-containing organic wastewater.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {472},
pmid = {41273495},
issn = {1573-0972},
support = {2024TSGC0781//Shandong Province Science and Technology Small and Medium sized Enterprise Inno vation Ability Enhancement Project/ ; 2024ZDYF010019//Key R&amp;D Program of Rizhao City/ ; ZR2021MB085//Shandong Provincial Natural Science Foundation/ ; },
mesh = {*Wastewater/chemistry/microbiology ; Anaerobiosis ; *Sulfates/metabolism/chemistry ; *Graphite/chemistry ; Methane/metabolism ; Biological Oxygen Demand Analysis ; *Iron/chemistry ; Bioreactors/microbiology ; Ferric Compounds/chemistry ; Biofuels ; Bacteria/metabolism/genetics/classification ; *Water Purification/methods ; },
abstract = {This study combined with the analysis of co-metabolic microbial communities and investigated the enhancing effects of graphene oxide (GO)/iron series (GO/Fe[0], GO/Fe3O4 and GO/Fe2O3) on anaerobic treatment of sulfate-laden organic wastewater at varying chemical oxygen demand to sulfate ion (COD/SO4[2-]) ratios (COD/SO4[2-]=2.5, COD/SO4[2-]=1.25 and COD/SO4[2-]=0.8). Our results indicate that all GO/iron series significantly improved CODCr and SO4[2-] removal efficiencies and methane production and the enhancement effect was more pronounced at lower COD/SO4[2-] ratios. At COD/SO4[2-]=0.8, compared to the blank control system, the CODCr and SO4[2-] removal efficiencies and the biogas production rate of the GO/Fe3O4 and GO/Fe2O3 system were enhanced by 14.1%, 18.3%, and 24.7%; 5.8%, 9.6%, and 23.3% respectively. Notably, with GO/Fe[0] exhibiting the most significant improvement, the CODCr removal efficiency, SO4[2-] removal efficiency and biogas production were improved by 34.4%, 41.1% and 42.5%, respectively, relative to the blank control. This mechanism is primarily attributed to the corrosion of Fe[0] under anaerobic conditions, which releases electrons and H2 (supplying electron donors for hydrogenotrophic methanogens) and produces elevated levels of soluble Fe[2+] which precipitates sulfide (reducing H2S toxicity). Furthermore, they optimized the system's pH (GO/Fe[0]:7.30-7.69; GO/Fe3O4: 7.30-7.57; GO/Fe2O3: 7.17-7.54; blank: 6.99-7.18), and oxidation-reduction potential (ORP) (GO/Fe[0]: -350~-370 mV; GO/Fe3O4 and GO/Fe2O3: -303~-325 mV; blank: -303~-325 mV) and enhanced the physicochemical properties of the activated sludge. Metagenomic sequencing revealed that the addition of GO/iron series maintained the stability of the microbial community structure, thereby conferring stronger shock resistance to the system. This research provides a scientific basis for exploring the application of anaerobic systems in treating sulfate-containing organic wastewater.},
}
@article {pmid41272806,
year = {2025},
author = {Zhang, CJ and Hou, J and Zhou, J and Zou, D and Zhang, H and Ma, Q and Li, M},
title = {Methane cycling microorganisms drive seasonal variation of methane emission in mangrove ecosystems.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {149},
pmid = {41272806},
issn = {2524-6372},
abstract = {Coastal mangroves are one of the significant hotspots of natural methane (CH4) emissions, yet the seasonal dynamics of these emissions and the underlying microbial drivers remain poorly understood. A clearer understanding of these processes is critical for predicting and mitigating methane emissions from these crucial ecosystems. In this study, we conducted a seasonal investigation (from March 2021 to January 2022) in mangrove sediments of the Futian Natural Reserve. We measured in situ methane fluxes and analyzed the microbial community structure via 16S rRNA gene sequencing, metagenomics and metatranscriptomics. Our results revealed significant seasonal variations in methane emissions, with the highest rates occurring in summer. Based on relative abundance of 16S rRNA gene amplicons and methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) gene sequences obtained from metagenomes, we identified three dominant methanogenic lineages (hydrogenotrophic Methanomicrobiales, acetoclastic Methanosaeta and H2-dependent methylotrophic Methanomassiliicoccales), two anaerobic methanotrophic archaea (ANME-1 and ANME-2b) and one group of aerobic methanotrophic bacteria (Methylococcaceae). Metatranscriptomic data further illuminated that the transcripts of methanogenic mcrA genes were significantly higher in summer and autumn, while the transcriptional activity of anaerobic (ANME-mcrA) and aerobic (pmoA) methanotrophs were most pronounced in autumn. Correlation analyses established a significantly negative relationship between methane emissions and salinity levels. This study highlights that salinity is a key environmental factor mediating methane emissions in mangroves, likely through suppressing methanogenic activity. Our findings thus reveal that seasonal microbial interactions regulate mangrove methane flux, providing critical insights for modeling global methane budgets and guiding climate-smart mangrove management.},
}
@article {pmid41272756,
year = {2025},
author = {Dubovitskiy, N and Kurskaya, O and Solomatina, M and Loginova, A and Derko, A and Khozyainova, A and Denisov, E and Shemyakin, E and Shestopalov, A and Sharshov, K},
title = {Metagenomic identification, isolation, and complete genome characterization of two novel picornaviruses in wild duck from Northeastern Siberia.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-025-03017-w},
pmid = {41272756},
issn = {1743-422X},
support = {225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; },
abstract = {Duck hepatitis A virus (DHAV, Avihepatovirus ahepati species) is a well-known pathogen of domestic ducks, causing fatal disease in ducklings and posing a significant burden to duck poultry farms. Avihepatovirus ahepati is the sole species within the genus Avihepatovirus and is classified into three distinct genotypes: DHAV-1, DHAV-2, and DHAV-3. In our study, we detected and isolated two strains belonging to the Picornaviridae family from Anas crecca in Northeastern Asia. One of the isolates is related to the DHAV-1 group; however, its polyprotein gene sequence shares only 77.83% nucleotide identity and 89.68% amino acid identity with the most closely related DHAV-1 sequence available, suggesting it represents a highly divergent lineage. The second isolated duck picornavirus shows 60.16% nucleotide identity to the polyprotein gene sequence of the previously described duck picornavirus strain detected during an outbreak in domestic ducks in China. The identification of these two novel picornaviruses in wild ducks, along with their efficient replication in duck embryos and primary cell cultures, emphasizes the need for comprehensive studies of their prevalence in wild ducks and their biological traits to assess potential risks for wildlife and poultry farming. The obtained complete genome sequences and viral isolates enhance our understanding of the diversity, evolution, and ecology of avian picornaviruses.},
}
@article {pmid41272260,
year = {2025},
author = {Akyazı, H and Güldür, F&#xc7; and Beyzi, E},
title = {Anode surface modification with reduced graphene oxide (rGO) and molybdenum (Mo) enhances microbial diversity and chemical oxygen demand (COD) removal in microbial fuel cells.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41272260},
issn = {1614-7499},
support = {FCD-2023-8721//Gazi &#xdc;niversitesi/ ; },
abstract = {This study aimed to investigate the effects of anode surface modifications on microbial community composition and chemical oxygen demand (COD) removal efficiency in microbial fuel cells (MFCs). Four different anode electrodes were fabricated: bare nickel foam (NF), reduced graphene oxide-coated nickel foam (rGO/NF), and rGO/NF modified with 30 wt% and 50 wt% molybdenum (Mo). These electrodes were tested in a single-chamber, membraneless, air-cathode MFC. Surface morphology was characterized using scanning electron microscopy (SEM), and microbial diversity was assessed through 16S rRNA metagenomic sequencing. Distinct microbial profiles were observed across the electrode types. The NF anode supported high abundances of Mesoterricola sediminis (22.2%), Klebsiella pneumoniae (10.1%), and other facultative species. The rGO/NF electrode promoted colonization by Cutibacterium acnes (8.1%) and Paracidovorax avenae (5.4%). On the 30Mo/rGO/NF electrode, notable species included Escherichia coli (8.4%) and Salmonella enterica (6.0%). The 50Mo/rGO/NF anode exhibited the highest microbial diversity, with species such as Streptomyces sp. RerS4 (6.9%) and Micromonospora endophytica (6.5%) being predominant. The highest COD removal efficiency (88.58%) was achieved using the 50Mo/rGO/NF anode. These findings demonstrate that molybdenum-modified rGO coatings enhance both microbial colonization and electrochemical performance, offering a promising strategy for improving MFC efficiency in wastewater treatment applications.},
}
@article {pmid41271719,
year = {2025},
author = {Martiny, HM and Munk, P and Fuschi, A and Becsei, &#xc1; and Pyrounakis, N and Brinch, C and , and Larsson, DGJ and Koopmans, M and Remondini, D and Csabai, I and Aarestrup, FM},
title = {Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10278},
pmid = {41271719},
issn = {2041-1723},
support = {NNF16OC0021856: Global Surveillance of Antimicrobial Resistance//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
mesh = {*Sewage/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; North America ; Geography ; Cities ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance genes (ARGs) have rapidly emerged and spread globally, but the pathways driving their spread remain poorly understood. We analyzed 1240 sewage samples from 351 cities across 111 countries, comparing ARGs known to be mobilized with those identified through functional metagenomics (FG). FG ARGs showed stronger associations with bacterial taxa than the acquired ARGs. Network analyses further confirmed this and showed potential for source attribution of both known and novel ARGs. The FG resistome was more evenly dispersed globally, whereas the acquired resistome followed distinct geographical patterns. City-wise distance-decay analyses revealed that the FG ARGs showed significant decay within countries but not across regions or globally. In contrast, acquired ARGs showed decay at both national and regional scales. At the variant level, both ARG groups had significant national and regional distance-decay effects, but only FG ARGs at a global scale. Additionally, we observed stronger distance effects in Sub-Saharan Africa and East Asia compared to North America. Our findings suggest that differential selection and niche competition, rather than dispersal, shape the global resistome patterns. A limited number of bacterial taxa may act as reservoirs of latent FG ARGs, highlighting the need of targeted surveillance to mitigate future resistance threats.},
}
@article {pmid41271709,
year = {2025},
author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C},
title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10295},
pmid = {41271709},
issn = {2041-1723},
mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; },
abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.},
}
@article {pmid41271554,
year = {2025},
author = {Wang, J and Chen, Y and Chen, T and Cai, H and Chen, Q and Sun, W and Ni, J},
title = {Genomic blueprint enables early intervention in cyanobacterial risk management.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2025.11.005},
pmid = {41271554},
issn = {2095-9281},
abstract = {While existing early-warning systems struggle to achieve cross-species cyanobacterial risk prediction with the required synchronicity and accuracy in aquatic ecosystems, our study pioneers a genome architecture-driven monitoring paradigm through decoding 317 cyanobacterial metagenome-assembled genomes from the world's largest phosphorus-limiting water transfer system, the Middle Route of the South-to-North Water Diversion Canal (MR-SNWDC). We found an evolutionary blueprint where genome minimization (<3 Mbp) confers ecological dominance under phosphorus scarcity. These streamlined genomes showed predominance and remarkable seasonal dynamics and demonstrated metabolic specialization in phosphorus turnover, light harvesting, and carbon fixation compared to larger genomes. Importantly, we identified a 3 Mbp genomic threshold distinguishing low-risk cyanobacterial consortia from their toxin-producing counterparts. This genome-proxy system enables preemptive risk mitigation by predicting toxic transitions through genome size tracking, fundamentally advancing algal management from reactive monitoring to proactive regulation in water transfer networks.},
}
@article {pmid41271358,
year = {2025},
author = {Li, Z and Chen, Y and Zheng, J and Su, J and Lu, Y and Xia, Y and Luo, H},
title = {From fungi to lactic acid bacteria: Dominant microorganisms govern stage-specific esters biosynthesis in pit microecology of strong-flavor baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 2},
pages = {117797},
doi = {10.1016/j.foodres.2025.117797},
pmid = {41271358},
issn = {1873-7145},
mesh = {*Esters/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Fungi/metabolism/genetics ; *Wine/microbiology/analysis ; *Flavoring Agents/metabolism ; Butyrates/metabolism ; Food Microbiology ; Taste ; },
abstract = {Esters are vital flavor compounds in strong-flavor baijiu (SFB). However, their biosynthetic mechanisms during pit fermentation are not fully understood. This study employed integrated metagenomic and metabolomic analyses to investigate stage-specific microecological dynamics governing ester biosynthesis and identified three distinct fermentation stages. Stage P1 (days 0-15) featured initial ester accumulation driven by fungal dominance (e.g., Saccharomyces, Aspergillus, and Rhizopus) and high α-diversity. Elevated esterase (EST) genes mainly involved to the ethyl acetate and ethyl butyrate synthesis. Stage P2 (15-35 d) exhibited minimal changes in esters content (except ethyl lactate increase linked to 42 EST genes). During this stage, acidogenic microorganisms, primarily Acetilactobacillus (> 64 % relative abundance), Lactobacillus, and Clostridium, proliferated and co-aggregated with methanogens, including Methanosarcina and Methanobacterium. In Stage P3 (35-117 d), Lactobacillus-Acetilactobacillus consortium (> 74 %) exhibited rapid ester accumulation alongside acids and alcohols increases, with high EST abundance for ethyl caproate and ethyl butyrate synthesis. Dominant microorganisms govern the ester synthesis, with catalytic dominance shifting from fungal (Aspergillus, Saccharomyces, etc.) to lactic acid bacteria (Lactobacillus, Acetilactobacillus, etc.) systems across stages. Five physicochemical properties exerted the stage-dependent control: pH and reducing sugars shaped the microbial structure in P1 (R[2] = 0.40, 0.46); temperature and ethanol drove community simplification in P2 (R[2] = 0.35, 0.64); Acidity and ethanol regulated functional dominance in P3 (R[2] = 0.85, 0.64). PLS-SEM confirmed direct inhibition/promotion effects on α/β-diversity. This microecology-guided framework provided references for manipulation of ester profiles via phase-specific environmental control, offering a scientific basis for improving the quality of SFB flavor.},
}
@article {pmid41270974,
year = {2025},
author = {Wang, L and Zhao, Z and Zhao, Y and Dong, S and Feng, S and Cao, L and Song, K},
title = {Comparative Diagnostic Accuracy of Metagenomic Next-Generation Sequencing and Targeted Next-Generation Sequencing for Periprosthetic Joint Infection: A Systematic Review and Meta-Analysis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106661},
doi = {10.1016/j.jinf.2025.106661},
pmid = {41270974},
issn = {1532-2742},
abstract = {OBJECTIVES: The aim of this meta-analysis was to assess the diagnostic performance of metagenomic next-generation sequencing and targeted next-generation sequencing for periprosthetic joint infection (PJI).<br><br>BACKGROUND: Next-generation sequencing (NGS) is increasingly used for diagnosing periprosthetic joint infection (PJI), but its clinical utility remains poorly defined. Discrepancies between metagenomic NGS (mNGS) and targeted NGS (tNGS) results pose a significant clinical challenge for PJI diagnosis. To address this, we conducted a systematic review and meta-analysis comparing the diagnostic accuracy of mNGS and tNGS for PJI.<br><br>METHODS: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We comprehensively searched PubMed, EMBASE, Cochrane Library, Web of Science, and Scopus from inception through June 1, 2025. Two reviewers independently extracted data and assessed study quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), and the area under the hierarchical summary receiver operating characteristic curve (AUC) were calculated.<br><br>RESULTS: Following screening and eligibility assessment, 23 studies were included in the analysis. The pooled sensitivity and specificity for diagnosing PJI were 0.89 (95% CI: 0.84-0.93) and 0.92 (95% CI: 0.89-0.95) for mNGS, and 0.84 (95% CI: 0.74-0.91) and 0.97 (95% CI: 0.88-0.99) for tNGS. The DORs were 58.56 (95% CI: 38.41-89.26) for mNGS and 106.67 (95% CI: 40.93-278.00) for tNGS. The areas under the summary receiver-operating characteristic curves (AUCs) were 0.935 (95% CI: 0.90-0.95) for mNGS and 0.911 (95% CI: 0.85-0.95) for tNGS. Comparisons of DOR and AUC between mNGS and tNGS revealed no statistically significant differences (P > 0.05).<br><br>CONCLUSIONS: This meta-analysis indicates that mNGS demonstrates higher sensitivity and a numerically greater AUC than tNGS for diagnosing PJI, with acceptable specificity, although the difference in AUC was not statistically significant. Conversely, tNGS exhibits higher specificity and DOR, alongside acceptable sensitivity, making it valuable for confirming PJI. Overall, the diagnostic accuracy of both next-generation sequencing (NGS) methods is comparable, with each possessing distinct advantages and limitations.},
}
@article {pmid41270973,
year = {2025},
author = {Zhu, TY and Guo, JY and Zhang, D and Weng, L and Yang, QW and Peng, JM and Du, B},
title = {A Comparative Study of DNA- and RNA-Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Tract Infections.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106659},
doi = {10.1016/j.jinf.2025.106659},
pmid = {41270973},
issn = {1532-2742},
abstract = {OBJECTIVES: To compare the clinical utility of DNA- and RNA-metagenomic next-generation sequencing (mNGS) for pathogen detection in lower respiratory tract infections (LRTIs), and evaluate strategies to optimize RNA-mNGS performance.<br><br>METHODS: We retrospectively analyzed 82 patients with suspected LRTI undergoing simultaneous DNA-mNGS and RNA-mNGS testing. The concordance of two methods in detecting microorganisms was assessed. Performance in detecting causative pathogens was compared using multi-label classification metrics. Impacts of RNA-mNGS workflow adjustments were evaluated using mock samples.<br><br>RESULTS: In a total of 196 microbial detections, DNA-mNGS and RNA-mNGS showed poor overall agreement (Cohen's &#x3ba;=0.166, p<0.01). In identifying causative pathogens, RNA-mNGS demonstrated significantly higher precision (1.00 vs. 0.50, p<0.05) and F1 scores (0.80 vs. 0.67, p<0.05) compared to DNA-mNGS. DNA-mNGS possessed higher sensitivity for bacteria, fungi, and atypical pathogens, while RNA-mNGS excelled in detecting RNA viruses. Improved RNA-mNGS sensitivity and significant DNA-RNA read correlations were observed in causative pathogens at high abundance. Neither homogenization nor increased sequencing depth improved RNA-mNGS testing.<br><br>CONCLUSIONS: DNA-mNGS and RNA-mNGS exhibited low overall consistency. However, RNA-mNGS showed superior precision in identifying causative pathogens in LRTI and additional capacity for RNA virus detections, while DNA-mNGS possessed essential sensitivity for low abundance pathogens.},
}
@article {pmid41270957,
year = {2025},
author = {Xu, Y and Zhao, J and Huang, N and Wang, Z and Liu, L and Wang, Y and Qu, Q and Li, Q and Yang, Q and Wang, G and Liu, G and Wang, Q and Wu, W},
title = {Metagenomic characterization of the resistome, bacteriome and mobilome in raw milk from intensive farming systems.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.017},
pmid = {41270957},
issn = {2090-1224},
abstract = {INTRODUCTION: Intensive farming, as the dominant paradigm in global dairy production, exacerbates antimicrobial resistance (AMR) risks via concentrated animal operations and routine antimicrobial prophylaxis. Nevertheless, the spatiotemporal dissemination patterns of antibiotic resistance genes (ARGs) in regional intensive dairy systems remain insufficiently elucidated.<br><br>OBJECTIVES: Elucidating the spatiotemporal dissemination patterns of ARGs in regional intensive dairy systems by characterizing ARGs across diverse sample matrices.<br><br>METHODS: This investigation employed an integrated approach, combining metagenomic sequencing with comprehensive experimental validation, including bacterial isolation, antimicrobial susceptibility testing, PCR based detection of ARGs, biofilm formation assays, and conjugation experiments to characterize the antibiotic resistome across 539 samples (encompassing raw milk, forage, water, and breast swabs) collected from 42 intensive farms in Shandong, China.<br><br>RESULTS: DY exhibited the most pronounced microbial diversity (16,347 species) and the highest ARG abundance (547 subtypes), which were predominantly &#x3b2;-lactamase genes (56.3&#x202f;%). Multidrug-resistant determinants were pervasive across all sample types. Klebsiella pneumoniae (K. pneumoniae) was identified as a high-risk vector, showing 96.43&#x202f;% resistance to &#x3b2;-lactam antibiotics and a 25&#x202f;% rate of multidrug resistance (MDR). Crucially, conjugation experiments confirmed the horizontal transfer of the blaSHV gene to Escherichia coli (E. coli), demonstrating its potential for cross-species transmission. Furthermore, a significant correlation (P&#x202f;<&#x202f;0.05) was found between biofilm formation and enhanced &#x3b2;-lactam resistance, implicating biofilms in the maintenance of resistance.<br><br>CONCLUSION: This pioneering regional ARG atlas delineates K. pneumoniae's epidemiological significance in Shandong's intensive dairy continuum. Our findings advocate for precision intervention strategies and establish the utility of metagenomics for operational surveillance.},
}
@article {pmid41270896,
year = {2025},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.<br><br>METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n&#x202f;=&#x202f;23) prior to any treatment initiation, and unrelated healthy controls (n&#x202f;=&#x202f;24) to elucidate their microbial diversity and relative abundance.<br><br>RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2]&#x202f;=&#x202f;0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.<br><br>CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}
@article {pmid41270740,
year = {2025},
author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z},
title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116517},
doi = {10.1016/j.celrep.2025.116517},
pmid = {41270740},
issn = {2211-1247},
abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.},
}
@article {pmid41270667,
year = {2025},
author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T},
title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.},
journal = {Chemosphere},
volume = {393},
number = {},
pages = {144767},
doi = {10.1016/j.chemosphere.2025.144767},
pmid = {41270667},
issn = {1879-1298},
abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.},
}
@article {pmid41270588,
year = {2025},
author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK},
title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180981},
doi = {10.1016/j.scitotenv.2025.180981},
pmid = {41270588},
issn = {1879-1026},
abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.},
}
@article {pmid41270407,
year = {2025},
author = {Zhang, T and Zhang, P and Zhang, J and Hu, Z and Zhang, J and Wah, TY and He, Y},
title = {Interfacial electron transfer between artificial carbon nanowires clusters and Cyt c: Enabling electron transport for methanogenesis.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124994},
doi = {10.1016/j.watres.2025.124994},
pmid = {41270407},
issn = {1879-2448},
abstract = {Intercellular electron transfer via microbial nanowires and Cytochrome c (Cyt c) is a key mechanism for syntrophic metabolism in anaerobic digestion, yet this functionality is encoded in only a limited number of microbial genomes. To address this limitation, we developed artificial carbon nanowire clusters (ACNCs) derived from plastic/sludge precursors, featuring densely arranged nanowires (Φ 20-60 nm), which form a conductive network supporting microbial colonization and electron transport. Calculations of pseudocapacitance and double-layer capacitance derived from cyclic voltammetry (CV), along with electrochemical impedance spectroscopy (EIS) characterization, revealed enhanced interfacial electron transfer between Cyt c and ACNC compared to biochar (BC) and, carbon nanotubes (CNT). Mott-Schottky analysis revealed superior energy level alignment between ACNC and Cyt c in comparison to BC/CNT, resulting in an enhanced current response in the ACNCCyt c complex, which is critical for efficient electron transfer. Circular dichroism and EPR spectroscopy revealed that ACNC induced an increase in β-sheet content in Cyt c, optimizing its electron transfer orientation. In microbial communities, ACNC supplementation enriched electroactive populations. Metagenomic analysis showed a 1.67-fold increase in Methanothrix abundance and a 1.16-fold upregulation of multiheme cytochromes (MtrC/Ech/Rnf), leading to a 123 % elevation in methanation rates compared to BC.},
}
@article {pmid41269405,
year = {2025},
author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q},
title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {102},
pmid = {41269405},
issn = {1559-0267},
support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; },
abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.},
}
@article {pmid41269281,
year = {2025},
author = {Yazhini, A and Morice, &#xc9; and Jochheim, A and Lieser, B and Söding, J},
title = {Evaluation of metagenome binning: advances and challenges.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf617},
pmid = {41269281},
issn = {1477-4054},
support = {101111457//Marie Sk&#x142;odowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; },
abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.},
}
@article {pmid41268511,
year = {2025},
author = {Almeida, NEC and Kalil, AC and Gomez, CA},
title = {Prostatic Abscess due to Ureaplasma parvum in a Heart Transplant Recipient: Diagnostic Challenges and Clinical Utility of Metagenomics Next-Generation Sequencing (NGS).},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {7511507},
pmid = {41268511},
issn = {2090-6625},
abstract = {Ureaplasma spp. are small and fastidious bacteria that may cause urogenital infections in healthy adults and, in rare cases, invasive disease. These bacteria have been increasingly recognized in immunocompromised patients and have been associated with hyperammonemia syndrome, particularly in lung transplant recipients. In this context, we present a unique clinical case of Ureaplasma parvum prostate abscess, a condition rarely observed in heart transplant recipients, diagnosed using next-generation sequencing (NGS).},
}
@article {pmid41268311,
year = {2025},
author = {Han, JA and Lee, J and An, HJ and Yi, ES and Kim, Y and Koo, BK and Lee, H and Kim, EY and Lee, HS},
title = {Exploring the Panax ginseng Meyer soil metagenome to uncover antagonistic bacteria against ginseng root rot disease.},
journal = {Journal of ginseng research},
volume = {49},
number = {6},
pages = {767-775},
pmid = {41268311},
issn = {1226-8453},
abstract = {BACKGROUND: Ginseng, renowned for its health benefits, is often cultivated with pesticides, which contradicts its health-enhancing properties. To address this, we identified Bacillus velezensis ARRI17 through a 5-year monitoring of ginseng yield on a national scale and comparative metagenome analysis. ARRI17 is a biocontrol agent that enhances ginseng growth and disease resistance under authentic field conditions.<br><br>METHODS: We identified ARRI17 through metagenomic analysis of soil samples collected from ginseng fields classified as high-yield (3.54&#xa0;&#xb1;&#xa0;0.46&#xa0;kg per 1.62&#xa0;m[2]) or low-yield (0.9&#xa0;&#xb1;&#xa0;0.21&#xa0;kg per 1.62&#xa0;m[2]), based on comparisons to the national 5-year average yield of 2.13&#xa0;&#xb1;&#xa0;0.35&#xa0;kg per 1.62&#xa0;m[2]. The biocontrol efficacy of ARRI17 was validated under laboratory conditions and field trials. Additionally, we analyzed the genomic and physiological characteristics of ARRI17 to clarify its antifungal mechanisms and adaptability to diverse environments.<br><br>RESULTS: ARRI17 exhibited strong inhibitory activity against multiple ginseng fungal pathogens, including Ilyonectria mors-panacis, in both controlled and field conditions. The application of ARRI17 improved ginseng growth parameters and reduced disease incidence in infested soil. Genomic analysis revealed that ARRI17 produces antimicrobial compounds, such as Iturin A, confirmed by HPLC. Furthermore, ARRI17 naturally thrived in rice straw compost, a traditional biofertilizer used in ginseng cultivation, suggesting its long-term presence and compatibility with standard ginseng farming practices.<br><br>CONCLUSION: Bacillus velezensis ARRI17 is an effective biocontrol agent that promotes ginseng growth and enhances disease resistance. Its natural compatibility with traditional farming practices, especially its presence with rice straw compost, positions ARRI17 as a promising and sustainable alternative.},
}
@article {pmid41268301,
year = {2025},
author = {Zhang, D and Zhou, M and Qiu, Y and Xu, H and Liu, H and Liu, Y and Xie, L},
title = {Cross-generational mechanisms of maternal gut microbiota in modulating offspring autism spectrum disorder risk: from the gut-brain axis to translational challenges in precision interventions.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1642240},
pmid = {41268301},
issn = {1663-4365},
abstract = {Autism Spectrum Disorder (ASD) manifests as a group of neurodevelopmental disorders with high clinical and genetic heterogeneity, characterized by core features including social communication deficits, repetitive behaviors, and restricted interests. Current research primarily focuses on genetic variations, immune dysregulation, synaptic dysfunction, and gene-environment interactions. Nowadays, accumulating evidence indicates that maternal gut microbiota dysbiosis, induced by high-fat diets, antibiotic overuse, and urbanization, significantly correlates with abnormal fetal neurodevelopment and increased ASD risk. This review systematically delineates three transplacental mechanisms whereby maternal dysbiosis regulates fetal neurodevelopment: Metabolite-mediated pathways, Immune pathway activation, and Epigenetic reprogramming. Meanwhile, the key translational challenges are highlighted. At last, metagenomics-metabolomics-fetal neuroimaging, Development of microbiota metabolite-treated brain organoids, and Artificial Intelligence-driven (AI-driven) probiotic screening were proposed as research directions in future.},
}
@article {pmid41268226,
year = {2025},
author = {Liu, Y and Zhang, Y and Li, Y and Yang, J},
title = {Liver abscess caused by Bacteroides thetaiotaomicron complicated by purulent pericarditis: a case report.},
journal = {American journal of translational research},
volume = {17},
number = {10},
pages = {8164-8170},
pmid = {41268226},
issn = {1943-8141},
abstract = {BACKGROUND: Liver abscess complicated by purulent pericarditis is a rare clinical condition. To date, no cases of liver abscess caused by Bacteroides thetaiotaomicron with concomitant purulent pericarditis have been reported. We present a rare case of this dual pathology to improve clinicians' understanding of liver abscess-related complications and uncommon pathogens.<br><br>CASE PRESENTATION: A 33-year-old female was admitted with hypothermia, chest tightness, and vomiting. Upon admission, laboratory tests showed elevated inflammatory markers. Ultrasound imaging revealed both pericardial effusion and a hepatic abscess, leading to a diagnosis of liver abscess complicated by purulent pericarditis. Metagenomic next-generation sequencing (mNGS) of pericardial fluid identified Bacteroides thetaiotaomicron. The patient received anti-infective therapy with meropenem and ornidazole, combined with pericardial effusion drainage. During the later stage of treatment, the patient developed thoracic empyema, necessitating thoracic drainage. Following treatment, the inflammatory markers significantly improved, the liver abscess reduced in size, and the pericardial effusion nearly resolved. At the 8-week follow-up after discharge, clinical and imaging findings were normal.<br><br>CONCLUSION: This case highlights the importance of recognizing atypical manifestations in immunocompromised patients and emphasizes the critical role of early comprehensive examination, prompt and effective anti-infective therapy, and puncture drainage for improving patient outcome. Pathogen identification methods such as mNGS can guide more precise treatment strategies, thereby shortening hospitalization and reducing complications.},
}
@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.<br><br>OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).<br><br>METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).<br><br>RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.<br><br>CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}
@article {pmid41267936,
year = {2025},
author = {Ogbuji, NG and Agogbua, JU},
title = {Genomics in plant pathogen identification and control.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1661432},
pmid = {41267936},
issn = {1664-462X},
abstract = {Recent advances in genomics have revolutionized plant pathogen detection and control by enabling faster and more accurate identification compared to traditional culture-based methods. Genomic tools like metagenomics and next generation sequencing (NGS) facilitate the detection of microorganisms (bacteria, fungi, viruses, and nematodes) directly from environmental samples. Genomics also provides information on plant-pathogen interactions, especially the detection of Resistance (R) genes and their role in plant defense against pathogens, aiding in the development of genetic markers for breeding disease-resistance crop species. Gene editing systems such as clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (CRISPR-Cas9), transcription activator-like effector nucleases (TALENs), and Zinc Finger nucleases (ZFNs) allow for precise genetic modification, either by incorporating a beneficial R genes or disabling susceptibility (S) genes of the host plant. RNA interference (RNAi) is another genomic tool used to suppress important pathogenic genes and inhibit disease development. Although the use of genomics in plant pathology is hampered by limitations such as high costs, complexity of data analysis and interpretation, and limited access to sequencing platforms, especially in developing countries, recent innovations and multi-disciplinary collaborations are tackling these issues. In general, genomics offers powerful tools that can be employed in the development of sustainable and effective plant disease management strategies, which will help to enhance crop protection and contribute to global food security.},
}
@article {pmid41267688,
year = {2025},
author = {Song, K and Ren, L and Guo, X and Ren, G and Sun, Y and Tian, X and Hu, C and Pan, M and Yu, Q and Luo, Z and Hao, Y and Lei, P and Yu, H and Yang, S and Chen, Q and Li, Y and Wang, S and He, Y and Hui, Z and Zheng, W and Jiang, J and Wang, L},
title = {Microbiota-responsive oral nano-amifostine enables colorectal-specific radioprotection and tumor immunity via gut microenvironment reprogramming.},
journal = {Advanced composites and hybrid materials},
volume = {8},
number = {6},
pages = {432},
pmid = {41267688},
issn = {2522-0136},
abstract = {UNLABELLED: Radiotherapy for abdominal malignancies is limited by intestinal toxicity and secondary colorectal cancers. Here, we develop an oral, microbiota-responsive nano-amifostine (CS/PEC-AMF NPs) system that achieves site-specific radioprotection in the colorectum without compromising antitumor efficacy. By conjugating amifostine to pectin and encapsulating it with chitosan, the nanoparticles enable pH- and microbiota-triggered release in the large bowel, safeguarding drug bioactivity during gastrointestinal transit. In murine models, CS/PEC-AMF NPs attenuate both acute and chronic radiation-induced bowel injury, restore epithelial integrity, preserve stem cell populations, and promote tight junction repair. Integrated metagenomic and metabolomic analyses reveal that the system normalizes gut microbiota diversity and composition, increases short-chain fatty acid production, and facilitates macrophage polarization towards the anti-inflammatory M2 phenotype. Notably, the formulation synergistically enhances tumor suppression and extends survival in orthotopic colorectal tumor models undergoing radiotherapy and reduces the incidence of secondary colorectal tumors post-irradiation. Mechanistically, transcriptomic analysis demonstrates the suppression of proinflammatory pathways and the promotion of DNA repair programs. This study provides a paradigm for leveraging functional nanomaterials to orchestrate precise, tissue-specific radioprotection and immune modulation, addressing a key challenge in abdominal cancer therapy.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42114-025-01492-x.},
}
@article {pmid41267624,
year = {2025},
author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J},
title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70234},
doi = {10.1111/1758-2229.70234},
pmid = {41267624},
issn = {1758-2229},
support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; },
mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; },
abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.},
}
@article {pmid41267035,
year = {2025},
author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z},
title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {236},
pmid = {41267035},
issn = {2049-2618},
support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; },
abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.<br><br>RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.<br><br>CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.},
}
@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}
@article {pmid41266391,
year = {2025},
author = {Pairoh, S and Mhuantong, W and Boonyapakron, K and Yuvaniyama, J and Kanokratana, P and Bunterngsook, B and Lekakarn, H and Arunrattanamook, N and Laothanachareon, T and Champreda, V},
title = {Machine learning-guided discovery of thermophilic carbonic anhydrases from environmental metagenomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40969},
pmid = {41266391},
issn = {2045-2322},
support = {B13F670055//Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation (PMU-B)/ ; },
mesh = {*Carbonic Anhydrases/genetics/chemistry/metabolism ; *Machine Learning ; *Metagenome ; Metagenomics/methods ; Hot Springs/microbiology ; },
abstract = {Thermophilic carbonic anhydrases (CAs) are promising biocatalysts for carbon capture utilization and storage (CCUS) due to their stability and efficiency at elevated temperatures. This study presents a machine learning (ML)-guided approach to discover thermostable γ-class CA (γ-CA) from metagenomic datasets derived from Fang Hot Spring, Northern Thailand. To develop classification models, two sets of protein descriptors-dipeptide composition (DPC) and physicochemical/biochemical properties (AAindex)-were used to train classification models. Fourteen ML algorithms were systematically evaluated for each feature set. AdaBoost achieved the best performance for the DPC-based model, while LightGBM performed best with AAindex-based features. External validation with known CA sequences confirmed the ability of the models to discriminate thermophilic from non-thermophilic proteins. Applying the optimized models, we screened 1,534 predicted CAs and identified three high-confidence candidates (TtCA, CrCA, and ToCA). These were heterologously expressed in E. coli, purified, and biochemically validated. All candidates exhibited carbonic anhydrase activity, trimeric oligomeric structures, and high melting temperatures (Tm ranging from 97.0 °C to 109.1 °C). Although their hydration activity was modest compared to α-class CAs, their thermal robustness highlights their potential for industrial CO2 capture. This study demonstrates an approach in which ML integrated with metagenomics enables efficient discovery and validation of robust enzymes from extreme environments, providing a scalable strategy for CCUS applications.},
}
@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}
@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}
@article {pmid41265635,
year = {2025},
author = {Wang, S and Huang, Y and Wang, N and Zhou, H and Ren, X and Li, K and Xia, Y and Xu, J and Huang, L and Cai, H},
title = {Epstein-Barr virus in suspected intracranial infection: a multicenter, retrospective study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108235},
doi = {10.1016/j.ijid.2025.108235},
pmid = {41265635},
issn = {1878-3511},
abstract = {OBJECTIVES: The clinical relevance of Epstein-Barr virus (EBV) detection in cerebrospinal fluid (CSF) using metagenomic next-generation sequencing (mNGS) in patients with suspected intracranial infections has not been fully clarified. This study aimed to assess the clinical features, imaging characteristics, and outcomes in EBV-positive patients.<br><br>METHODS: We retrospectively enrolled patients with suspected intracranial infection who underwent commercial mNGS of CSF samples between December 2019 and October 2023 across 13 hospitals in four cities. Clinical data were collected, and multivariable logistic regression was performed to assess the association between EBV positivity and unfavorable outcomes.<br><br>RESULTS: Among 507 patients, 51 (10.1%) were EBV-positive in CSF. EBV-positive cases showed higher CSF mononuclear cell proportions (83.8% vs. 32.8%, p<0.001), lower chloride levels (123.0 vs. 126.1 mmol/L, p=0.019), and more frequent herpesvirus co-detection (21.6% vs. 8.6%, p=0.007). Imaging abnormalities did not differ significantly. After adjustment, multivariable logistic regression showed that EBV was not an independent risk factor for clinical outcomes (OR 1.005, 95% CI 0.516 - 1.972, p&#x202f;=&#x202f;0.988).<br><br>CONCLUSIONS: EBV was detected in 10.1% of patients in CSF samples from patients with suspected intracranial infections. EBV positivity correlated with a lymphocytic CSF profile and co-detection of other herpesviruses but was not independently associated with unfavorable outcomes.},
}
@article {pmid41265331,
year = {2025},
author = {Zeng, Y and Gao, H and Huang, H and Xiong, W and Bin, L and Liao, B and Chen, W and Chen, X and Wen, S and Li, P and Huang, S and Tang, B},
title = {Performance, metabolism, and resistance of an SMX-stressed continuous-flow AGS-MBR system: Microscopic mechanism of macroscopic instability phenomena.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124968},
doi = {10.1016/j.watres.2025.124968},
pmid = {41265331},
issn = {1879-2448},
abstract = {To clarify how long-term sulfamethoxazole (SMX) pressure converts macro-scale performance loss into micro-level mechanistic change, a continuous-flow aerobic granular sludge membrane bioreactor (AGS-MBR) was operated for 140 days at SMX concentrations ranging from 0 to 5 mg L[-1]. At 0.2-1 mg L[-1], the system remained resilient: TN and TP removal stabilized at 90 % and 72.8 %, respectively, and the volume-mean granule diameter remained 282 µm. Metagenomics revealed significant up-regulation of the glycogen-metabolising gene glk and the polyphosphate gene ppk, which fuelled an energy-compensation pathway that supplied ATP and precursors for TB-EPS synthesis and reinforced granule scaffolding. When influent SMX rose to 5 mg L[-1] this compensation collapsed: EPS dropped 45 %, Dv shrank 38 %, granules disintegrated, TN removal fell to 70 % and TP to 44.8 %. The community shifted to a filamentous bacteria dominated state with Thiothrix >25 % relative abundance. Concurrently, the non-pathogen Rubrivivax became a shared host for antibiotic resistance genes (sul1, sul2) and multiple transposases; mobile genetic elements mediated the co-transfer of resistance and virulence genes and eroded functional redundancy. LC-MS further showed that the major transformation products P4 and P6 exhibited 2.3 folds higher chronic toxicity than the parent compound and imposed additional chemical stress on the already impaired granule microbiota. SMX dose dictated a cascade in which metabolic compensation was followed by selection of filamentous hosts prone to gene mobility and finally by chemical toxicity, progressively dismantling granule structure, nutrient removal services and ecological safety. These results elucidate the dose-dependent macro-to-micro cascade under SMX stress and provide insights for mitigating ecological risks in antibiotic laden wastewater.},
}
@article {pmid41264852,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00349},
pmid = {41264852},
issn = {1520-4995},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}
@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}
@article {pmid41263111,
year = {2025},
author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC},
title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1234},
pmid = {41263111},
issn = {1362-4962},
support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; },
abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.},
}
@article {pmid41263098,
year = {2025},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1185},
pmid = {41263098},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}
@article {pmid41262935,
year = {2025},
author = {Zhang, B and Meng, D and Wang, X and Hu, J and Fan, J and Li, X and Yang, Z and He, W and Zhou, D and Cheng, Y and Li, J and Zou, J and Liu, Z},
title = {Additive of cow dung weakened the influences of microbial interactions on nitrogen dynamic during composting of rice husks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641502},
pmid = {41262935},
issn = {1664-302X},
abstract = {Rice husk (RH) and cow dung (CD) are two of the most abundant agricultural solid waste. Converting these residues into peat-free substrates through co-composting supports sustainable agricultural development. A 40-day rice husk composting experiment was conducted to assess the effects of cow dung addition on microbial networks and carbon-nitrogen dynamics using 16S rRNA and metagenomic analyses. Furthermore, Furthermore, we prepared seedling substrates from composts of RH alone and RH combined with CD (RHCD), and evaluated their plant growth-promoting effects. The addition of cow dung (CD) to rice husk (RH) composting increased the average temperature from 52.8 °C to 60.1 °C and acted as a pH buffer, maintaining values around 7.4. CD significantly (p < 0.05) enhanced microbial network complexity, as indicated by larger network size and higher average degree, but disrupted the linear correlations between network properties and carbon or nitrate nitrogen contents (p > 0.05). This decoupling suggests that CD weakened the linkage between microbial interactions and carbon or nitrogen biotransformation processes. CD also significantly suppressed (p < 0.05) denitrification-related genes (norB, nir and nar) after the thermophilic phase, implying reduced nitrogen loss during compost maturation. We further found that larger network size or higher average degree reduced the abundance of key genes involved in assimilatory nitrite reduction (e.g., nirBD), while increasing those related to denitrification (e.g., nirK and nirS). Moreover, seedling substrates derived from RH (95.06%) and RHCD (93.21%) composts achieved higher germination rates of Solanaceae crops than the commercial peat-based substrate (81.48%). Germination rate and seedling biomass were positively correlated with dissolved organic carbon (r = 0.820, p = 0.045) and ammonium nitrogen (r = 0.858, p = 0.029), respectively. These findings advance the understanding of microbial interaction regulating carbon and nitrogen cycling during RH composting, and support the sustainable production of peat-free seedling substrates from agricultural waste.},
}
@article {pmid41262931,
year = {2025},
author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A},
title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1704392},
pmid = {41262931},
issn = {1664-302X},
abstract = {INTRODUCTION: Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neurocognitive issues in people without HIV. Recently characterized, the brain and cerebrospinal fluid (CSF) viromes represent a new avenue to understand brain and mental health in PWH.<br><br>METHODS: This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA and RNA viruses. Taxonomic composition (reads and contigs), diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV status, markers of neuroinflammation/neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of hEV, non-human viruses (NHV) and blood-brain barrier permeability were performed. Multivariable models assessed the relationship between cognition and clusters.<br><br>RESULTS: Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. PWH displayed lower &#x3b1; diversity, although p > 0.05. At &#x3b2; diversity analysis, HIV status explained 3.4% of the variation in viral composition (p = 0.016). Contigs assembly yielded 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100&#x3b2; (rho 0.36, p = 0.002) and &#x3b2;-Amyloid 1-42 fragment (&#x3b2;A-42, rho 0.27, p = 0.026), whereas higher RA of nhEV with poorer cognitive performance (rho 0.26, p = 0.022). Conversely, higher RA of hEV correlated with better cognition (rho -0.38, p = 0.003) and lower &#x3b2;A-42 (rho -0.30, p = 0.012). Sensitivity analyses restricted to only CSF samples with detectable reads confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, &#x3b2;A-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and NHV-enriched CSF (all p < 0.05).<br><br>CONCLUSION: This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.},
}
@article {pmid41262456,
year = {2025},
author = {Ma, Y and Li, Z and Liu, P and Wei, Y and Jiang, K and Yue, Y and Zhang, A and Wang, W and Li, L and Zhang, P and Gu, X and Liu, Q and Lu, L},
title = {Metagenomics research on the gut microbiota of the Marmota himalayana of the Sanjiangyuan National Nature Reserve in Qinghai Province, China.},
journal = {Biosafety and health},
volume = {7},
number = {5},
pages = {281-294},
pmid = {41262456},
issn = {2590-0536},
abstract = {With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau, the scope of human activities has continuously expanded, increasing opportunities for contact with wildlife, also exacerbating the outbreak rate of zoonotic emerging infectious diseases. Currently, research on the gut microbiota of wildlife, especially Marmota himalayana (M. himalayana), which are reservoir hosts for plague, is scarce. In this study, we investigated the composition, function, and regional variations of the gut microbiota in M. himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province. The results indicated that at the phylum level, the dominant bacterial phyla in the gut microbiota of the M. himalayana were Firmicutes, Bacteroidota, and Proteobacteria, collectively accounting for 74.16 % of the community. At the genus level, the top three most abundant genera were Alistipes (11.86 % ± 1.56 %), Bacteroides (6.68 % ± 0.95 %), and Clostridium (4.92 % ± 1.04 %). Kyoto encyclopedia of genes and genomes (KEGG) database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism, genetic information processing (GIP), and environmental information processing (EIP). These active functions played a crucial role in food digestion, nutrient absorption, metabolic balance maintenance, and pathogen defense, aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau. The study provided critical insights into host-microbe interactions, highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.},
}
@article {pmid41262425,
year = {2025},
author = {Morelle-Hungría, E},
title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {244},
doi = {10.12688/openreseurope.21126.2},
pmid = {41262425},
issn = {2732-5121},
abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.},
}
@article {pmid41261745,
year = {2025},
author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z},
title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1243},
pmid = {41261745},
issn = {1362-4962},
support = {2022FY100905//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; },
abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.},
}
@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}
@article {pmid41261035,
year = {2025},
author = {Rahman, T and Samia, NSN and Moon, SB and Islam, MS and Mahmud, ZH and Kabir, MS and Karim, MM and Rahman, M and Jubair, M},
title = {2024 Bangladesh Floodwaters Harbour Regional Hotspots of Pathogens and Antimicrobial Resistance.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70240},
doi = {10.1111/1758-2229.70240},
pmid = {41261035},
issn = {1758-2229},
support = {//International Centre for Diarrhoeal Disease Research, Bangladesh/ ; //Government of Bangladesh/ ; //Global Affairs Canada/ ; },
mesh = {Bangladesh ; *Floods ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Water Microbiology ; },
abstract = {Seasonal flooding in Bangladesh poses severe public health risks through waterborne disease, yet a comprehensive, genomic-level understanding of the associated microbial hazards is lacking. This study presents a comprehensive shotgun metagenomic analysis of floodwaters from four districts of Bangladesh (Cumilla, Feni, Lakshmipur, and Noakhali) during the devastating 2024 floods, profiling the distribution of pathogenic bacteria, antimicrobial resistance genes, and virulence factors. A total of 12 samples were collected during peak flooding periods and processed using Illumina sequencing. Taxonomic profiling and resistome analysis were performed using MetaPhlAn4, ABRicate, and MEGAHIT, referencing the NCBI and CZ ID databases. Across all regions, 301 operational taxonomic units were identified. Feni exhibited the highest diversity of pathogenic species, including multidrug-resistant Klebsiella pneumoniae, toxigenic Pseudomonas aeruginosa, and mobilizable resistance plasmids (e.g., IncP1, Col440I). Noakhali samples revealed co-detection of zoonotic and emerging pathogens such as Aliarcobacter spp. and Streptococcus suis, along with key resistance genes like blaOXA and ermB. Microbial community clustering revealed strong spatial heterogeneity. This study provides genomic evidence that floodwaters harbour emerging pathogens and AMR. It strongly advocates for incorporating metagenomic tools into Bangladesh's national flood response and AMR monitoring frameworks.},
}
@article {pmid41260473,
year = {2025},
author = {Dyukova, K and Paloyan, A and Khoyetsyan, L and Mkhitaryan, A and Antranikian, G and Hambardzumyan, A},
title = {Characterization of thermostable β-glucosidase immobilized on linen fabric.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27014},
pmid = {41260473},
issn = {1525-3198},
abstract = {In this study, a thermostable β-glucosidase derived from a hot spring metagenome was successfully immobilized on linen fabric to create an eco-friendly and reusable biocatalyst for lactose hydrolysis. The enzyme is derived from a metagenome of the high-temperature Pisciarelli hot springs, an extreme environment known to yield robust biocatalysts with industrial relevance. Two immobilization strategies were employed: direct covalent binding (Lf-β-glucosidase) and binding via a spacer arm (LfEG-β-glucosidase). The latter exhibited superior enzymatic performance, retaining 76.6% of its initial activity and demonstrating enhanced thermal and operational stability. Both free and immobilized forms of enzyme showed similar pH and temperature optima, with the immobilized form exhibiting significantly improved long-term thermostability and storage stability-retaining full activity after 1 yr at 4°C. The LfEG-β-glucosidase biocatalyst was effectively applied in the enzymatic treatment of cheese whey, retaining 90% activity after 15 reuse cycles, yielding more than 6.4 g of glucose. These findings highlight the promising use of biodegradable, low-cost linen fabric as a carrier for thermostable enzymes in food biotechnology. The high efficiency and reusability of the developed biocatalyst offer a compelling solution for lactose hydrolysis and valorization of dairy industry by-products, particularly whey, within a circular and environmentally conscious production model.},
}
@article {pmid41260470,
year = {2025},
author = {Dilireba, E and Lu, Q and Chang, L and Luo, F},
title = {Antibiotic resistance profile and molecular mechanism of enterococci in traditional fermented yogurts.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27212},
pmid = {41260470},
issn = {1525-3198},
abstract = {Enterococci are present in traditional fermented foods, but their potential role as reservoirs of antibiotic resistance and virulence genes has raised concerns about food safety. To evaluate the prevalence of antibiotic-resistant enterococci in traditional fermented yogurt, microbial sequencing and culture methods were used to analyze the microbiota and Enterococcus composition in a total of 75 yogurts from Xinjiang Uygur Autonomous Region (Xinjiang, China). Enterococcus faecium and Enterococcus durans were the predominant enterococcal species and belonged to 20 and 5 biotypes, respectively, according to randomly amplified polymorphic DNA PCR analysis. Antibiotic resistance testing revealed that 98.92% of Enterococcus strains were resistant to at least one kind of antibiotic, of which E. faecium showed high resistance to gentamicin (96.92%), erythromycin (55.38%), and ciprofloxacin (49.23%), whereas E. durans was most resistant to tetracycline (58.82%) and chloramphenicol (55.82%), followed by gentamicin (47.06%). Multidrug-resistant strains were more abundant in E. faecium (37.3%). Furthermore, vancomycin resistance was observed in E. faecium strains, highlighting the risk of resistance spread. Molecular analysis revealed vancomycin and tetracycline resistance phenotypes were consistent with genotypes, but not for penicillin, gentamicin and erythromycin. Moreover, mobile genetic elements were detected, such as 5'ococs/3'ococs and IntI3, which facilitate gene transfer. Metagenomic sequencing further revealed the high abundance of antibiotic resistance genes, such as mlaF, macB, and ImrD. Additionally, the microbial co-occurrence network analysis revealed significant positive correlations between E. faecium and Acetobacter in the Zhaosu region. This study highlights that traditional fermented yogurt may serve as a reservoir for multidrug-resistant enterococci, posing a potential risk to public health.},
}
@article {pmid41161417,
year = {2025},
author = {Mussert, CMA and Miesbach, W and Chowdary, P and Lillicrap, D and Mahlangu, J and Peyvandi, F and Pipe, SW and Srivastava, A and Voorberg, J and Pierce, GF and Kaczmarek, R and Batty, P and Cutica, I and Nathwani, A and Leebeek, FWG},
title = {A comprehensive care pathway of gene therapy for hemophilia based on current guideline documents and summary of product characteristics: communication from the ISTH SSC working group on gene therapy.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2025.09.041},
pmid = {41161417},
issn = {1538-7836},
abstract = {BACKGROUND: Gene therapy for hemophilia has recently been implemented as standard clinical care, requiring organizational and multistakeholder preparedness and clear guidelines. In addition to pharmaceutical summaries of product characteristics (SMPCs), various (inter)national guidance documents have been published. However, no guidance document or SMPC covers the entire gene therapy care pathway.<br><br>OBJECTIVES: This study provides a complete and comprehensive overview of current guidance documents and SMPCs to develop a comprehensive care pathway for hemophilia gene therapy delivery.<br><br>METHODS: Published gene therapy guidance documents and collected SMPCs were complemented by a selective search in online databases, including PubMed and scientific societies' websites. Reference lists were checked for additional relevant articles.<br><br>RESULTS: Four SMPCs and 11 (inter)national guidance documents and recommendations were collected. The documents were focused on either the intervention or the care pathway, and none were comprehensive covering all aspects of hemophilia gene therapy delivery. Considerable differences were found between the 2 approved gene therapy products and between the SMPCs issued by the 2 regulatory authorities, the Food and Drug Administration and the European Medicines Agency. (Inter)national guidance documents provided additional information and recommendations not covered in SMPCs.<br><br>CONCLUSION: Based on SMPCs and (inter)national guidance documents and recommendations a care pathway has been developed and visualized in a Metro Map. This provides a clear and comprehensive overview of all activities, contact moments, and responsibilities within the longitudinal gene therapy treatment process. This comprehensive care pathway may help navigate gene therapy implementation, providing guidance to clinicians, patients, and caregivers.},
}
@article {pmid41260397,
year = {2025},
author = {Abbasi, E},
title = {Metagenomic Surveillance of Emerging Viruses in Mosquito Populations from High-Risk Regions of Iran.},
journal = {Journal of virological methods},
volume = {},
number = {},
pages = {115301},
doi = {10.1016/j.jviromet.2025.115301},
pmid = {41260397},
issn = {1879-0984},
abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.},
}
@article {pmid41260011,
year = {2025},
author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J},
title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119004},
doi = {10.1016/j.marpolbul.2025.119004},
pmid = {41260011},
issn = {1879-3363},
abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.},
}
@article {pmid41259923,
year = {2025},
author = {Wang, YC and He, LY and Wu, DL and Gao, FZ and Liu, YS and Ying, GG},
title = {Long-term manure applications promote persistent antibiotic resistance in soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140476},
doi = {10.1016/j.jhazmat.2025.140476},
pmid = {41259923},
issn = {1873-3336},
abstract = {Manure application has the potential to influence soil microbial composition and the antibiotic resistome; however, its long-term effects remain largely unknown. This study investigated the prolonged impacts of manure applications (pig and chicken manure/compost) on soil antibiotic resistance over a two-year period. Compared with the control (51.9-85.1 ng/g), manure-amended soils contained markedly higher antibiotic concentrations (356-26100 ng/g), remaining 4-300 times higher after 730 days, especially in pig compost treatments. The abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in amended soils (4.48 × 10[8]-2.74 × 10 [12] copies/g) consistently exceeded those in controls (1.24 × 10[7]-6.10 × 10[7] copies/g). Notably, 62.5 % of ARGs were located on plasmid-associated contigs, and high-risk genes such as floR and aph(3')-III persisted throughout incubation. Elevated MGE levels after 730 days indicated sustained horizontal gene transfer (HGT) potential under antibiotic selection pressure. Overall, these results reveal the long-lasting enrichment of ARGs and highlight the need for improved manure management and long-term.},
}
@article {pmid41259914,
year = {2025},
author = {Yang, W and Wang, X},
title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140523},
doi = {10.1016/j.jhazmat.2025.140523},
pmid = {41259914},
issn = {1873-3336},
abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.},
}
@article {pmid41260377,
year = {2025},
author = {Chen, Z and Zhu, S and Gao, S and Wu, H and Tian, S and Wen, X},
title = {Fe3O4-Enhanced continuous production of medium-chain fatty acids from Sludge: Metagenomic Perspective on microbial synergy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133673},
doi = {10.1016/j.biortech.2025.133673},
pmid = {41260377},
issn = {1873-2976},
abstract = {Fe3O4 exhibits promising potential in enhancing chain elongation (CE) for medium-chain fatty acids (MCFAs) production from sludge, yet its application in continuous flow processes remains underexplored. In this study, MCFAs were continuously produced from sludge via a Fe3O4-enhanced CE process. Optimal performance was achieved with 20 g/L Fe3O4, 5.8 g COD/L/d ethanol loading rate (ELR), and 3-day hydraulic retention time (HRT), yielding 11.4 ± 0.8 g COD/L MCFAs and a production rate of 3.7 ± 0.1 g COD/L/d. n-Caproate and n-caprylate accounted for 40.9 % and 54.4 % of total MCFAs, respectively. Fe3O4 addition halved CE start-up time and increased MCFA production fourfold. Metagenomic analysis identified Clostridium kluyveri, Petrimonas sp., Alcaligenes faecalis, Proteiniphilum acetatigenes, and Anaerosalibacter sp. as biomarkers enhancing the fatty acid biosynthesis (FAB) cycle. These taxa could increase malonyl-ACP availability, improve reductive reaction efficiency, and promote acetyl-CoA generation, facilitating a streamlined microbial community with Pseudomonas caeni. This investigation offers strategic insights and data support for the high-value utilization of excess sludge.},
}
@article {pmid41260374,
year = {2025},
author = {Zhang, Q and Lin, L and Hu, T and Liu, Q and Wang, Y and Mo, H and Jin, W and Zhang, W and Chen, J and Zeng, H and Wang, X and Chen, S and Zhang, Y},
title = {Nitrogen removal driven by zonal supply of thiosulfate and pyrite in an up-flow blanket filter (UBF) reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133677},
doi = {10.1016/j.biortech.2025.133677},
pmid = {41260374},
issn = {1873-2976},
abstract = {Despite its effectiveness in nitrogen removal, the anammox process faces challenges in practical applications due to NO3[-]-N accumulation, which can lead to effluent breaches of discharge standards. This study developed a single-stage up-flow blanket filter (UBF) reactor featuring three axially stratified functional zones with multi-point supplementation of thiosulfate and pyrite. During stable operation, the high-intensity anammox layer (L1) contributed to 82.3 % of total nitrogen (TN) removal and generated alkalinity to support subsequent sulfur autotrophic denitrification (SAD). The SAD-coupled anammox layer (L2) effectively removed accumulated NO3[-]-N, reducing TN from 42.8 mg/L to 25.2 mg/L. The advanced nitrogen removal layer (L3) further polished the effluent to a TN concentration of 4.3 ± 2.8 mg/L and a pH of 7.1 ± 0.1, achieving advanced nitrogen removal and pH self-regulation. Anammox bacteria exhibited an inhibition-recovery response to thiosulfate addition, while pyrite served a triple role as a filter medium, metabolic accelerator, and electron donor. Metagenomic analysis revealed that thiosulfate supplementation selectively enrichedThiobacillusandPFJX01in each functional zone, with denitrification gene abundance increasing along the reactor's height. Notably, functional and associated microorganisms showed layer-specific gene expression and co-metabolism patterns. Even within the same genus, differential gene regulation in response to local microenvironments drove functional divergence at the genetic level. In summary, this work innovatively establishes spatially segregated functional layers within a single UBF reactor, offering a novel low-carbon strategy for advanced nitrogen removal and facilitating the resource utilization of tailings.},
}
@article {pmid41260114,
year = {2025},
author = {Ahmad, W and Ray, R and Khan, AL},
title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.},
journal = {The Science of the total environment},
volume = {1007},
number = {},
pages = {180812},
doi = {10.1016/j.scitotenv.2025.180812},
pmid = {41260114},
issn = {1879-1026},
abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.},
}
@article {pmid41259660,
year = {2025},
author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A},
title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf620},
pmid = {41259660},
issn = {1367-4811},
abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.<br><br>RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.<br><br>raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.},
}
@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.<br><br>METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.<br><br>RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p&#x2264;0.05, LDA&#x2265;2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.<br><br>CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}
@article {pmid41258718,
year = {2025},
author = {Markkanen, M and Pezzutto, D and Virta, M and Karkman, A},
title = {Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0085725},
doi = {10.1128/spectrum.00857-25},
pmid = {41258718},
issn = {2165-0497},
abstract = {UNLABELLED: The introduction of the first broad-spectrum antibiotics, sulfonamide drugs, fundamentally revolutionized medicine in the 1930s. Shortly after, and ever since, sulfonamide resistance genes (sul genes) have been widely detected. Still, the most recent variant of these genes, sul4, was first described only in 2017, and its host range and transmission mechanisms are still largely unknown. Here, we applied PacBio long-read metagenomic sequencing and bacterial methylation signals to investigate the genetic contexts and bacterial carriage of the sul4 gene in wastewater. Furthermore, we extended our description of sul4 carriers to previously published data sets. Our results indicate that sul4 is prominently found in sludge and hosted by various bacteria, such as the species from the phyla Myxococcota and Chloroflexota and genera Trichlorobacter and Desulfobacillus, which are commonly found in activated sludge. Additionally, according to our results, sul4 has already spread into multiple strains of opportunistic human pathogens, such as Aeromonas and Moraxella, in addition to the previously described Salmonella. The sequence region flanking sul4 included a truncated folK gene and an ISCR28 element and exhibited a high degree of conservation across the investigated sequences. Furthermore, the module was associated with various integron integrase genes. Also, other mobility-related elements that could further increase the likelihood of sul4 mobilization were detected. Altogether, our results describing the sul4 hosts of bacteria from distant lineages indicate the efficient mobility of sul4 by genetic elements that traverse both clinical and environmental bacteria. Finally, we suggest that wastewater may provide favorable conditions for such horizontal gene transfer events.<br><br>IMPORTANCE: Antibiotic resistance is an ancient phenomenon and a common trait of many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacteria's ability to exchange genetic material across different lineages, have drastically increased the spread of resistance traits among bacteria from various niches. The primary concern is the resistance genes encoded by infections causing pathogens, already causing over 1 million deaths annually and indirectly contributing to nearly 4 million more. Therefore, understanding the bacteria that harbor ARGs and the genetic mechanisms driving their mobilization is crucial for understanding the dynamics and emerging trends of resistance. Here, we focus on revealing these crucial aspects of the newly discovered sulfonamide resistance gene, sul4. Given the limitations of the metagenomic approach in linking the functional genes to their host genomes, the significance of our research lies in our workflow, which allows this linkage through the identification of shared methylation profiles.},
}
@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}
@article {pmid41258552,
year = {2025},
author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK},
title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1354},
pmid = {41258552},
issn = {1573-2959},
support = {core funding//Zoological Survey of India/ ; },
mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; },
abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.},
}
@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}
@article {pmid41258468,
year = {2025},
author = {Bui, HT and Bui, ATP and Ngo, HT and Ngo, XT and Nguyen, HT and Nguyen, AH and Tran, VC and Pham, TD and Nguyen, ATV},
title = {Vaginal-spray Bacillus spore probiotics as a potential treatment and reducing recurrence of bacterial vaginosis: randomized, double-blind, and controlled pilot study.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-025-01236-4},
pmid = {41258468},
issn = {2730-664X},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal disorder characterized by reduced beneficial species and overgrowth of pathogens. Probiotics, especially direct vaginal sprays, offer a promising alternative to antibiotics by restoring healthy vaginal microbiota, relieving symptoms, and preventing recurrence.<br><br>METHODS: We conducted a clinical trial (ClinicalTrials.gov: NCT06165354; 8/12/2023) to evaluate the effectiveness of the vaginal-spray probiotic LiveSpo X-Secret, containing Bacillus subtilis, B. clausii, and B. coagulans spores (&#x2265;1 billion CFU/mL). A total of 120 women were randomized equally into Control and X-Secret groups at Bac Ninh CDC. Outcomes were assessed at day 7 (end of standard treatment) for symptom resolution and day 28 (21 days post-treatment) for recurrence. Both Per-Protocol and Intention-to-Treat analyses were performed to assess efficacy and account for attrition.<br><br>RESULTS: Here we show that no adverse events occur in either group. Compared to the Control, the X-Secret group exhibits a faster reduction in BV symptoms (odor, discharge, pH >4.5, and itching) by days 7 and 28, with odds ratios at day 28 of 3.61, 4.87, 2.95, and 3.34, respectively. Vaginal swab analysis reveals a 3.7-225.3-fold greater reduction in Gardnerella vaginalis. By day 28, metagenomic profiling indicates increases in beneficial species Lactobacillus crispatus (3.71-fold) and Streptococcus salivarius (from non-detectable to 2.1%), along with reductions in harmful species G. vaginalis (14.29-fold) and Sneathia sanguinegens (806-fold).<br><br>CONCLUSIONS: The vaginal-spray Bacillus spore probiotic (LiveSpo X-Secret) provides a safe, convenient, and effective approach for BV treatment and reducing recurrence, supporting its potential as an adjunctive therapy for maintaining vaginal health.<br><br>CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT06165354, first posted 8/12/2023.},
}
@article {pmid41258374,
year = {2025},
author = {Aydin, E and Karaynir, A and Ozkan, RG and Bozdogan, B},
title = {Metagenomic analysis of bacteriome and phageome of wastewater from a ceramic factory in Türkiye.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41258374},
issn = {1618-1905},
abstract = {Bacteriophages are major determinants of bacterial community dynamics. Industrial wastewaters constitute distinctive microbe-phage ecosystems shaped by heavy-metal and chemical stressors, yet they remain sparsely characterized by metagenomics. Most existing studies focus on municipal or hospital wastewaters, while phage and bacteriome communities in industrial effluents such as ceramic wastewater are largely unexplored. This study aimed to comprehensively characterize bacterial and phage communities in influent and effluent samples from a ceramic factory using metagenomic approaches. Phage DNA was sequenced on an Illumina NextSeq and processed with a standard bioinformatics pipeline for taxonomic and functional annotation. Of 657 million raw reads, 66% mapped to phage sequences. Caudovirales predominated, with Autographiviridae comprising 59% of classified viral reads. Functional annotation indicated that 64% of assigned genes encoded structural or replication functions. For the bacteriome, 16 S rRNA (V3-V4) amplicons were sequenced on an Illumina NovaSeq 6000 and classified with Kraken2. Proteobacteria dominated both sample types, but community structure shifted along the treatment line: the influent was enriched in environmental-water genera-Flavobacterium (25%), Aeromonas (16%), and Acinetobacter (11%) -whereas the effluent was dominated by Flavobacterium (37%), Hydrogenophaga (25%), and Rhodoferax (14%). Genus-level richness contracted from 228 (influent) to 67 (effluent), and the number of reads entering taxonomic classification declined sharply (1,482,914 vs. 55,847), consistent with selective removal and physicochemical filtering during treatment. Collectively, these results demonstrate that ceramic wastewater harbors a distinct microbe-phage ecosystem molded by chemical and particulate stress. By illuminating an understudied industrial niche, this work provides actionable insights for wastewater treatment, environmental bioremediation, and microbial risk assessment.},
}
@article {pmid41258115,
year = {2025},
author = {Yepes-García, J and Novoa-Montenegro, N and Otero-Jiménez, V and Uribe-Vélez, D and Barreto-Hernández, E and Falquet, L},
title = {Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1823},
pmid = {41258115},
issn = {2052-4463},
mesh = {*Oryza ; Colombia ; Metagenomics ; *Metagenome ; *Soil Microbiology ; Bacillus/genetics ; Agriculture ; Fermentation ; },
abstract = {Extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. In the quest for enhanced RS degradation systems, we recovered 146 Metagenome-Assembled Genomes (MAGs) from experiments aiming at decomposing RS. Such assays included the application of a Bacillus strain, a Trichoderma-based commercial product, organic and inorganic compounds in different combinations during a solid-state fermentation in Colombian rice fields. The set of MAGs comprises 30 MAGs from bulk soil and 116 MAGs from RS surface, for which taxonomic classification indicates that 67% of them may constitute novel taxa. Furthermore, functional analysis through different approaches suggests the presence of both mid-quality and high-quality MAGs with potential to biotransform RS within this dataset. Finally, these MAGs represent a valuable resource for exploring uncharacterized microbial diversity in Colombian agricultural ecosystems.},
}
@article {pmid41258100,
year = {2025},
author = {Wang, C and Zheng, R and Sun, C},
title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10134},
pmid = {41258100},
issn = {2041-1723},
mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; },
abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.},
}
@article {pmid41258067,
year = {2025},
author = {Zhang, Q and Sun, Y and Liu, W and Zhao, Q and Yuan, K and Chen, D},
title = {Clinical characteristics of Torquetenovirus infected immunocompromised patients explored by metagenomic next-generation sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40857},
pmid = {41258067},
issn = {2045-2322},
support = {Grant No. MTP2022D027//Medical Talent Program for High-hroughput Sequencing Technology in Infectious Diseases, China/ ; },
mesh = {Humans ; *Immunocompromised Host ; *Torque teno virus/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; *DNA Virus Infections/virology/immunology/diagnosis ; *Metagenomics/methods ; Adult ; Aged ; },
abstract = {Since the recent application of metagenomic next-generation sequencing (mNGS) techniques to clinics, Torquetenoviruses (TTV) have received much attention due to their high positive rates. However, there is an insufficient understanding in clinical settings of the pathogen, especially in immunocompromised patients. This study explores the clinical characteristics of TTV infection in immunocompromised patients using mNGS. We enrolled a total of 120 TTV-infected patients in the study, including 81 immunocompromised and 39 immunocompetent individuals. The prevalence, diagnosis, treatment, and co-pathogens were compared between the two groups. The microbial diversity and presence of co-pathogens in patients infected with Torquetenovirus (TTV) were elucidated through comprehensive analysis. T-tests compared the normally distributed continuous data. The immunocompromised patients exhibited significantly elevated TTV loads, and a notable proportion of these patients also presented with hematopoietic disorders. Importantly, our investigation revealed that current treatments showed no efficacy against TTV infection.Furthermore, the presence of copathogens such as Staphylococcus, Bacillus, Mycobacterium, and Acinetobacter was observed in TTV-infected individuals. Immunocompromised patients exhibited a significantly higher abundance of Staphylococcus and Shewanella compared to immunocompetent patients (p < 0.05). Cautious use of antiviral therapy is recommended for patients with TTV mono-infection. However, greater attention should be given to co-pathogens, such as Staphylococcus spp. and Shewanella spp. This cohort study provides valuable insights into the clinical significance of TTV infection, particularly in immunocompromised patients. We found that TTV is frequently detected in this population, often with higher viral loads and an increased burden of co-pathogens. These findings suggest that TTV may serve primarily as a marker of immune dysfunction rather than as a sole pathogen. Incorporating TTV monitoring into mNGS-based diagnostics could help identify high-risk patients, support early intervention, and guide tailored management strategies in immunocompromised settings.},
}
@article {pmid41257635,
year = {2025},
author = {Liu, J and Wu, J and Zheng, Z and Xue, J and Zhang, W},
title = {Clinical spectrum of Talaromyces marneffei infections in HIV-negative patients: an 18-case series including a rare presentation with gastrointestinal onset, adrenal mass, and hemophagocytic lymphohistiocytosis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1616},
pmid = {41257635},
issn = {1471-2334},
support = {2024J0112//Nature Science Foundation of Fujian Province of China/ ; },
mesh = {Humans ; Male ; Female ; *Talaromyces/isolation &amp; purification/genetics ; Middle Aged ; *Lymphohistiocytosis, Hemophagocytic/microbiology ; *Mycoses/diagnosis/microbiology/pathology/complications ; Retrospective Studies ; Aged ; Adult ; Coinfection ; *Gastrointestinal Diseases/microbiology ; HIV Seronegativity ; },
abstract = {BACKGROUND: The diverse manifestations of Talaromyces marneffei (TM) infection in HIV-negative patients complicate and often delay diagnosis. This study reviews 18 cases to better characterize the clinical spectrum of this disease, with the goal of improving recognition of its varied presentations.<br><br>METHODS: Retrospective analysis of 18 patients assessing underlying diseases, manifestations, co-infections, diagnostics, treatment, and outcomes. Diagnosis required TM positivity via culture, histopathology, or metagenomic next-generation sequencing(mNGS).<br><br>RESULTS: This cohort (14 males and 4 females; mean age 57.94&#x2009;&#xb1;&#x2009;11.12 years) exhibited diverse comorbidities, including renal transplantation (27.8%), tuberculosis (22.2%), cancer (16.7%), bronchiectasis (16.7%), and anti-interferon-&#x3b3; autoantibody (AIGA) syndrome (11.1%). Common manifestations included respiratory symptoms (72.2%), fever (55.6%), and anemia (50.0%). Immunodeficiency was frequent, with an abnormal CD4/CD8 ratio in in 10/15 patients (66.7%). Notably, 94.4% of cases were initially misdiagnosed-often as tuberculosis (35.3%) or bacterial pneumonia (23.5%)-leading to a mean diagnostic delay of 8.97&#x2009;&#xb1;&#x2009;7.02 weeks. mNGS provided diagnosis in 77.8% of cases. Overall mortality was 22.2%, with two relapses linked to AIGA syndrome. We report the first documented TM triad in a patient with systemic lupus erythematosus (SLE) and Epstein-Barr virus (EBV) coinfection: concurrent gastrointestinal onset (manifesting as ileocolonic ulcers), adrenal mass, and hemophagocytic lymphohistiocytosis (HLH).<br><br>CONCLUSIONS: TM infection in HIV-negative hosts demonstrates broad clinical heterogeneity, often masked by comorbidities and leading to delayed diagnosis. mNGS is critical for early identification. The unprecedented triad of gastrointestinal onset, adrenal mass, and HLH underscores TM's capacity for atypical dissemination. AIGA may predict relapse.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid41257101,
year = {2025},
author = {He, X and Wang, M and Sun, T and Tang, J and Zeng, Y},
title = {Metagenomic Next-Generation Sequencing Diagnosis of Streptococcus agalactiae Meningitis in a Diabetic Patient.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94759},
pmid = {41257101},
issn = {2168-8184},
abstract = {Streptococcus agalactiae meningitis is primarily observed among neonates and is uncommon in adults. We present a rare case of Streptococcus agalactiae meningitis in an adult. The patient was a 74-year-old male with a history of gastric perforation surgery, chemotherapy for neck lymphoma, and hypertension. He presented to the emergency department with an 11-day history of neck pain, one day of limited mouth opening and dysphagia, and eight hours of altered consciousness. On examination, he exhibited impaired consciousness (Glasgow Coma Scale score: 8) and cervical rigidity. He was intubated and received oxygen therapy. Laboratory findings revealed elevated infection markers and turbid cerebrospinal fluid (CSF). Metagenomic next-generation sequencing (mNGS) of the CSF detected Streptococcus agalactiae. Enhanced MRI of the head and neck showed a small subdural effusion, spinal cord edema at C5-C6, thickening and enhancement of the anterior and posterior longitudinal ligaments and meninges at the skull base, suggestive of Streptococcus agalactiae infection. After 10 days of anti-infective treatment with ceftriaxone, the patient's condition improved, and he was transferred to a local hospital for continued management.},
}
@article {pmid41256608,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.02.680046},
pmid = {41256608},
issn = {2692-8205},
abstract = {UNLABELLED: Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, 'reverse translation' experiments are performed where intact fecal microbiomes collected from trial participants prior to and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because 'no treatment' control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes microbial gene expression consistent with a less virulent gut ecosystem and changes in expression of (i) components of gut epithelial cell junctions in the enterocytic and goblet cell lineages, (ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and (iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.<br><br>SIGNIFICANCE STATEMENT: Undernutrition is a global health problem. Recent clinical trials of a gut microbiome-directed complementary food (MDCF-2) designed to repair the perturbed gut microbiomes of undernourished Bangladesh children produced superior growth outcomes versus a standard nutritional supplement. Given ethical considerations and tissue sampling constraints associated with these types of studies, we colonized gnotobiotic mice postnatally with microbiome samples obtained from trial participants before and after treatment to model "unrepaired" and "repaired" gut ecosystems. Using a multi-omics approach, we uncover heretofore unappreciated changes in expressed chemosensory tuft cell, mucus-producing goblet cell and absorptive enterocytic functions and interactions accompanying microbiome repair. Extending microbiome clinical trials back to preclinical models ('reverse translation') provides mechanistic insights that can inform design/interpretation of future interventions.},
}
@article {pmid41256588,
year = {2025},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandon, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.679827},
pmid = {41256588},
issn = {2692-8205},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.<br><br>METHODS: In this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.<br><br>RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8 [+] and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA [+] cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.<br><br>CONCLUSIONS: These results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.},
}
@article {pmid41256293,
year = {2025},
author = {Agrawal, H and Agarwal, N and Gupta, N},
title = {Impact of gut microbiome on outcomes following endoscopic interventions in gastrointestinal disease.},
journal = {World journal of gastrointestinal endoscopy},
volume = {17},
number = {11},
pages = {110207},
pmid = {41256293},
issn = {1948-5190},
abstract = {BACKGROUND: Endoscopic interventions play a vital role in diagnosing and managing gastrointestinal diseases, but complications such as bleeding, infection, and delayed healing can adversely affect patient outcomes. The influence of the gut microbiome on these outcomes is increasingly being recognized.<br><br>AIM: To evaluate the role of the gut microbiome in influencing clinical outcomes after endoscopic interventions, focusing on microbial diversity, specific taxa, metabolic functions, and emerging predictive models.<br><br>METHODS: A systematic literature search was conducted in PubMed, EMBASE, and Cochrane databases up to May 2025, selecting human studies that analyzed gut microbiome composition or function in relation to endoscopic interventions and clinical outcomes. Microbiome analysis techniques included 16S rRNA gene sequencing, metagenomics, and metabolomics.<br><br>RESULTS: Forty-two studies met the inclusion criteria. Our review identifies key beneficial microbes, such as Faecalibacterium prausnitzii and Bacteroides spp., which support mucosal healing. In contrast, dysbiosis (e.g., an increased abundance of Proteo bacteria) is associated with poorer healing and higher complication rates. Notably, microbiome-informed predictive models have shown strong potential for forecasting post-procedural complications, offering a pathway to personalized treatment strategies. Probiotics have also emerged as a promising intervention, helping to restore microbial balance and reduce complications such as infection and delayed healing.<br><br>CONCLUSION: The gut microbiome plays a significant role in recovery after endoscopy. Integrating microbiome analysis into clinical decision-making could improve outcomes through personalized predictions and targeted therapies. Future research should focus on standardizing microbiome assessment protocols and validating predictive models to optimize patient care.},
}
@article {pmid41255950,
year = {2025},
author = {Li, S and Peng, X and Tang, Z and Li, W and Song, X},
title = {Talaromyces marneffei Infection in Non-Endemic Areas: Two Case Reports, Diagnostic Insights, and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5895-5903},
pmid = {41255950},
issn = {1178-6973},
abstract = {PURPOSE: Talaromycosis is an invasive fungal infection caused by the pathogenic fungus Talaromyces marneffei (T. marneffei), prevalent in Southeast Asia and Southern China. This disease is rare in non-endemic areas and primarily affects the respiratory system with atypical manifestations. Therefore, the condition is often misdiagnosed as other respiratory infections. This article presents two cases of talaromycosis in non-endemic areas, aiming to provide diagnostic and therapeutic references for this rare fungal infection.<br><br>CASE PRESENTATION: Two cases of talaromycosis in non-endemic areas were retrospectively analyzed. The first case involved a human immunodeficiency virus (HIV)-infected patient with tracheobronchial talaromycosis. Bronchoscopy revealed multiple nodular neoplasms in the trachea and bilateral main bronchi. Histopathological examination of the biopsy tissue showed histiocyte aggregation and intracellular pathogens. T. marneffei was identified by microbial culture of bronchoalveolar lavage fluid (BALF). The second case was an HIV-negative patient with pulmonary talaromycosis. Bronchoscopy revealed mucosal congestion and edema, and T. marneffei was detected by metagenomics next-generation sequencing (mNGS) of BALF.<br><br>CONCLUSION: Talaromycosis warrants more clinical attention in both HIV-negative individuals and non-endemic areas. In addition, clinicians should improve diagnostic recognition of this disease for timely management. Bronchoscopy combined with mNGS can facilitate early diagnosis of talaromycosis, particularly in culture-negative cases where conventional methods fail. This strategy directly addresses a major diagnostic challenge and improves patient prognosis.},
}
@article {pmid41255826,
year = {2025},
author = {Jin, J and Chao, X and Zhu, Z and Zhang, B and Fu, Y and Xu, J and Ma, S and Chen, T and Wang, Y and Ding, J},
title = {Metagenomic Analysis of Tick-Borne Viruses Associated With Hyalomma asiaticum From Different Hosts in the Surrounding Areas of Urumqi, China.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {9985595},
pmid = {41255826},
issn = {1865-1682},
mesh = {Animals ; China/epidemiology ; Metagenomics ; *Ixodidae/virology ; Phylogeny ; Horses ; Sheep ; Tick-Borne Diseases/veterinary/epidemiology/virology ; *RNA Viruses/isolation &amp; purification/genetics/classification ; },
abstract = {Tick-borne viruses (TBVs) represent a serious risk to global public and animal health. Despite the remarkable species diversity of ticks documented in Urumqi and its adjacent regions of China, scientific investigations into TBVs in this ecologically significant area have been strikingly scarce. In this study, we conducted metagenomic sequencing on 752 Hyalomma asiaticum (H. asiaticum), including questing ticks from Wujiaqu and blood-feeding ticks collected from sheep and horses in the Changji area. A total of 11 different RNA viruses were detected, belonging to six viral families and some unclassified families, with double-stranded RNA viruses being the most prevalent (49.1%), including Totiviridae and Sedoreoviridae. Single-stranded RNA viruses accounted for 11.9% of the virome, encompassing Chuviridae, Flaviviridae, Rhabdoviridae, and Phenuiviridae. Notably, 39.0% of the viral sequences remained unclassified, highlighting a substantial reservoir of uncharacterized viral diversity. Genomic and phylogenetic characterizations were performed on six highly abundant viruses, including Bole tick virus 1, Mivirus boleense, Bole tick virus 4, Lonestar tick totivirus, Hubei toti-like virus 24, and a novel strain of Hulunbuir Totiv tick virus 1. However, their zoonotic potential requires further investigation. By integrating cytochrome c oxidase subunit Ⅰ (COI) gene-based tick species identification with viral metagenomics, this study provided a comprehensive assessment of tick species and TBVs diversity in Urumqi and its surrounding areas, China. These results provide new insights into both the genetic diversity of tick-borne RNA viruses and their phylogenetic connections, while also expanding knowledge about the geographical distribution patterns of these pathogens.},
}
@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}
@article {pmid41255157,
year = {2025},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}
@article {pmid41254499,
year = {2025},
author = {Bring Horvath, ER and Winter, JM},
title = {SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {280},
pmid = {41254499},
issn = {1471-2105},
support = {1R01AI155694/NH/NIH HHS/United States ; },
mesh = {*Software ; *Sequence Alignment/methods ; Databases, Genetic ; *Genomics/methods ; Amino Acid Motifs ; Metagenomics/methods ; },
abstract = {BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST + remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers.<br><br>RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST&#x2009;+&#x2009;database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage.<br><br>CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.},
}
@article {pmid41254331,
year = {2025},
author = {Bersch-Ferreira, &#xc2;C and Fonseca, DC and Tramujas, L and Schiavon, CA and Nakagawa Santos, RH and V Machado, RH and Biasi Cavalcanti, A and Marcadenti, A},
title = {Gut Microbiota Composition and Arterial Hypertension Improvement Post-Roux-en-Y Gastric Bypass: GATEWAY Trial Sub-Analysis After 5 Years.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41254331},
issn = {1708-0428},
abstract = {INTRODUCTION: The aim of this study was to explore the relationship between gut microbiota composition and hypertension remission in individuals with obesity and hypertension who underwent Roux-en-Y gastric bypass (RYGB) surgery five years prior.<br><br>METHODS: This is a sub-analysis of the GATEWAY trial using cross-sectional data from participants five years post-surgery. Three groups were included: patients who underwent RYGB and achieved hypertension remission (Group 1, n&#x2009;=&#x2009;12), patients who underwent RYGB but did not achieve remission (Group 2, n&#x2009;=&#x2009;12), and a control group of individuals with obesity and hypertension who did not undergo surgery (Group 3, n&#x2009;=&#x2009;15). Gut microbiota composition was evaluated using metagenomic sequencing of fecal samples, with taxonomic classification at the phylum, class, and order levels.<br><br>RESULTS: No statistically significant differences were found in overall microbiota composition between the groups. However, microbial richness was higher in both surgical groups compared to the control group, suggesting a potential link between bariatric surgery and increased gut microbial diversity.<br><br>CONCLUSION: While gut microbiota composition did not significantly differ between individuals with and without hypertension remission, the observed increase in microbial richness among those undergoing bariatric surgery underscores the complex interplay between obesity treatment, gut microbiota, and blood pressure regulation. Further research is needed to elucidate these long-term relationships.},
}
@article {pmid41253025,
year = {2025},
author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP},
title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157550},
doi = {10.1016/j.phymed.2025.157550},
pmid = {41253025},
issn = {1618-095X},
abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.<br><br>PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.<br><br>METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-&#x3ba;B), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.<br><br>RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-&#x3b1;, IL-17, and IFN-&#x3b3;), inhibit the expression of TLR4/NF-&#x3ba;B, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.<br><br>CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-&#x3ba;B and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.},
}
@article {pmid41252983,
year = {2025},
author = {Cao, S and Zhu, J and Gan, X and Fu, Q and Hu, H and Huang, Q},
title = {Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140491},
doi = {10.1016/j.jhazmat.2025.140491},
pmid = {41252983},
issn = {1873-3336},
abstract = {The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ[13]C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.},
}
@article {pmid41252855,
year = {2025},
author = {Oh, S and Wijaya, J},
title = {Predictive surveillance and diagnosis of COVID-19: An integrative machine learning and wastewater multi-omics approach.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124981},
doi = {10.1016/j.watres.2025.124981},
pmid = {41252855},
issn = {1879-2448},
abstract = {COVID-19 has had major global impacts, highlighting the importance of robust predictive surveillance and diagnostic systems to ensure effective public health responses. Traditional surveillance methods based on passive case counting and diagnostic testing of individual patients often suffer from delays and resource constraints, preventing timely responses. This study proposed an integrative framework integrating machine learning (ML)-derived predictive surveillance with wastewater-based diagnosis, aiming to predict temporal trends in Korea and identify disease-causing agents. The ML model utilized crowdsourced COVID-19-related keywords, climatic, and environmental data, optimized via model selection and feature selection. The integrated data-driven model predicted COVID-19 cases over three years more accurately than those using single source data (i.e., baseline model). The explainable AI technique (i.e., helping to inform how the model made those predictive decisions) identified six keywords (reducing phlegm, throat pain, long COVID-19, sore throat, COVID-19 self-kit, and COVID-19 kit) as robust predictors of disease trends. In a proof-of-concept experiment, wastewater-based genotyping of disease-causing agents and affected human communities in sewershed areas was conducted. Metatranscriptomics of municipal wastewater was conducted to identify COVID-19 viral variants, evolutionarily related to those clinically isolated strains, distinguishable from conventional diagnostic testing of individual patients. Wastewater-derived metagenomics was also performed to assess genomic variation in the affected human populations. The integrative framework proposed in this study offers a rapid, cost-effective approach for the surveillance and diagnosis of COVID-19 and other infectious diseases, thus strengthening or complementing existing health systems.},
}
@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&amp;D Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; },
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.<br><br>RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.<br><br>TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}
@article {pmid41189540,
year = {2026},
author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S},
title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70066},
doi = {10.1111/1755-0998.70066},
pmid = {41189540},
issn = {1755-0998},
support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project &#x201b;Ocean DNA'/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; },
abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.},
}
@article {pmid41168956,
year = {2026},
author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD},
title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70069},
doi = {10.1111/1755-0998.70069},
pmid = {41168956},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; },
abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.},
}
@article {pmid41257040,
year = {2023},
author = {Gündoğdu, A and Charyyeva, A and Nalbantoğlu, &#xd6;U},
title = {Metagenomic Profiling of Human Protozoan Parasites in Wastewater and Hospital Effluents.},
journal = {Journal of clinical practice and research},
volume = {45},
number = {5},
pages = {435-446},
pmid = {41257040},
issn = {2980-2156},
abstract = {OBJECTIVE: Advancements in metagenomic techniques have provided new tools for profiling human parasites in environmental matrices such as wastewater. This study aimed to profile protozoan parasites in wastewater from a major city, rural area, and hospital in Kayseri, Türkiye, using metagenomic techniques.<br><br>MATERIALS AND METHODS: Shotgun metagenome sequencing was conducted on ten water samples collected from five sampling sites over a two-week period. The sequences were aligned to 80 human parasite genomes to evaluate the presence and relative abundance of each parasite species. A comparative bioinformatic analysis was performed on the metagenomes from each sampling point.<br><br>RESULTS: The diversity of parasites in the city wastewater exceeded that of the rural and hospital sampling points. Blastocystis spp. subtypes and Giardia intestinalis were dominant in rural wastewater, while Plasmodium falciparum, Plasmodium ovale, Toxoplasma gondii, and Acanthamoeba species showed significant abundance in hospital effluent (p<0.01). Moreover, protozoan parasites not previously reported in a clinical setting were identified in the water samples.<br><br>CONCLUSION: This is the first study in T&#xfc;rkiye investigating the presence of human parasites in wastewater using metagenomics. The study highlights the risk posed by human parasites in treated wastewater to population using natural resources. Implementing a specialized wastewater treatment targeting parasites could mitigate the potential spread of these pathogens in the environment. The study revealed certain sequences associated with species not previously identified in clinical instances. This finding may result from genomic resemblances with other eukaryotic organisms that were not systematically excluded, or alternatively, the displacement of protozoa linked to the increasing influx of refugees.},
}
@article {pmid41252801,
year = {2025},
author = {Gacem, A and Soltane, R and Wanale, SG and Mohammed, SA and Almulla, N and Eltayeb, LB and Alreshidi, MA and Alasiri, A and Albakri, GS and Raghuvanshi, U and Abdulmonem, WA and Qasim, MT and Gupta, R and Islam, S and Yadav, KK},
title = {Advances in molecular methodologies and nanotechnology-enabled drug delivery in biomedicine: An overview of current progress.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 1},
pages = {108765},
doi = {10.1016/j.compbiolchem.2025.108765},
pmid = {41252801},
issn = {1476-928X},
abstract = {Recent advances in molecular techniques and nanosystems have significantly transformed biomedical research, particularly in pathogen detection and drug delivery. Traditional culture-based methods are being increasingly replaced by rapid and precise molecular approaches, offering greater accuracy in identifying pathogens and uncovering the genetic mechanisms underlying antimicrobial resistance (AMR). This review highlights key molecular tools, including matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing, DNA microarrays, metagenomics, and polymerase chain reaction (PCR) and others with a critical evaluation of their strengths, limitations, and applications in global surveillance. Alongside, the integration of nanostructured systems has opened new avenues for designing advanced drug-delivery platforms with improved bioavailability, targeted action, and reduced toxicity. Together, these innovations emphasize the potential of molecular and nanoscale technologies to address pressing challenges in diagnostics, therapeutics, and the management of infectious diseases.},
}
@article {pmid41252568,
year = {2025},
author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G},
title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2592078},
pmid = {41252568},
issn = {1747-4132},
abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.<br><br>AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.<br><br>EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.},
}
@article {pmid41252442,
year = {2025},
author = {Zentgraf, J and Schmitz, JE and Rahmann, S},
title = {Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf632},
pmid = {41252442},
issn = {1367-4811},
abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.<br><br>RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.<br><br>Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).<br><br>SUPPLEMENTARY INFORMATION: Available online.},
}
@article {pmid41252249,
year = {2025},
author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS},
title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116573},
doi = {10.1016/j.celrep.2025.116573},
pmid = {41252249},
issn = {2211-1247},
abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.},
}
@article {pmid41251845,
year = {2025},
author = {Saggu, SK and Kumar, M and Kumar, S},
title = {Metagenomics and its impact on environmental and therapeutic microbiology.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {24},
pmid = {41251845},
issn = {1432-072X},
mesh = {*Metagenomics/methods ; *Environmental Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Humans ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metagenomics has significantly advanced our understanding of microbial life by enabling the direct analysis of environmental DNA, thereby deciphering the vast microbial dark matter comprising unknown and uncultivable microbial diversity that remains inaccessible through conventional culture-dependent methods. The culture-independent approach provides a comprehensive view of microbial composition, function, and evolution, facilitating discoveries across environmental and clinical domains. Recent developments in high-throughput sequencing, hybrid long-read assemblies, and AI/ML-based genome binning have enhanced our understanding to reconstruct complete genomes, predict metabolic pathways, and engineer microbial consortia. This review summarizes the impact of metagenomics on environmental and therapeutic microbiology, emphasizing its contributions in the field of bioremediation, greenhouse gas mitigation, sustainable agriculture, industrial enzyme discovery, and novel drug development. It further explores metagenomics-driven innovations in pathogen detection, antimicrobial resistance surveillance, and multi-omics integration. Furthermore, it discusses methodological developments, computational challenges, and translational limitations, offering future perspectives for harnessing metagenomic insights in sustainable biotechnology and precision medicine.},
}
@article {pmid41251544,
year = {2025},
author = {Pang, X and Zhang, B and Zhang, Q and Jiang, J},
title = {Freeze-Thaw Cycling Accelerates Microbial Reduction and Immobilization of Vanadium(V) in Groundwater.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11332},
pmid = {41251544},
issn = {1520-5851},
abstract = {As global warming intensifies, freeze-thaw cycling has become more pronounced, significantly impacting microbial metabolic processes. In this study, microbial vanadium(V) [V(V)] reduction under freeze-thaw conditions was investigated. Temperature fluctuations between -4 and +4 °C accelerated V(V) reduction, together with the faster decrease in organic matter and total nitrogen in the sediment, compared to constant-temperature incubations at either -4 or +4 °C. V(V) was bioreduced to vanadium(IV) precipitates, increasing the acid-soluble, reducible, and oxidizable fractions of vanadium in the sediment. Freeze-thaw cycling enhanced microbial carbon and nitrogen utilization, as well as the richness and diversity of the microbial community. Metagenomics, real-time quantitative polymerase chain reaction quantification, and electron-transfer measurements revealed the underlying mechanisms. During thawing, microorganisms such as Flavobacterium sp., Stutzerimonas sp., and Giebergeria sp. reduced V(V) via denitrification genes (narG, nirS, and nosZ). Under freezing conditions, enriched Pseudomonas sp. and Acinetobacter sp. achieved V(V) reduction through the electron-transfer gene (mtrC), with increased cytochrome c concentration. Key cold-adaptation genes, including cspA, HSP, SOD, katG, and SCD, were prevalent in these microorganisms, supporting antifreeze activities. This study offers insights into microbial V(V) reduction under freeze-thaw cycling scenarios and is helpful in developing pertinent remediation strategies.},
}
@article {pmid41251358,
year = {2025},
author = {Wilson, A and Jauregui, R and Bueno, R and Begg, D and Hannah, M and Sheeba, E and Bestbier, M and Green, D and O'Keefe, J and McCulley, M},
title = {Genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0108325},
doi = {10.1128/mra.01083-25},
pmid = {41251358},
issn = {2576-098X},
abstract = {We report the draft genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand. A high-quality near-complete genome, comprised of an apicoplast, mitochondrion, and four chromosomes, was produced through long-read metagenomic sequencing.},
}
@article {pmid41251138,
year = {2025},
author = {Shukla, M and Wattam, AR and Aleman, A and Bhattacharya, R and Bowers, N and Brettin, T and Capria, A and Chia, N and Cucinell, C and Davis, JJ and Dempsey, DM and Dickerman, A and Dietrich, EM and Gokdemir, O and Hendrickson, RC and Kenyon, RW and Klahn, B and Kuscuoglu, M and Lefkowitz, EJ and Ma, H and Machi, D and Macken, C and Mann, CM and Mao, C and Nguyen, M and Olsen, GJ and Olson, RD and Overbeek, R and Owens, SM and Parrello, B and Poretsky, R and Pusch, GD and Ramanathan, A and Sheriff, JT and Singh, I and Stewart, L and VanOeffelen, M and Vonstein, V and Warren, AS and Wilke, A and Zmasek, CM and Zuniga, A and Stevens, RL},
title = {BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1254},
pmid = {41251138},
issn = {1362-4962},
support = {//National Institute of Allergy and Infectious Diseases/ ; /NH/NIH HHS/United States ; U24AI183849/HH/HHS/United States ; },
abstract = {The Bacterial and Viral Bioinformatics Resource Center (BV-BRC; https://www.bv-brc.org) is a comprehensive resource supporting research on bacterial and viral pathogens. It currently hosts over 14 million publicly available genomes and 33 high-throughput bioinformatic analysis services with numerous visual analytic tools allowing researchers to analyze their private data, generate comparisons with public data, and share data and results with colleagues. In recent years, the BV-BRC has added several new analysis services to support rapid comparative genomics and epidemiological analysis, viral genome assembly and annotation, viral subspecies classification, wastewater analysis, and molecular docking. In addition, several existing services have been updated to incorporate state-of-the-art tools, including assembly, annotation, taxonomic classification, metagenomic read mapping, and RNA-seq analysis. A new tool, called BV-BRC Copilot, provides an AI-powered natural-language interface that combines large language models with retrieval-augmented generation to guide users through data exploration, analysis workflows, and knowledge integration. With expanded outbreak tracking pages, training and educator engagement, and continued development of novel AI-driven analytics, BV-BRC continues to provide a unified resource to meet the evolving needs of the global research community.},
}
@article {pmid41250695,
year = {2025},
author = {Pathi, B and Sahoo, JP and Mahapatra, A and Panigrahy, R and Padhi, S and Lenka, PR and Mohanty, I and Ramadass, B and Panigrahi, K and Dixit, S and Das, MK},
title = {Genome Sequencing to Prevent Hospital-Acquired Infections Caused by Carbapenem-Resistant Acinetobacter baumannii Due to Importation and Intra-facility Transmission in a Regional Hospital Network: Study Protocol for Implementation Research.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94812},
pmid = {41250695},
issn = {2168-8184},
abstract = {BACKGROUND AND OBJECTIVES: Carbapenem-resistant Acinetobacter baumannii (CRAb) is among India's leading bacteria responsible for hospital-acquired infections (HAIs). The CRAb causing intra-facility and inter-facility (or importation) HAI transmissions may differ phylogenetically. For control and prevention of CRAb-associated HAIs within and across facilities, information about the phylogenetic lineage characterization and contextual risk factors is critical. To our knowledge, there is no preliminary state-level data available from Odisha state in India regarding the dynamics of CRAb transmission (intra- and inter-facility), phylogenetic lineages, risk factors, and geospatial epidemiology. This study shall document the dynamics of CRAb-associated HAIs, the phylogenetic lineages responsible for intra-facility and inter-facility transmissions, and the risk factors. We shall leverage the CRAb phylogenetic data and risk factors identified through an integrated laboratory-clinical-epidemiological-genomic surveillance for tackling the intra-facility and inter-facility transmissions and outbreaks using implementation research approaches with adoption of contextualized hospital infection control and prevention measures and antibiotic stewardship efforts in a hospital network in Odisha state, India.<br><br>METHODS: This study adopts an integrated prospective facility-based surveillance with a quasi-experimental design using the plan-do-study-act (PDSA) implementation research cycles with mixed-methods data collection approaches. The study will be conducted over three years at six tertiary care medical institutions in Odisha. Prospective surveillance over 24 months at these hospitals will monitor the CRAb isolates to identify HAI outbreaks and intra- and inter-facility transmissions. The metagenomic and genome-wide sequencing (GWS) shall document CRAb phylogenetic lineages for outbreaks and intra- and inter-facility transmissions. Geospatial mapping shall document the spatial characterization of CRAb transmission for the index cases. Formative research shall identify potential risk factors at various levels for HAIs, outbreaks, intra- and inter-facility CRAb transmissions, hospital infection prevention, surveillance, and antibiotic stewardship efforts, using the Consolidated Framework for Implementation Research (CFIR). Based on this information, contextualized strategies and interventions to strengthen hospital infection prevention, surveillance, and antibiotic stewardship efforts shall be implemented at these facilities using incremental PDSA cycles. Data from these PDSA cycles shall be compared to document the impact on CRAb outbreaks and process indicators. The practices' and interventions' feasibility, acceptability, and sustainability shall be documented.<br><br>RESULTS: We do not have any observations, as we have not started the study yet.<br><br>CONCLUSION: The study shall generate evidence on genoepidemiology, transmission dynamics of HAIs due to CRAb in Odisha, India, and the associated risk factors. The lessons from context-specific implementation strategies (covering infection surveillance, prevention strategies, and antibiotic stewardship domains) to tackle CRAb-associated HAIs outbreaks and the feasibility, acceptability, and sustainability shall inform the policy and practices. The geographic signatures of horizontal CRAb-associated HAIs will generate a new knowledge base to design future intervention measures.},
}
@article {pmid41250675,
year = {2025},
author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X},
title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf257},
pmid = {41250675},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.<br><br>RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.<br><br>Code is available at https://github.com/Ying-Lab/ICCTax.},
}
@article {pmid41250628,
year = {2025},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41250628},
issn = {2191-0286},
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}
@article {pmid41250240,
year = {2025},
author = {Gwak, HJ and Rho, M},
title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {393},
pmid = {41250240},
issn = {1474-760X},
support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; },
abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.},
}
@article {pmid41250148,
year = {2025},
author = {Lam, AY and Lau, CH and Tam, WY and Chan, CT and Lok, TM and Suen, LK and Lee, LK and Yeung, EY and Lam, TK and Cheung, WK and Chui, MW and Soong, HS and Chow, FW and Lam, SC and So, SN and Yuen, SK and Siu, GK},
title = {Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {143},
pmid = {41250148},
issn = {2524-6372},
support = {2023-00-51 CRG230402//Tung Wah College/ ; 1-ZVZL//The Hong Kong Polytechnic University/ ; },
abstract = {BACKGROUND: Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities.<br><br>RESULTS: From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n&#x2009;=&#x2009;10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n&#x2009;=&#x2009;5), and methicillin-resistant Staphylococcus aureus (MRSA, n&#x2009;=&#x2009;2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area.<br><br>CONCLUSIONS: Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.},
}
@article {pmid41250124,
year = {2025},
author = {Huang, SW and Lin, CR and Chang, YH and Ni, YH and Chen, HL and Liu, HH},
title = {Cross-country multi-modal evidence links Aspergillus to biliary atresia.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {94},
pmid = {41250124},
issn = {1757-4749},
abstract = {BACKGROUND: Biliary atresia (BA) is the leading cause of pediatric liver transplantation. It is characterized by progressive extrahepatic bile duct obstruction in young infants. Inspired by the success of antifungal treatment in a newborn with BA-related obstructive cholangitis, we explored a potential link between BA and fungi, particularly Aspergillus. Fecal DNA was analyzed using 18S ribosomal sequencing and validated with a published fecal metagenomic dataset. Epidemiological data from the UK, Taiwan, and Japan were also examined.<br><br>RESULTS: Gut Aspergillus was exclusively detected in BA cases, suggesting it may be a potential trigger. Independent fecal metagenomic data from China and epidemiological correlations further supported this hypothesis. In the UK, BA presentations strongly correlated (r = 0.98, 95% CI [0.36, 1.0], p = 0.02) with Aspergillosis, but not with Candidiasis, during the COVID-19 lockdown. In Taiwan, a decade of data showed BA incidence was significantly associated (r = 0.78, 95% CI [0.29, 0.94], p = 0.01) with yearly Aspergillus-positive isolates among cancer-adjusted hospital admissions. In Japan, BA cases over 25 years correlated significantly (r = 0.85, 95% CI [0.37, 0.97], p = 0.01) with visceral Aspergillus burdens in autopsied cases, but not with other fungal infections.<br><br>CONCLUSIONS: The resolution of obstructive cholangitis in the antifungal-treated index case, together with multi-modal, cross-country evidence, highlights a potential link between gut Aspergillus and BA. Although limited by small sample size, retrospective design, and lack of mechanistic validation, the study may still be interpreted as hypothesis-generating and underscores the need for prospective studies to validate and extend these observations.},
}
@article {pmid41249836,
year = {2025},
author = {Huang, Y and Sun, Y and Ronda, C and Mavros, CF and Li, J and Jacobse, J and Huang, LH and Resnick, SJ and Giddins, M and Freedberg, DE and Chavez, A and Goettel, JA and Wang, HH},
title = {Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41249836},
issn = {1546-1696},
support = {MCB-2025515//National Science Foundation (NSF)/ ; 1R01DK118044//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R01CA272898//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5U19AI067773//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R03DK123489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; N00014-17-1-2353//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; HR00111920009//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; S-168-4X5-001//United States Department of Defense | United States Air Force | AFMC | Air Force Research Laboratory (AFRL)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; 1061046//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; 1513935//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; IRIS Award//Columbia University/ ; },
abstract = {Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.},
}
@article {pmid41249624,
year = {2025},
author = {Kocher, A and Krause, J and Spyrou, MA},
title = {Insights into infectious diseases through ancient pathogen genomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41249624},
issn = {1740-1534},
abstract = {Major advances in metagenomic and biomolecular techniques have opened avenues for the recovery and sequencing of rare and highly fragmented DNA molecules from ancient biological samples, including those of pathogens that may persist in the remains of infected hosts long after their death. Initially consisting of relatively rare findings for a few disease-causing agents of historical importance, the field of ancient pathogen genomics is rapidly progressing towards genome-level analyses of larger sample sets encompassing a wider range of bacterial, viral and eukaryotic taxa. These advances have provided important insights into past pathogen distribution and genomic make-up, and the unprecedented opportunity to track their evolution 'in action' over large timescales. In this Review, we explore the major contributions of ancient DNA research to the understanding of pathogen evolution and its association with past epidemics, as well as human sociocultural and migration history, including numerous important studies that have been published in recent years. Moreover, we discuss existing limitations and future prospects of ancient pathogen genomics and the relevance of the field to current public health challenges.},
}
@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}
@article {pmid41249299,
year = {2025},
author = {Wu, Y and Meng, X and Han, X and Bu, Z and Li, Y and Zhan, H and Zhang, S},
title = {Integrated metagenomic and metabolomic analysis reveals microbial metabolite interactions involved in the quality formation of Codonopsis Radix.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40278},
pmid = {41249299},
issn = {2045-2322},
mesh = {*Codonopsis/metabolism/microbiology/growth &amp; development/chemistry ; *Metabolomics/methods ; *Metagenomics/methods ; Soil Microbiology ; *Drugs, Chinese Herbal/metabolism ; Plants, Medicinal/metabolism/microbiology ; },
abstract = {Due to the impact of various environmental factors, in conjunction with the ecological adaptability and biochemical diversity of Chinese medicinal materials, Codonopsis Radix from Shanxi Province has developed into two distinct commercial specifications, namely Tai Codonopsis Radix (TCP) and Lu Codonopsis Radix (LCP). The present study examined the relationships between TCP and LCP from Shanxi Province regarding their environment, secondary metabolites, and Traditional Chinese Medicinal plant authenticity using metagenomic, metabolomic, and comprehensive quality assessment methods. The findings revealed that the two types of CPs met the quality standards. With respect to the growing environment, TCP and LCP grow in the same longitudinal extent, with a maximum longitudinal span of only 53'. Both regions presented similar natural environments conducive to the growth of CP. Additionally, the Lobetyolin content in TCP was greater than that in LCP. The soil microbial abundance in the TCP group was considerably significantly greater than that in the LCP group, and a new genus, Ascobolus, was found in TCP. Additionally, comparison of the metallic element data of the two groups soils revealed that the contents of Ti, Mg, Cr (P < 0.01) in the TCP group were significantly greater than those in the LCP group. Through correlation analysis, the ternary network of microbial-metal-metabolite interactions was constructed. The rhizosphere fungus Ascobolus was found to enhance the bioavailability of Zn via mineralization processes, thereby underscoring the significance of rhizosphere microecology in promoting plant growth. This study offers novel insights and approaches for the cultivation and processing of Codonopsis Radix.},
}
@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth &amp; development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}
@article {pmid41229281,
year = {2026},
author = {Richardson, RT and Avalos, G and Garland, CJ and Trott, R and Hager, O and Hepner, MJ and Raines, C and Goodell, K},
title = {Sensitive Environmental DNA Methods for Low-Risk Surveillance of At-Risk Bumble Bees.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70073},
doi = {10.1111/1755-0998.70073},
pmid = {41229281},
issn = {1755-0998},
support = {RC22-B5-7373//Environmental Security Technology Certification Program/ ; //Maryland Department of Natural Resources/ ; //University of Maryland/ ; },
mesh = {Animals ; Bees/genetics/classification/physiology ; *DNA, Environmental/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; },
abstract = {Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.},
}
@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&amp;D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}
@article {pmid41248761,
year = {2025},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhanced anaerobic digestion performance of food waste by Fe-Mn MOF-derived carbon composite: Methane production, microbial response, and intrinsic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133667},
doi = {10.1016/j.biortech.2025.133667},
pmid = {41248761},
issn = {1873-2976},
abstract = {This study investigated the effects of Fe-Mn MOF-derived carbon composite (Fe-Mn MDC) on anaerobic digestion (AD) performance of food waste (FW) and elucidated the underlying mechanisms. The methane yield increased to 457.44 ± 14.21 mL/g VS under 0.05 g/g TS Fe-Mn MDC addition, representing a 36.47 % increase compared to the control group. Metagenomics analysis indicated that Fe-Mn MDC altered the microbial community structure, enriched the abundance and mutualism of exoelectrogenic bacteria (Geobacter) and electroactive methanogenic microorganisms (Methanothrix) involved in direct interspecies electron transfer. The metabolic activity of hydrogenotrophic methanogens was enhanced under Fe-Mn MDC addition, and the content of dehydrogenase and coenzyme F420 was also stimulated, thereby accelerating substrate consumption and methane production. The physicochemical characterization results of Fe-Mn MDC demonstrated that it could act as an electron shuttle and facilitate proton transfer. Besides, AD system exhibited not only an increase in e-pili and c-type genes abundance, but also an enhanced representation of gene modules linked to the biosynthesis of V/A-type ATPases (M00159) and F-type (M00157), which further indicated that Fe-Mn MDC enhanced the proton-coupled electron transfer in AD system. These results provided potential applications in FW management and new insights into the mechanism of renewable energy recovery from AD.},
}
@article {pmid41248576,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127958},
doi = {10.1016/j.jenvman.2025.127958},
pmid = {41248576},
issn = {1095-8630},
abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.},
}
@article {pmid41249156,
year = {2025},
author = {Liu, L and Wang, Z and Zhang, W and Lin, W},
title = {Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1795},
pmid = {41249156},
issn = {2052-4463},
support = {T2225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Genome, Viral ; Desert Climate ; *Soil Microbiology ; *Mars ; *Genome, Microbial ; Metagenome ; Metagenomics ; Tibet ; },
abstract = {The Qaidam Basin on the northern Tibetan Plateau represents a terrestrial Mars-analog desert characterized by hyperaridity, low temperatures, intense ultraviolet radiation, and high-salinity soils. To unveil the largely unexplored genomic diversity of microbes and viruses in this extreme environment, we collected 58 soil samples from various landforms and depths for metagenomic sequencing and analysis. We reconstructed 1,773 microbial metagenome-assembled genomes (mMAGs) and 2,060 viral MAGs (vMAGs), the vast majority (>94%) of which represent novel taxa. Among these, 327 mMAGs (completeness ≥ 90% and contamination ≤ 5%) and 325 vMAGs (completeness ≥ 90%) were classified as high-quality genomes. Taxonomic classification revealed that the bacterial, archaeal, and viral phyla with the largest numbers of genomes were Actinomycetota (n = 565), Halobacteriota (n = 111), and Uroviricota (n = 836), respectively. This metagenomic and genomic dataset provides valuable reference data for advancing our understanding of the diversity and function of microbial and viral communities across global desert ecosystems. Furthermore, these data offer astrobiological insights for research on life in Mars-analog extreme environments.},
}
@article {pmid41248707,
year = {2025},
author = {Mizuno, S and Horiba, K and Nakahashi, T and Atsumi, Y and Takahara, T and Hashino, M and Ito, Y and Kamimura, K},
title = {A 1-year-old boy presenting with roseola accompanied by bilateral eyelid oedema and acute infectious mononucleosis syndrome caused by human herpesuvirus-6B: a case report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108213},
doi = {10.1016/j.ijid.2025.108213},
pmid = {41248707},
issn = {1878-3511},
abstract = {Bilateral eyelid oedema, also known as Hoagland sign, is a specific physical sign of infectious mononucleosis (IM) syndrome caused by Epstein-Barr virus (EBV) infection in older children and adolescents. IM syndrome, which is mainly caused by EBV or cytomegalovirus infection, has milder symptoms in young children than in older children and adolescents. The human herpesvirus 6B (HHV-6B) causes roseola infantum (sixth disease) and various complications in children younger than 2 years; however, bilateral eyelid oedema and IM syndrome are rarely reported. We report the case of a 1-year-old boy with bilateral upper eyelid oedema and severe IM syndrome, including pancytopenia with an increased atypical lymphocyte count, purpura due to thrombocytopenia, and elevated liver enzyme and ferritin levels. Metagenomic next-generation sequencing indicated active HHV-6B infection. The patient improved within 1 week without any specific treatment. Our experience with this case suggests that the presentations observed should be considered rare complications of HHV-6B infection.},
}
@article {pmid41247052,
year = {2025},
author = {Huang, X and Zeng, J and Yang, F and Liu, Y and Chen, J and Wang, H and Li, S and Li, C and Zhang, S},
title = {Microbial succession in human tissues postmortem: insights from 2bRAD-M sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266624},
doi = {10.1128/spectrum.02666-24},
pmid = {41247052},
issn = {2165-0497},
abstract = {Microbial communities play a crucial role in decomposition, yet their patterns in human tissues remain underexplored. Most previous research has often focused on animal models such as mice and swine, with limited studies on human samples, primarily targeting specific environments like the gut and skin. Consequently, gaps persist in understanding postmortem microbial dynamics within internal human organs. The 2bRAD-M sequencing technology offers a powerful approach for human thanatomicrobiome research, overcoming key limitations of 16S rRNA and metagenomic sequencing methods. In this study, we used 2bRAD-M to profile microbial succession across seven human tissues-heart, liver, spleen, lung, kidney, calf muscle, and gut-at various postmortem intervals (PMIs). Significant variations in microbial community composition were observed across organs and decomposition stages, with Proteobacteria dominating early and Firmicutes later. A comparison of frozen and unfrozen cadavers (PMI 1-7 days) revealed divergent microbial shifts in the liver and spleen, while other tissues exhibited limited variation. These findings highlight complex, organ-specific microbial trajectories and suggest that microbial signatures could serve as biomarkers for PMI estimation. This research deepens our understanding of the microbial succession within internal human organs postmortem and contributes to elucidating the identity and role of microorganisms in human decomposition.IMPORTANCEHumans host a diverse array of microbial communities that play a crucial role in the decomposition process after death. Understanding these postmortem microbial dynamics is essential, as they offer valuable insights into the progression of decomposition with significant implications for forensic science. The role of microorganisms in corpse decomposition has gained increasing attention in both forensic and ecological research, but studies in this area remain in their early stages, requiring further in-depth exploration. This work pioneers the use of 2bRAD-M sequencing to investigate microbial changes across various human organs over increasing postmortem intervals. By enhancing knowledge of postmortem microbiota dynamics, the study contributes to refining and improving the accuracy of forensic methodologies.},
}
@article {pmid41247049,
year = {2025},
author = {Ma, J and Yu, L and Zhao, K and Qiao, Q and Zhu, X and Wu, T and Rong, H and Ning, S and Guo, J and Ding, Y and Chi, Y and Cui, L and Ge, Y},
title = {A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0290825},
doi = {10.1128/spectrum.02908-25},
pmid = {41247049},
issn = {2165-0497},
abstract = {UNLABELLED: Emerging respiratory infectious diseases represented by COVID-19, along with traditional respiratory infections, pose a serious threat to human health. High-throughput sequencing (NGS), with its high sensitivity and ultra-high throughput, is particularly suitable for the detection of respiratory pathogens (RP) that are extremely diverse in types and frequently involved in mixed infections. In this study, by integrating a Micro-Targets Hybrid Capture (MT-Capture) system, we developed previously with NGS, we developed a novel assay (termed RP-MT-Capture NGS) for the detection of multiple respiratory pathogens (more than 300 species/types). By optimizing probe design and hybridization capture procedures, RP-MT-Capture NGS achieved high detection sensitivity for different types of pathogens. For influenza viruses, this assay could acquire full-length sequences of hemagglutinin (HA) and neuraminidase (NA) genes for samples with CT values < 32, offering a robust tool for viral mutation surveillance and recombination analysis. The results of clinical sample detection showed that RP-MT-Capture NGS exhibited superior accuracy and sensitivity compared to TaqMan array and metagenomic NGS (mNGS) technologies for respiratory pathogen detection. Compared with traditional probe hybridization-based targeted NGS (tNGS), RP-MT-Capture NGS significantly shortens the wet lab experiment time to within 6 h. In summary, the RP-MT-Capture NGS assay developed in this study offers a novel tool for detecting multiple respiratory pathogens, with substantial clinical and public health relevance.<br><br>IMPORTANCE: Emerging and traditional respiratory infections pose threats to human health. These diseases are caused by a variety of pathogens, which often lead to co-infections and, thus, make detection difficult. This study combines a novel probe hybridization capture system with high-throughput sequencing to develop a new detection tool (RP-MT-Capture NGS), which can identify over 300 types of respiratory pathogens. For influenza viruses, it can reveal complete details of key viral genes, facilitating the tracking of viral mutations. Compared with existing detection methods, this new tool is more accurate, more sensitive, and has a higher throughput. It provides great value for clinical practice and public health in respiratory pathogen detection.},
}
@article {pmid41246284,
year = {2025},
author = {Yang, C and Lv, M and Li, Y and He, Y and Zhang, S and Zhang, G and Lan, J and Guo, Z and Cheng, Y and Yang, Y and Sun, J and Ma, L and Zhang, L},
title = {The interactions between psychological stress, gut microbiota, and fecal metabolites: A longitudinal multi-omics study in Chinese adolescents.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100498},
doi = {10.1016/j.crmicr.2025.100498},
pmid = {41246284},
issn = {2666-5174},
abstract = {OBJECTIVES: This study investigated the bidirectional associations between psychological stress, gut microbiota, and fecal metabolites in a cohort of Chinese adolescents using a multi-omics approach.<br><br>METHODS: Baseline fecal samples from 124 adolescents were subjected to 16S rRNA gene amplicon sequencing, with 51 participants providing samples for metagenomic sequencing and untargeted metabolomics at baseline and follow-up. Psychological stress was assessed via the Adolescent Self-Rating Life Events Checklist.<br><br>RESULTS: After covariates adjustment, baseline total stress was associated with depleted alpha- and beta-diversity and abundances of the genera Lachnospiraceae NK4A136 group and unclassified Muribaculaceae.In longitudinal analyses, with the same covariates, baseline total stress was associated with six follow-up microbial species (Pfdr < 0.1; Actinomyces spp. HMSC035G02, Actinomyces sp. ICM58, Actinomyces sp. oral taxon 172, Schaalia odontolytica, Blautia sp. AF17-9LB, and Blautia sp. AM47-4) and 83 metabolites, predominantly lipids. These metabolites were primarily enriched in Kyoto Encyclopedia of Genes and Genomes pathways of lipid metabolism. Schaalia odontolytica, Actinomyces sp. ICM58, and Actinomyces spp. HMSC035G02 mediated associations between the total stress score and five lipids, with Schaalia odontolytica demonstrating the strongest effect (26.3 % mediated). Seven baseline metabolites but no microbial species were predictive of follow-up total stress. These metabolites exhibited an area under the curve of 0.72 for differentiating adolescents with high versus low stress, with 5-oxo-eicosatetraenoic acid being the strongest predictor.<br><br>CONCLUSIONS: This study suggests that psychological stress is associated with specific gut microbes and lipid metabolites change, and in turn, specific metabolites contribute to psychological stress change. These findings provide insights into bidirectional interactions between psychological stress and gut microbiota in adolescents.},
}
@article {pmid41246108,
year = {2025},
author = {Benghanem, S and Pérot, P and Rodriguez, C and Fourgeaud, J and Bouguerra, M and Mathon, B and Seilhean, DD and Bielle, F and Plu, I and Jamet, A and Weiss, N and Marois, C and Rohaut, B and Eloit, M and Demeret, S},
title = {Diagnostic Yield of Next-Generation Sequencing in CSF or Brain Biopsy for Severe Encephalitis Requiring Intensive Care.},
journal = {Neurology. Clinical practice},
volume = {15},
number = {6},
pages = {e200558},
doi = {10.1212/CPJ.0000000000200558},
pmid = {41246108},
issn = {2163-0402},
abstract = {OBJECTIVES: The aim of this study was to evaluate the contribution of metagenomic next-generation sequencing (mNGS) in critically ill patients with encephalitis of unknown etiology.<br><br>METHODS: This retrospective study (2016-2023) was conducted in a tertiary care referral neuro-ICU at La Piti&#xe9;-Salp&#xea;tri&#xe8;re Hospital (Paris, France). The inclusion criteria were encephalitis with unknown etiology and mNGS performed on CSF, brain biopsy, and/or autopsy. We assessed the yield of mNGS and whether specific treatments were initiated. Neurologic outcome at 1 year was assessed using the Glasgow Outcome Scale-Extended (GOSE-1: death; GOSE-8: upper good recovery).<br><br>RESULTS: A total of 49 patients were included, of whom 44.9% were immunosuppressed. At 1 year, 38.8% had a GOSE score 4-8 and 47.7% died. mNGS was performed on the CSF of 40 of 49 patients (81.6%) and on brain biopsy of 19 of 49 patients (38.8%), including 12 patients who underwent both CSF and biopsy testing. Among the 40 mNGS analyses performed on the CSF, 7 (17.5%) yielded positive results but only 1 (2.5%) was likely causative. Conversely, 7 of 19 mNGS analyses (36.8%) on biopsies were positive and causative. Regarding the yield of mNGS in the entire cohort, 15 of 49 patients (30.6%) had a positive result but only 7 of 49 (14.3%) were causative (dengue virus, measles virus, rubella virus, Nocardia spp, HHV6, astrovirus, and orthobunyavirus), all from brain biopsies of immunocompromised patients. Conversely, 8 of 49 mNGS analyses (16.3%) were noncausative (polyomavirus, HHV8, HHV7, EBV, 2 pegiviruses, and 2 rhinoviruses). Specific treatments were initiated in 4 of 7 patients (57%). Among the 34 patients with a negative mNGS result, 5 (14.7%) were diagnosed with infectious encephalitis using conventional methods.<br><br>CONCLUSION: In critically ill patients with encephalitis of unknown etiology, mNGS performed on brain biopsy could reduce diagnostic uncertainty.},
}
@article {pmid41245671,
year = {2025},
author = {Orbea, M and Fortini, M and Amerson-Brown, MH and Palazzi, DL and Dunn, JJ},
title = {Mycetohabitans rhizoxinica bacteremia in the setting of invasive fungal disease in an immunocompromised patient.},
journal = {ASM case reports},
volume = {1},
number = {4},
pages = {},
doi = {10.1128/asmcr.00014-24},
pmid = {41245671},
issn = {2996-2684},
abstract = {BACKGROUND: Mycetohabitans [Burkholderia] rhizoxinica is an endosymbiotic bacteria of Rhizopus microsporus that normally causes rice seedling blight. In our case report, we present one of the first known cases of concomitant bacteremia with M. rhizoxinica and invasive mold infection due to Rhizopus spp. in an immunocompromised child.<br><br>CASE SUMMARY: A 3 year old male recently diagnosed with B-cell acute lymphoblastic leukemia developed febrile neutropenia. His workup was significant for invasive fungal sinusitis due to Exserohilum spp. based on histopathology and culture, a right middle lobe infiltrate, and a blood culture positive for gram-negative coccobacilli, later identified as M. rhizoxinica. Additionally, metagenomics next-generation sequencing was positive for R. microsporus as was broad-range fungal PCR testing of a lung biopsy sample. His surgical treatments included sinus debridement and a near total right pneumonectomy, and his antimicrobial treatment included 10 days of cefepime for his bacteremia, 4 weeks of liposomal amphotericin B, 4 weeks of micafungin following his pneumonectomy, and approximately 12 months of posaconazole.<br><br>CONCLUSION: This case highlights the association of M. rhizoxinica with Rhizopus spp., wherein the isolation of M. rhizoxinica led to a high index of suspicion of Rhizopus infection in an immunocompromised patient who developed bacteremia with a slow-growing, oxidase positive, gram-negative bacteria not able to be identified by traditional identification methods.},
}
@article {pmid41245635,
year = {2025},
author = {Wongwattanarat, S and Schorn, A and Klose, L and Carré, C and Malvis Romero, A and Liese, A and Pérez-García, P and Streit, WR},
title = {A combined chemo-enzymatic treatment for the oxidation of epoxy-based carbon fiber-reinforced polymers (CFRPs).},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1670548},
doi = {10.3389/fbioe.2025.1670548},
pmid = {41245635},
issn = {2296-4185},
abstract = {Carbon fiber-reinforced polymers (CFRPs), particularly epoxy-based composites, have become essential in the aerospace, automotive, and wind energy industries due to their robust mechanical properties, and lightweight nature. However, there is a lack of recycling technologies that are environmentally sustainable while also ensuring the recovery of carbon fibers in their original state. Although certain bacterial and fungal strains can colonize epoxy polymers, enzymes capable of efficiently degrading these materials have not yet been reported. Consequently, there is an urgent need for an effective, sustainable, and biologically inspired solution for CFRP recycling. Here, a chemo-enzymatic two-step oxidation process was developed. A chemical pre-treatment with propionic acid and hydrogen peroxide was used to recover imbedded carbon fibers. Additionally, three novel bacterial laccases isolated from a European spruce bark beetle gut metagenome (Ips typographus) demonstrated the ability to oxidize three epoxy resin scaffolds derived from TGMDA-based epoxy resin system, a high-performance material commonly used in aerospace applications. The sequential combination of both oxidative steps enabled the retrieval of clean carbon fibers and showed the potential of the laccase to partially further modify the pre-treated cured epoxy. This bio-inspired approach marks an initial step toward developing a bio-based recycling method for epoxy CFRPs.},
}
@article {pmid41245257,
year = {2025},
author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J},
title = {Correction: Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1706582},
doi = {10.3389/fcimb.2025.1706582},
pmid = {41245257},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1649384.].},
}
@article {pmid41244979,
year = {2025},
author = {Ladines-Lim, JB and Yang, WT and Tebas, P and O'Donnell, J and Koenig, H and Kreider, E and Dyer, K and Anwar, M and Rodriguez, E and Patel, S and Rodino, K and Glaser, L and Richterman, A},
title = {Delayed diagnosis of disseminated Mycobacterium intracellulare subsp. chimaera infective endocarditis via cell-free metagenomic next-generation sequencing: a case report.},
journal = {ASM case reports},
volume = {1},
number = {5},
pages = {},
doi = {10.1128/asmcr.00003-25},
pmid = {41244979},
issn = {2996-2684},
abstract = {BACKGROUND: Mycobacterium intracellulare subsp. chimaera infective endocarditis associated with contaminated heater-cooler units has been well documented, leading to the discontinuation of these devices in most hospitals by 2018. The rarity of this infection and its nonspecific symptoms often result in delayed diagnosis.<br><br>CASE SUMMARY: We describe a 56-year-old female diagnosed with M. intracellulare subsp. chimaera infective endocarditis with disseminated intracranial abscess 7 years after aortic and mitral valve replacement. Diagnosis was achieved using cell-free microbial DNA next-generation sequencing (cfmNGS). She underwent left temporal craniotomy for abscess drainage and aortic and mitral valve replacement. Diagnosis was confirmed via mycobacterial culture from blood, brain tissue, and explanted valve tissue. Treatment included rifabutin, ethambutol, azithromycin, and amikacin, alongside a prednisone taper prescribed for a previously diagnosed undifferentiated inflammatory process. Amikacin was discontinued 6 weeks after valve surgery because of unilateral hearing loss. She remained clinically stable 5 months after valve surgery.<br><br>CONCLUSION: This case highlights that M. intracellulare subsp. chimaera infections may continue to emerge years after heater-cool unit discontinuation, suggesting that the time window for case incidence may still be active. cfmNGS may serve as a valuable diagnostic tool for disseminated M. intracellulare subsp. chimaera. Finally, we discuss pharmacotherapeutic factors, including the need for multiple agents over long durations, in this case with specific considerations given to the dissemination of infection into the central nervous system and potential drug-drug interactions, including steroids.},
}
@article {pmid41244776,
year = {2025},
author = {Tan, J and Liu, L and Wang, L and Qu, Y and Sun, Z and Wang, Q and Liu, Y},
title = {Case Report: First pulmonary infection caused by Mycobacterium colombiense in a non-immunosuppressed host with bronchiectasis: diagnosis facilitated by synergistic mNGS and culture.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1671968},
doi = {10.3389/fmed.2025.1671968},
pmid = {41244776},
issn = {2296-858X},
abstract = {Mycobacterium colombiense, a rare slow-growing mycobacterium within the Mycobacterium avium complex (MAC), causes disseminated disease almost exclusively in immunocompromised hosts, with no prior reports of localized pulmonary infection in non-immunosuppressed individuals. A 47-year-old non-immunosuppressed male with bronchiectasis presented with progressive cough, night sweats, and fatigue. Computed tomography (CT) revealed bronchiectasis with nodules in the right middle and lower lobes. Empirical β-lactam therapy failed, and conventional bronchoalveolar lavage fluid (BALF) tests (smears, cultures, PCR) yielded no pathogens at 48 h. Although metagenomic next-generation sequencing (mNGS) of BALF detected a low number of M. colombiense sequences (eight reads), definitive confirmation was achieved through extended culture, which is considered the gold standard for the diagnosis of nontuberculous mycobacteria. This culture revealed acid-fast bacilli within 12 days (160 CFU), confirming the presence of viable M. colombiense. Subsequent mNGS of the isolated colonies further confirmed the species identity with high sequence reads (25,787 reads). Guideline-based triple therapy (guided by drug susceptibility testing and guidelines) with clarithromycin, rifampicin, and ethambutol achieved significant radiographic resolution at 24 weeks. This case demonstrates that M. colombiense pulmonary infection is diagnostically elusive and mimics non-specific respiratory syndromes. It defines the clinical features of this pathogen in non-immunosuppressed hosts and highlights the need for heightened surveillance for nontuberculous mycobacteria (NTM) in bronchiectasis patients, given the likelihood of underdiagnosis.},
}
@article {pmid41244772,
year = {2025},
author = {Li, Q and Song, XC and Li, K and Wang, J},
title = {Gut-lung immunometabolic crosstalk in sepsis: from microbiota to respiratory failure.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1685044},
doi = {10.3389/fmed.2025.1685044},
pmid = {41244772},
issn = {2296-858X},
abstract = {Sepsis is a systemic immune-metabolic disorder syndrome caused by infection, in which gut microbiota dysbiosis plays a central role in the occurrence and development of multi-organ dysfunction. This paper systematically elaborates on the bidirectional regulatory mechanism of the "gut-lung axis" in sepsis. Gut microbiota dysregulation damages the gut barrier function, reduces the production of short-chain fatty acids (SCFAs), and increases endotoxin translocation. Subsequently, it activates alveolar macrophage polarization, promotes the formation of neutrophil extracellular traps (NETs), and leads to an imbalance in the Treg/Th17 cell ratio, ultimately exacerbating the pathological process of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). Conversely, the pulmonary inflammatory response can also aggravate gut barrier damage through circulating inflammatory mediators, forming a vicious cycle. Mechanistically, HIF-1α, mTOR, and Sirtuins do not act in isolation. Instead, they jointly regulate the metabolic fate of immune cells through spatiotemporally dynamic interactions. During the evolution of sepsis, these signals exhibit opposite regulatory polarities during the hyper-inflammatory phase and the immunosuppressive phase, and mitochondrial dysfunction and oxidative stress further amplify the inflammatory cascade reaction. Preclinical research evidence shows that microbiota-based intervention measures (including probiotic preparations, fecal microbiota transplantation, and SCFA supplementation) and vagus nerve electrical stimulation can effectively alleviate sepsis-related lung injury and improve prognosis, but there is significant individual heterogeneity in their therapeutic effects. Future research should not be restricted to descriptive associations. Instead, it is essential to conduct in-depth analyses of the specific logic of the aforementioned signaling networks in terms of cell types, subcellular compartments, and disease course timings, and clarify their context-dependent controversies to promote the transformation of mechanistic understanding into precision treatment. Meanwhile, research efforts should focus on constructing a multi-omics dynamic biomarker system integrating metagenomics, metabolomics, and immunophenotyping analysis and designing clinical trials through precise patient stratification to facilitate the clinical translation of individualized treatment strategies based on gut-lung axis regulation.},
}
@article {pmid41244681,
year = {2025},
author = {Ru, J and Jiang, Z and Li, J and Li, X and Su, Z and Li, T and Xu, M},
title = {Screening of microbial consortium with high efficiency of lignin-degrading and its synergistic metabolic mechanism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1709019},
doi = {10.3389/fmicb.2025.1709019},
pmid = {41244681},
issn = {1664-302X},
abstract = {INTRODUCTION: Lignin is difficult to degrade, which makes its high-value utilization a challenge. So finding an efficient method to degrade lignin is very important. At present, microbial degradation is considered to be one of the most effective and environmentally friendly degradation methods that is widely accepted.<br><br>METHODS: This study enriched three lignin-degrading microbial consortia R0, R1 and R2 using alkali lignin as the sole carbon source under 15&#x202f;&#xb0;C conditions. Using the methods of 16S rRNA sequencing, metagenomics, and metabolomics, the degradation mechanism of these three microbial consortia were systematically analyzed.<br><br>RESULTS: The microbial consortium R0, which has the best degradation efficiency, can degrade more than 80% within 6&#x202f;days, with dominant genera being Achromobacter and Pseudomonas. The dominant genera in other two microbial consortia R1 and R2 are Pseudomonas and Achromobacter in R1, Pseudomonas and Sphingobacterium in R2. Protocatechuic acid is a central intermediate in the degradation of lignin, its degradation pathway was fully annotated in microbial consortia R0 and R1. Microbial consortium R0 has the most abundant of AA (Auxiliary Activities) family genes annotated as carbohydrate annotation enzymes. The dominant genera in the microbial consortium R0 based on AA family gene abundance were Pseudomonas and Achromobacter.<br><br>DISCUSSION: Our results indicated that Pseudomonas is the dominant genus in lignin degradation, the metabolic potential of other abundant genera suggests a possible complementary role in the lignin degradation process. In the lignin degradation system with Pseudomonas as the dominant genera, the degradation of protocatechuic acid is the core of the degradation process. This study could enrich the mechanism of efficient and stable lignin degradation by microbial consortium, and could provide theoretical guidance for the development of lignin biodegradation technology in industry.},
}
@article {pmid41244617,
year = {2025},
author = {Ma, ZS},
title = {Microbial Biomarkers of Breast Tumor and Mastitis: Deciphering the Delicate Balance between Potentially "Evil" and "Benign" Alliances in Mammary Microbiomes.},
journal = {Breast care (Basel, Switzerland)},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548037},
pmid = {41244617},
issn = {1661-3791},
abstract = {INTRODUCTION: Breast cancer and mastitis significantly impact women's health and their infants' wellbeing. The advent of metagenomic sequencing technology has opened new avenues to explore the relationships between mammary microbiomes and these diseases. Despite recent extensive studies, detailed understanding of the mammary microbiome-disease relationships remains incomplete.<br><br>METHODS AND RESULTS: Here, we apply the Specificity and Specificity Diversity framework (Ma 2024, BMC Biology) to identify unique/enriched species (US/ES) associated with mastitis, breast cancer, or their healthy controls. The US/ES lists contain potential biomarkers and offer fresh insights into the intricacies of mastitis etiology and the relationship between breast tissue microbiomes and breast cancer.<br><br>CONCLUSIONS: (i) The dynamic balance between coexisting alliances of beneficial microbes and harmful microbes (including opportunistic pathogens) holds key to understanding mastitis etiology. (ii) Intra-tumor microbes may serve multiple roles - as oncogenic microbes, neutral bystanders, or tumor suppressors, and their dynamic balance can influence breast cancer onset and progression. (iii) Significant challenges remain in developing effective probiotics, prebiotics and infant formulas due to complex entanglements between beneficial and harmful microbes. This complexity suggests that broad-spectrum or one-size-fits-all probiotic approaches may prove inadequate, pointing instead to the need for personalized prebiotic/probiotic/infant-formula solutions to restore and maintain healthy mammary microbiomes.},
}
@article {pmid41244590,
year = {2025},
author = {An, Z and Cha, JH and Lee, KH and Lee, I},
title = {Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113772},
doi = {10.1016/j.isci.2025.113772},
pmid = {41244590},
issn = {2589-0042},
abstract = {Whole genome sequencing (WGS) offers advantages over DNA chip-based genotyping, typically using blood-derived DNA. However, saliva and buccal samples-popular in direct-to-consumer tests-suffer reduced accuracy because of oral bacterial contamination. Decontamination strategies using decoy bacterial genomes yielded limited improvements, likely because they cover only a subset of oral bacteria with available isolate genomes. To overcome this, we developed a decontamination pipeline leveraging metagenome-assembled genomes (MAGs). Concordance analysis of variant calling between blood and matched oral samples confirmed the superiority of MAG-augmented decontamination over conventional methods relying mainly on isolate genomes. Although the underlying mechanism remains unclear, it particularly improves variant calls in GC-rich regions, recovering many likely pathogenic variants. Additionally, we demonstrate that certain bacterial genomic regions mimic human regions with clinically relevant variants, potentially confounding genotyping. These results highlight the need for MAG-based bacterial read decontamination to achieve accurate personal genotyping from non-invasive, self-collected oral samples.},
}
@article {pmid41244294,
year = {2025},
author = {Fuller, R and Petersen, BE and Hussein, S and Salib, C and Duffield, A and Gaglia, R and Gabrilove, JL and Hernández, C and Ramirez, JD and Jacobs, SE and Paniz-Mondolfi, A},
title = {Expedited diagnosis of disseminated Mycobacterium kansasii infection using targeted (amplicon-based) next-generation sequencing in an immunocompromised patient.},
journal = {ASM case reports},
volume = {1},
number = {6},
pages = {},
doi = {10.1128/asmcr.00110-24},
pmid = {41244294},
issn = {2996-2684},
abstract = {BACKGROUND: Mycobacterium kansasii is typically associated with pulmonary disease and is an uncommon cause of disseminated infection and thus can be challenging to diagnose and treat.<br><br>CASE SUMMARY: We present a 59-year-old female with a history of renal cell carcinoma (RCC) and T-cell large granular lymphocytic leukemia (T-LGLL) who developed disseminated Mycobacterium kansasii infection. Targeted next-generation sequencing (tNGS) facilitated the rapid detection of M. kansasii from formalin-fixed, paraffin-embedded (FFPE) tissue, aiding in clinical decision-making prior to culture confirmation.<br><br>CONCLUSION: The case highlights the diagnostic challenges posed by overlapping clinical features and chronic granulomatous inflammation in immunocompromised patients, as well as the utility of amplicon-based sequencing in expediting diagnostic turnaround and guiding therapeutic interventions.},
}
@article {pmid41244270,
year = {2025},
author = {Rabinowitz, PM and Walia, R and Pottinger, P and Lieberman, JA},
title = {Tropheryma whipplei native valve endocarditis diagnosed by sequencing of microbial cell-free DNA in plasma.},
journal = {ASM case reports},
volume = {1},
number = {6},
pages = {},
doi = {10.1128/asmcr.00070-25},
pmid = {41244270},
issn = {2996-2684},
abstract = {BACKGROUND: Endocarditis is an important manifestation of extra-intestinal Whipple's disease. The etiologic agent, the bacterium Tropheryma whipplei, cannot be cultivated in clinical laboratories, making the diagnosis of this culture-negative infection challenging. Molecular methods have emerged as useful adjuncts for the diagnosis of culture-negative endocarditis.<br><br>CASE SUMMARY: A 67-year-old male was seen in an infectious disease clinic for evaluation of a possible infectious etiology of chronic musculoskeletal pain with exercise intolerance. He had a history of an embolic stroke 2 years earlier, echocardiographic evidence of aortic valve thickening, and multiple negative blood cultures. Following an evaluation that included serology and extended incubation blood culture, plasma was sent for metagenomic sequencing of microbial cell-free DNA, which was positive for Tropheryma whipplei.<br><br>CONCLUSION: The patient's musculoskeletal complaints and his exercise intolerance resolved after treatment with ceftriaxone and trimethoprim-sulfamethoxazole. To our knowledge, this is the first report of T. whipplei native valve endocarditis diagnosed by metagenomic sequencing.},
}
@article {pmid41244037,
year = {2025},
author = {Leys, SP and Hentschel, U and Easson, CG and Stimson, D and Lopez, JV and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the fragile freshwater sponge, Eunapius fragilis (Leidy, 1851) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {268},
doi = {10.12688/wellcomeopenres.24165.1},
pmid = {41244037},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Eunapius fragilis (fragile freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence has a total length of 218.91 megabases. Most of the assembly (99.98%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,614 protein-coding genes. Additionally, eight high-quality bacterial metagenomes belonging to the Bacteroidota and Pseudomonadota phyla were assembled.},
}
@article {pmid41243980,
year = {2025},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1083},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; //Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}
@article {pmid41243635,
year = {2025},
author = {Wu, S and Wei, Z and He, Z and Li, M and Zeng, W},
title = {Clinical characteristics of tracheobronchial mucormycosis: a retrospective analysis of twenty cases.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2584286},
doi = {10.1080/07853890.2025.2584286},
pmid = {41243635},
issn = {1365-2060},
mesh = {Humans ; *Mucormycosis/diagnosis/drug therapy ; Middle Aged ; Male ; Female ; Retrospective Studies ; Aged ; *Antifungal Agents/therapeutic use/administration &amp; dosage ; Adult ; Amphotericin B/therapeutic use/administration &amp; dosage ; Bronchoscopy ; Tomography, X-Ray Computed ; *Bronchial Diseases/diagnosis/microbiology/drug therapy ; Immunocompromised Host ; Treatment Outcome ; },
abstract = {BACKGROUND: Tracheobronchial mucormycosis (TM) is a rare and potentially fatal disease commonly occurred in immunocompromised individuals, with death risk from massive hemoptysis or asphyxia.To enhance clinical understanding, we retrospectively analyzed the clinical features, therapeutic regimen, and outcomes of TM patients.<br><br>METHODS: We conducted a comprehensive analysis of hospitalized patients diagnosed with TM between January 1, 2010, and April 30, 2025, systematically collecting and evaluating data on clinical manifestations, treatment strategies, and clinical outcomes.<br><br>RESULTS: Twenty patients were included in this study, with a median age of 56&#x2009;years. Most patients had diabetes mellitus, followed by those with hematological malignancies. Common symptoms included cough, expectoration, hemoptysis, and fever. Chest CT revealed pulmonary infiltrates, bronchial stenosis or occlusion, obstructive pneumonia, and pleural effusion, while bronchoscopy revealed neoplasms, purulent secretions, and bronchial obstruction or stenosis.Metagenomic next-generation sequencing demonstrated a higher positive diagnostic rate and shorter time to diagnosis compared to histopathology and culture. Three patients received intravenous amphotericin B (AmB) monotherapy, eight patients were treated with a combination of intravenous and intratracheal AmB, one patient was treated with intravenous triazole drug alone, two patients received a regimen consisting of intravenous triazole drugs combined with intratracheal AmB, and five patients underwent triple therapy involving both intravenous triazole drugs and concurrent intravenous and intratracheal AmB administration. Additionally, one patient underwent bronchoscopic intervention, and two patients underwent lobectomy. Fourteen patients demonstrated clinical improvement, whereas six died. Massive hemoptysis was the leading cause of mortality.<br><br>CONCLUSIONS: TM is a highly lethal disease that is often underdiagnosed. Bronchoscopy plays an essential role in both diagnosis and management. Systemic antifungal therapy, combined with intratracheal administration of AmB, has shown favorable therapeutic outcomes.},
}
@article {pmid41243436,
year = {2025},
author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A},
title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2576657},
doi = {10.1080/19490976.2025.2576657},
pmid = {41243436},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; },
abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.},
}
@article {pmid41243097,
year = {2025},
author = {Hang, WJ and Yin, R and Kang, XW and He, L and Cao, X and Chen, J},
title = {Berberine ameliorates high-fat diet-induced metabolic disorders through promoting gut Akkermansia and modulating bile acid metabolism.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {190},
pmid = {41243097},
issn = {1749-8546},
support = {82100402//National Natural Science Foundation of China/ ; 82370837//National Natural Science Foundation of China/ ; 2022CFB201//Bureau of Science and Technology of Hubei Province/ ; 2022YFE0209900//National Key Research and Development Program of China/ ; WZ21A02//Wuhan Municipal Health Commission's Scientific Research/ ; },
abstract = {BACKGROUND: Coptidis Rhizoma, the rhizome of Coptis chinensis Franch., has long been employed in the treatment of diabetes. Its active component, berberine, has been utilized in clinical practice; however, the underlying mechanisms of its protective effects remain to be fully elucidated.<br><br>METHODS: Metabolomics and lipidomics analyzed plasma metabolite and lipid changes in mice fed a high-fat diet and treated with 25&#xa0;mg/kg/day berberine for three months. Metagenomics and microbiota transplantation identified gut microbiota responding to berberine. Co-administration of berberine and Akkermansia was studied for metabolic effects, analyzing plasma and fecal metabolomics.<br><br>RESULTS: Berberine reduced triglycerides and cholesterol, showing metabolic protective effects. Metagenomics identified Akkermansia as key to berberine's benefits, validated by microbiota transplantation. Berberine enhanced Akkermansia growth, preserving intestinal mucus and tight junctions. It promotes the conversion of cholesterol to bile acids by inhibiting adenosine 5 '-monophosphate -activated protein kinase (AMPK), which promotes the expression of cholesterol 7-alpha hydroxylase (CYP7A1). Co-administration of berberine and Akkermansia amplified these effects. Potential metabolites, including linoleic acid and N-acetylputrescine, contributed to the observed benefits.<br><br>CONCLUSION: Berberine, through Akkermansia, maintains intestinal integrity and reduces cholesterol, highlighting its potential as a therapeutic agent for metabolic disorders. Combining berberine with Akkermansia enhances its efficacy against hyperlipidemia.},
}
@article {pmid41243094,
year = {2025},
author = {Andreani-Gerard, CM and Jiménez, NE and Palma, R and Muller, C and Hamon-Giraud, P and Le Cunff, Y and Cambiazo, V and González, M and Siegel, A and Frioux, C and Maass, A},
title = {Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {142},
pmid = {41243094},
issn = {2524-6372},
support = {Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.<br><br>RESULTS: We propose a computational framework for the simulation of the metabolic potential of microbiomes,&#xa0;as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and&#xa0;species from six contrasting soil samples across the Talabre Lej&#xed;a transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for&#xa0;sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or&#xa0;sensitive to environmental shifts, through putative cooperation events.<br><br>CONCLUSION: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.},
}
@article {pmid41243090,
year = {2025},
author = {Liu, Z and Xiao, L and Tang, X and He, Y and Nan, X and Wang, H and Guo, Y and Xiong, B},
title = {Salvianolic acid C inhibits methane emissions in dairy cows by targeting MCR and reshaping the rumen microbial community.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {151},
pmid = {41243090},
issn = {1674-9782},
support = {2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; 2024-YWF-ZYSQ-10//State Key Laboratory for Diagnosis and Treatment of Infectious Diseases/ ; },
abstract = {BACKGROUND: Methane (CH4) emissions from ruminants significantly contribute to greenhouse gas effects and energy loss in livestock production. Methyl-coenzyme M reductase (MCR) is the key enzyme in methanogenesis, making it a promising target for CH4 mitigation. This study aimed to identify and validate plant-derived inhibitors by using molecular docking to screen compounds with strong binding affinity to the F430 active site of MCR and assessing their efficacy in reducing CH4 emissions.<br><br>RESULTS: Molecular docking analysis identified salvianolic acid C (SAC) as a potent inhibitor of MCR, showing a strong binding affinity to the F430 active site (binding energy:&#x2009;-8.2&#xa0;kcal/mol). Enzymatic inhibition assays confirmed its inhibitory effect, with a half-maximal inhibitory concentration (IC50) of 692.3&#xa0;&#xb5;mol/L. In vitro rumen fermentation experiments demonstrated that SAC supplementation (1.5&#xa0;mg/g DM) significantly reduced CH4 production (P&#x2009;<&#x2009;0.01) without negatively affecting major fermentation parameters. Microbial community analysis using 16S rRNA sequencing and metagenomics revealed that SAC selectively altered the rumen microbiota, increasing the relative abundance of Bacteroidota while significantly reducing Methanobrevibacter (P&#x2009;=&#x2009;0.04). Moreover, metagenomic analysis showed the downregulation of key methanogenesis-related genes (mcrA&#xa0;and rnfC), suggesting a dual mechanism involving direct enzymatic inhibition and microbial community modulation.<br><br>CONCLUSIONS: These findings indicate that SAC effectively reduces CH4 production by inhibiting MCR activity and reshaping the rumen microbial community. As a plant-derived compound with strong inhibitory effects on methanogenesis, SAC presents a promising and sustainable alternative to synthetic CH4 inhibitors, offering potential applications for mitigating CH4 emissions in livestock production.},
}
@article {pmid41242690,
year = {2025},
author = {Li, X and Pan, L and Li, Z and Li, Y and Yang, L and Ye, X and Wubuli, A and Ye, Q and Yang, F and Yi, H and Maitusong, R and Liang, Y and Cai, Y and Chen, Z},
title = {Etiology and Clinical Characteristics of Pathogen Co-detection in Pediatric Mycoplasma pneumoniae Pneumonia: A Multicenter Retrospective Study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108230},
doi = {10.1016/j.ijid.2025.108230},
pmid = {41242690},
issn = {1878-3511},
abstract = {OBJECTIVES: Co-detection are frequent in pediatric Mycoplasma pneumoniae pneumonia (MPP), yet their full pathogen spectrum and clinical impact remain incompletely characterized. This study aimed to characterize co-detection etiology and clinical impacts of MPP in hospitalized children.<br><br>METHODS: A multicenter retrospective cohort study was conducted among hospitalized children under 14 years with MPP, diagnosed by metagenomic or targeted next-generation sequencing of bronchoalveolar lavage fluid, from June 2023 to July 2024. Multivariate logistic regression models were used to assess differences in clinical characteristics among various Mycoplasma pneumoniae (MP) co-detection patterns.<br><br>RESULTS: Among 570 MPP cases, co-detection occurred in 338 (59.3%) cases: viral-only (29.3%), bacterial-only (30.2%), and viral-bacterial (40.5%). The main bacteria were Streptococcus pneumoniae and Haemophilus influenzae, while human adenovirus and Epstein-Barr virus were the most common viruses. Co-detection rates inversely correlated with age, decreasing from 91.1% in infants to 48.1% in adolescents. Younger age (36-72mo vs 72-168mo, OR: 1.57), non-summer seasons (Spring, OR: 2.44; Autumn, OR: 1.93; Winter, OR: 2.77), and elevated white blood cell count (OR: 1.18) were associated with higher risk of co-detection, whereas higher fibrinogen and pleural effusion reduced risk (all P < 0.01).<br><br>CONCLUSIONS: The high prevalence of co-detection in pediatric MPP, notably viral-bacterial, exhibits distinct age and seasonal patterns essential for informing targeted control strategies. Study limitations include its retrospective design and potential heterogeneity from multicenter differences in NGS methodologies.},
}
@article {pmid41242396,
year = {2025},
author = {Sharma, R and Walia, A and Lakhanpal, D},
title = {Human metapneumovirus: an underdiagnosed public health threat.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105189},
doi = {10.1016/j.idnow.2025.105189},
pmid = {41242396},
issn = {2666-9919},
abstract = {Human metapneumovirus (hMPV), a negative-sense RNA virus in the Pneumoviridae family, has emerged as a major yet under-recognized cause of acute respiratory infections worldwide. Since its identification in 2001, hMPV has shown steady genetic evolution into genotypes A and B, with newer sublineages such as A2.2.1, A2.2.2, and B2 currently detected across continents. A recent global rise in hMPV detections, detailed in reports from China, Europe, and the USA, likely reflects both expanded testing and the re-establishment of seasonal circulation following the COVID-19 pandemic. Co-infections with respiratory viruses, including RSV and influenza, contribute to severe clinical outcomes and hospital burden. Multiplex RT-PCR remains the most sensitive and widely used diagnostic method for detection of hMPV, outperforming conventional PCR approaches, while metagenomic sequencing and CRISPR-based assays are primarily research tools. Diagnostic sensitivity also varies with sample source, and access to advanced technologies remains globally uneven. Despite its growing clinical impact, no approved antiviral is available. Promising candidates, including monoclonal antibodies against the fusion protein, siRNA therapies, and mRNA-based vaccines, are in the early stages of development. This review encompasses recent evidence on hMPV epidemiology, molecular evolution, diagnostic approaches, and therapeutic and vaccine development, underscoring a need for sustained surveillance, equitable diagnostic capacity, and proactive vaccine research more effectively addressing a largely overlooked respiratory pathogen.},
}
@article {pmid41242241,
year = {2025},
author = {Yang, L and Chen, J and Chen, Z and Gao, Y and Su, Y and Zeng, S and He, Q and Qiu, Q},
title = {Integrated metagenomic and metabolomic analyses reveal that nitrogen fertilizer reduction combined with biochar application improves the soil microenvironment of Phoebe bournei seedlings.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127954},
doi = {10.1016/j.jenvman.2025.127954},
pmid = {41242241},
issn = {1095-8630},
abstract = {Biochar has emerged as a globally recognized soil amendment, yet its synergistic effects with nitrogen fertilization on rhizosphere ecosystems remain underexplored. This study employed non-targeted metabolomics and metagenomic analyses to investigate the soil microenvironment of Phoebe bournei seedlings under four treatments: control (CK), optimum nitrogen application (F1), 20 % nitrogen fertilizer reduction with biochar application (F2B1), and 40 % nitrogen fertilizer reduction with biochar application (F3B2). A total of 842 (421 up-/421 down-regulated) and 789 (415 up-/374 down-regulated) differential metabolites were identified in the F2B1 and F3B2 treatments, respectively. Nitrogen fertilizer reduction combined with biochar application significantly reshaped soil metabolomic profiles, with pronounced enrichment in eight key metabolic pathways, including ascorbate and aldarate metabolism pathways and arachidonic acid metabolism pathways. Streptomyces, Pseudomonas, and Afipia exhibited higher relative abundance levels in both F2B1 and F3B2 treatments. Redundancy analysis indicated that soil pH was the dominant influence on the variation of microbial communities. The topological complexity and stability of bacterial co-occurrence networks were significantly improved by F3B2. An upregulation of functional genes involved in soil nitrification (amoAB, hao, and nxrAB) resulted from F3B2. Furthermore, network analysis revealed significant correlations between microbial taxa and differential metabolites, with a preponderance of positive correlations. Our results indicate that nitrogen fertilizer reduction combined with biochar application significantly influences soil microbial metabolism, establishing a theoretical foundation for enhancing soil quality in Phoebe bournei woodlands and for the judicious use of nitrogen fertilizer and biochar in forestry.},
}
@article {pmid41242205,
year = {2025},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}
@article {pmid41241245,
year = {2025},
author = {Li, L and Yu, X and Wang, M and Sun, H and Zhu, J and Wang, X and Chen, S and Hu, S},
title = {Salicylic acid as a pathway inducer for improved bioremediation of oil-polluted saline-alkali soils by chemotactic S. Stutzeri M3.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133647},
doi = {10.1016/j.biortech.2025.133647},
pmid = {41241245},
issn = {1873-2976},
abstract = {The bioremediation would be inhibited by low-efficiency of mass transfer and persistent high-molecular weight polycyclic aromatic hydrocarbons (PAHs). In this study, chemotactic strain named as Stutzerimonas stutzeri M3 and salicylic acid were employed for enhancing biodegradation of petroleum hydrocarbon. The addition of salicylic acid significantly enhanced the activities of alkane hydroxylase and catechol 1,2-dioxygenase, as well as the biodegradation rate of petroleum hydrocarbons. Moreover, the inputs of salicylic acid reshaped microbial community, and obviously affected their cooperative metabolic process by increasing relative abundance of petroleum-degrading bacteria, such as Stutzerimonas, Pontibacillus, Halobacillus and Virgibacillus. Metagenomic analysis furtherly confirmed that overall metabolic pathways of microbial communities and expression of functional genes associated with petroleum degradation (e.g., fad, cat and nah) were enhanced. Furthermore, chemotactic gene expression in strain M3 was significantly increased, thereby facilitating petroleum hydrocarbons degradation. These findings provide a new regulating strategy for effective bioremediation in oil-contaminated sites.},
}
@article {pmid41241073,
year = {2025},
author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W},
title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120709},
doi = {10.1016/j.jad.2025.120709},
pmid = {41241073},
issn = {1573-2517},
abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.<br><br>METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12&#x202f;&#xb1;&#x202f;15.79&#x202f;years, 8 males), while 14 were non-responders (40.14&#x202f;&#xb1;&#x202f;17.28&#x202f;years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).<br><br>RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.<br><br>CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.},
}
@article {pmid41240828,
year = {2025},
author = {Liu, J and Xie, S and Ji, Y and Fan, X and Luo, S and Xu, X and Wang, C and Zhu, L},
title = {Dual suppression of methanogenesis by dichloromethane and salinity: Competitive methyltransferase inhibition and energy-coupling disruption.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140408},
doi = {10.1016/j.jhazmat.2025.140408},
pmid = {41240828},
issn = {1873-3336},
abstract = {The pervasive co-occurrence of dichloromethane (DCM), a prevalent chlorinated solvent, with high salinity in industrial wastewater poses a poorly understood combined ecological stress on anaerobic microbial ecosystems. This study deciphered the molecular mechanisms underlying the dual inhibition of methanogenesis under such combined stress. Metagenomic analysis revealed that methanogens (particularly Methanobacterium and Methanothrix) were more sensitive to DCM and salinity stress, while fermentative bacteria and acetogens exhibited better resilience. Under salinity stress, methanogens primarily expelled extra Na[+] was via the Na[+] pump coupled with methyltransferase (Mtr). However, density functional theory (DFT) calculations demonstrated that DCM competitively bound to the cobamide cofactor in Mtr (ΔG = -10.5 kcal/mol for DCM vs. +14.6 kcal/mol for methylated carrier), thereby impairing sodium extrusion (58 % downregulation in mtrH gene abundance) and subsequent ATP synthesis. Concurrently, elevated Na[+] levels forced a metabolic shift towards energy-intensive sodium extrusion pathways, as evidenced by the upregulation of mrpA (Na[+]/H[+] antiporter, +20 %) and natA/natB (ABC sodium transporters, +162 %). These disruptions culminated in a severe bioenergetic crisis, indicated by decreased coenzyme F420 activity (31.11 ± 1.58 vs. 48.66 ± 2.09 U/L in control) and suppression of methane yield (22.31 ± 3.63 CH4/g COD vs. 178.91 ± 1.28 mL CH4/g COD in control). Our findings uncovered a novel dual inhibition mechanism, combining molecular-level competitive enzyme inhibition with cellular-scale energy uncoupling, providing critical insights into the microbial toxicological effects of co-occurring chlorinated solvents and salinity.},
}
@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
doi = {10.1016/j.psj.2025.106092},
pmid = {41240707},
issn = {1525-3171},
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}
@article {pmid39617895,
year = {2024},
author = {Perrin, AJ and Dorrell, RG},
title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {279},
pmid = {39617895},
issn = {1741-7007},
mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; },
abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.},
}
@article {pmid34286093,
year = {2021},
author = {Cheng, CT and Jeng, ML and Tsai, JF and Li, CL and Wu, LW},
title = {Two mitochondrial genomes of Taiwanese rhinoceros beetles, Oryctes rhinoceros and Eophileurus chinensis (Coleoptera: Scarabaeidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {8},
pages = {2260-2262},
pmid = {34286093},
issn = {2380-2359},
abstract = {Two mitochondrial genomes of the dynastine beetles, Oryctes rhinoceros (Linnaeus, 1758) and Eophileurus chinensis (Faldermann, 1835), were assembled via high-throughput sequencing (HTS). Each of the mitogenomes has 37 genes, showing standard gene order and annotation as the other insects, except for the transfer genes, presenting tQ-tI-tM order. To examine their phylogenetic positions, 118 public mitogenomes of Scarabaeidae were used to infer a ML tree. Overall, our scarabaeid phylogeny reveals clear relationships with high nodal supports, and the two rhinoceros beetles are both grouped with the subfamily Dynastinae. The feeding habit of the two clades seems to represent coprophagous and phytophagous types. However, polyphyletic relationships were observed in the subfamily Melolothinae and in the tribes of Onthophagini and Oniticellini. Further systematic revision is needed.},
}
@article {pmid33898751,
year = {2021},
author = {Jeng, ML and Chen, MY and Wu, LW},
title = {Two complete mitochondrial genomes of Papilio butterflies obtained from historical specimens (Lepidoptera: Papilionidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1341-1343},
pmid = {33898751},
issn = {2380-2359},
abstract = {Museum specimens are collected for education, exhibition, and various multiple scientific purposes. However, millions of specimens remain in their collection boxes for years without being analyzed. Historical specimens have been known to contain low-quality DNA; hence, it is difficult to utilize their sequence information in phylogenetic studies. However, recent advances in high-throughput sequencing (HTS) make these collections amenable to phylogenomic studies. In this study, two historical specimens (Papilio xuthus Linnaeus, 1767, and Papilio thoas Linnaeus, 1771) were sampled and DNA extracted for HTS via the Miseq platform. Two complete mitogenomes were assembled, even though the DNA quality of those specimens was highly fragmented, below 250 bp in length. The 37 genes of 60 mitogenomes were aligned and used for inferring the phylogenetic relationships of Papilioninae. These two newly sequenced mitogenomes are correctly grouped in the genus Papilio, and this result indicates that historical specimens show great potential for phylogenetic studies with HTS technology.},
}
@article {pmid32019036,
year = {2020},
author = {Brandon, TA and Stamps, BW and Cummings, A and Zhang, T and Wang, X and Jiang, D},
title = {Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations.},
journal = {The Science of the total environment},
volume = {713},
number = {},
pages = {136698},
doi = {10.1016/j.scitotenv.2020.136698},
pmid = {32019036},
issn = {1879-1026},
mesh = {Biofilms ; Bioreactors ; *Denitrification ; Nitrates ; Thiobacillus ; },
abstract = {Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.},
}
@article {pmid31974023,
year = {2020},
author = {Gladding, PA and Legget, M and Fatkin, D and Larsen, P and Doughty, R},
title = {Polygenic Risk Scores in Coronary Artery Disease and Atrial Fibrillation.},
journal = {Heart, lung &amp; circulation},
volume = {29},
number = {4},
pages = {634-640},
doi = {10.1016/j.hlc.2019.12.004},
pmid = {31974023},
issn = {1444-2892},
mesh = {*Atrial Fibrillation/genetics/physiopathology/therapy ; *Coronary Artery Disease/genetics/physiopathology/therapy ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; *Multifactorial Inheritance ; *Polymorphism, Single Nucleotide ; Risk Factors ; },
abstract = {Coronary artery disease (CAD) and atrial fibrillation (AF) are two highly prevalent cardiovascular disorders that are associated with substantial morbidity and mortality. Conventional clinical risk factors for these disorders may not be identified prior to mid-adult life when pathophysiological processes are already established. A better understanding of the genetic underpinnings of disease should facilitate early detection of individuals at risk and preventative intervention. Single rare variants of large effect size that are causative for CAD, AF, or predisposing factors such as hypertension or hyperlipidaemia, may give rise to familial forms of disease. However, in most individuals, CAD and AF are complex traits in which combinations of genetic and acquired factors play a role. Common genetic variants that affect disease susceptibility have been identified by genome-wide association studies, but the predictive value of any single variant is limited. To address this issue, polygenic risk scores (PRS), comprised of suites of disease-associated common variants have been devised. In CAD and AF, incorporation of PRS into risk stratification algorithms has provided incremental prognostic information to clinical factors alone. The long-term health and economic benefits of PRS-guided clinical management remain to be determined however, and further evidence-based data are required.},
}
@article {pmid31942825,
year = {2020},
author = {Ho, J and Yeoh, YK and Barua, N and Chen, Z and Lui, G and Wong, SH and Yang, X and Chan, MC and Chan, PK and Hawkey, PM and Ip, M},
title = {Systematic review of human gut resistome studies revealed variable definitions and approaches.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1700755},
pmid = {31942825},
issn = {1949-0984},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; },
abstract = {In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.},
}
@article {pmid31248111,
year = {2019},
author = {Richardson, E and Dacks, JB},
title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.},
journal = {Microorganisms},
volume = {7},
number = {6},
pages = {},
pmid = {31248111},
issn = {2076-2607},
support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.},
}
@article {pmid31226241,
year = {2019},
author = {Roth, H and Gallo, S and Badger, P and Hillwig, M},
title = {Changes in microbial communities of a passive coal mine drainage bioremediation system.},
journal = {Canadian journal of microbiology},
volume = {65},
number = {10},
pages = {775-782},
doi = {10.1139/cjm-2018-0612},
pmid = {31226241},
issn = {1480-3275},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Coal Mining ; *Microbiota ; *Wetlands ; },
abstract = {Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%-43%), Bacteroidetes (12%-37%), Firmicutes (3%-11%), and Verrucomicrobia (6%-11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.},
}
@article {pmid30769763,
year = {2019},
author = {, and Singh, BR and Gupta, VK and Deeba, F and Bajpai, R and Pandey, V and Naqvi, AH and Upreti, DK and Gathergood, N and Jiang, Y and El Enshasy, HA and Sholkamy, EN and Mostafa, AA and Hesham, AE and Singh, BN},
title = {Non-Toxic and Ultra-Small Biosilver Nanoclusters Trigger Apoptotic Cell Death in Fluconazole-Resistant Candida albicans via Ras Signaling.},
journal = {Biomolecules},
volume = {9},
number = {2},
pages = {},
pmid = {30769763},
issn = {2218-273X},
mesh = {Antifungal Agents/chemistry/*pharmacology ; Candida albicans/cytology/*drug effects ; Cell Death ; Cell Survival/drug effects ; Drug Resistance, Fungal/*drug effects ; Fluconazole/chemistry/*pharmacology ; Lichens/chemistry/metabolism ; Metal Nanoparticles/*chemistry ; Particle Size ; Proto-Oncogene Proteins p21(ras)/*antagonists &amp; inhibitors/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Silver/chemistry/*metabolism ; Surface Properties ; },
abstract = {Silver-based nanostructures are suitable for many biomedical applications, but to be useful therapeutic agents, the high toxicity of these nanomaterials must be eliminated. Here, we biosynthesize nontoxic and ultra-small silver nanoclusters (rsAg@NCs) using metabolites of usnioid lichen (a symbiotic association of algae and fungi) that exhibit excellent antimicrobial activity against fluconazole (FCZ)-resistant Candida albicans that is many times higher than chemically synthesized silver nanoparticles (AgNPs) and FCZ. The rsAg@NCs trigger apoptosis via reactive oxygen species accumulation that leads to the loss of mitochondrial membrane potential, DNA fragmentation, chromosomal condensation, and the activation of metacaspases. The proteomic analysis clearly demonstrates that rsAg@NCs exposure significantly alters protein expression. Most remarkable among the down-regulated proteins are those related to glycolysis, metabolism, free radical scavenging, anti-apoptosis, and mitochondrial function. In contrast, proteins involved in plasma membrane function, oxidative stress, cell death, and apoptosis were upregulated. Eventually, we also established that the apoptosis-inducing potential of rsAg@NCs is due to the activation of Ras signaling, which confirms their application in combating FCZ-resistant C. albicans infections.},
}
@article {pmid30278254,
year = {2019},
author = {Wu, LW and Chiba, H and Lees, DC and Ohshima, Y and Jeng, ML},
title = {Unravelling relationships among the shared stripes of sailors: Mitogenomic phylogeny of Limenitidini butterflies (Lepidoptera, Nymphalidae, Limenitidinae), focusing on the genera Athyma and Limenitis.},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {60-66},
doi = {10.1016/j.ympev.2018.09.020},
pmid = {30278254},
issn = {1095-9513},
mesh = {Animals ; Asia ; Butterflies/*classification/*genetics ; Genome, Insect/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; },
abstract = {The phylogenetic relationships of the nymphalid butterfly tribe Limenitidini are best known for the genera Limenitis and Adelpha, model taxa for evolutionary processes such as Batesian mimicry and rapid adaptive radiations. Whereas these American limenitidines have received the most attention, phylogenetic relationships of their Asian relatives are still controversial and largely unexplored. Even one of the largest genera in Asia, Athyma, is polyphyletic. To clarify the phylogenetic relationships of these Asian Limenitidini, a total of 53 representatives were sampled; 37 have their mitogenomes sequenced for the first time. Our phylogenetic results confirm that mitogenomic data provides well-resolved relationships at most major levels of the phylogeny, even using different partition schemes or different inference methods. Interestingly, our results show that some Athyma taxa are embedded within the genus Limenitis, whereas the genus Tacola, previously considered to be a synonym of Athyma, needs to be recognized as a valid clade. Additionally, the other Limenitidini genera in Asia (namely Tarattia, Litinga, Sumalia, Pandita and Patsuia) are now grouped either within Athyma or Limenitis, so these genera need to be sunk. Importantly, we also show that the mainly Old World Limenitis and entirely New World Adelpha are sister groups, confirming the relevance of Asian lineages to global studies of Limenitis evolution.},
}
@article {pmid28105307,
year = {2016},
author = {Ankenbrand, MJ and Terhoeven, N and Hohlfeld, S and Förster, F and Keller, A},
title = {biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.},
journal = {F1000Research},
volume = {5},
number = {},
pages = {2348},
pmid = {28105307},
issn = {2046-1402},
abstract = {The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.},
}
@article {pmid41240515,
year = {2025},
author = {Wang, S and Xu, R and Xiao, M and Yu, J and Yu, L and Heng, Z and Li, Z and Du, Q and Zhou, Y and Li, Y and Zhu, G},
title = {Comammox ammonia oxidization and N2O production in vadose and saturated zone soils.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124899},
doi = {10.1016/j.watres.2025.124899},
pmid = {41240515},
issn = {1879-2448},
abstract = {Riparian zones are biogeochemical hotspots of N2O emission. The important role of ammonia oxidation in N2O production has been reported in rivers, even higher than heterotrophic denitrification, however, the mechanisms controlling riparian N2O production remain unknown. Here, we found that complete ammonia oxidation (comammox) process significantly contributes to ammonia oxidation and N2O production in subsurface riparian zone. The contribution of comammox to ammonia oxidation in surface soils (38.7 ± 6.5 %) is equivalent to that of bacterial ammonia oxidation (49.4 ± 6.9 %), and both processes are significantly more important than archaeal ammonia oxidation (11.9 ± 4.1 %). Moreover, comammox dominates ammonia oxidation in both vadose and saturated zone soils, especially in summer with the average contributions of over 67.9 %. However, as a biotic N2O production pathway, comammox produces more N2O in vadose (up to 72 %) and saturated zone (up to 100.0 %) soils, significantly higher than that produced by archaeal ammonia oxidation (32.0 ± 4.0 %) and bacterial ammonia oxidation (18.0 ± 5.7 %). We obtained the first metagenome-assembled genomes (MAGs) of comammox bacteria in a riparian profile, and metagenomic binning analysis revealed that the wide niche of comammox may attribute to its diverse metabolic pathways, which not only perform ammonia oxidation but also nitrate reduction to ammonia. This research enhances the understanding of the biogeochemical ammonia cycle in riparian zone systems and provides new insights for the control of nitrogen pollution in riparian zones.},
}
@article {pmid41240423,
year = {2025},
author = {Alzeer, S and Almaghrabi, RS and Magrashi, A and Alzahrani, T and Bakheet, R and Alqasabi, A and Tayeb, H},
title = {Revealing co-infections in pneumonia: A case report on advancing diagnosis with metagenomic sequencing technologies.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103036},
doi = {10.1016/j.jiph.2025.103036},
pmid = {41240423},
issn = {1876-035X},
abstract = {Pneumonia, a frequent and serious complication in kidney transplant recipients, is significantly increased by long-term immunosuppressive medication. This case report details a patient with lung cavitation, in which conventional microbiological methods revealed Escherichia coli as the principal pathogen. Metagenomic long-read sequencing also identified Klebsiella pneumoniae as a co-pathogen, underscoring the shortcomings of traditional diagnostic techniques. In identifying infectious pathogens, this case illustrates the superior diagnostic accuracy of long-read sequencing, offering crucial information that conventional methods might miss. The implementation of sophisticated sequencing technologies may overcome these diagnostic deficiencies, improving infection care in challenging and immunocompromised patients.},
}
@article {pmid41240163,
year = {2025},
author = {Perez-Hernandez, C and Aldaroub, J and Barth, ZK and Aylward, FO},
title = {A novel lineage of large aquatic bacteriophages identified through metagenomics.},
journal = {Archives of virology},
volume = {170},
number = {12},
pages = {253},
pmid = {41240163},
issn = {1432-8798},
support = {#2141862//National Science Foundation/ ; },
mesh = {*Metagenomics ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Phylogeny ; },
abstract = {"Jumbo phages" are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as "moraphages", from the Gaelic word 'mór', for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylum Bacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the order Flavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere.},
}
@article {pmid41240088,
year = {2025},
author = {V, C and Lal, SB and Mishra, DC and Sharma, A and Kumar, S and Chaturvedi, KK and Behera, BK},
title = {In Silico Identification of Enzymes Involved in Bioremediation from Metagenomic Sequence of River Ganga.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {115},
number = {6},
pages = {64},
pmid = {41240088},
issn = {1432-0800},
mesh = {Biodegradation, Environmental ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; Metagenomics ; Computer Simulation ; Environmental Monitoring ; Metagenome ; },
abstract = {Environmental pollution, particularly in aquatic ecosystems, poses a major global threat. The Ganga River, vital to millions, suffers from severe contamination despite multiple remediation efforts. Bioremediation, especially enzyme-mediated approaches, offers an eco-friendly and efficient alternative to conventional methods. This study utilizes metagenomic reads to identify bioremediating enzymes, their host microorganisms, target pollutants, and enzyme abundance at two Ganga sites: Nawabganj, Kanpur (highly polluted), and Below Farakka Bridge, West Bengal (less polluted). In-silico analysis was conducted using RemeDB for enzyme identification and MG-RAST for microbial abundance. Enzyme abundance was determined by integrating microbial profiles with the RemeDB enzyme database. Key enzymes identified include Phenylacetaldehyde dehydrogenase (plastic), Biphenyl dioxygenase (hydrocarbons), and Catechol 1,2-dioxygenase (dyes). Results indicate higher bioremediating enzyme diversity in the more polluted Nawabganj site. The findings highlight the potential of native enzymes for pollutant degradation and support further exploration for environmental cleanup strategies.},
}
@article {pmid41239457,
year = {2025},
author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K},
title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1287},
pmid = {41239457},
issn = {1479-5876},
mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; },
abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.<br><br>METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16&#xa0;S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).<br><br>RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.<br><br>CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.},
}
@article {pmid41239428,
year = {2025},
author = {Chen, W and Zhang, Y and Gong, H and Cao, Z and Yang, K and Mi, J},
title = {Exploring diversity and distribution patterns of chicken gut bacteriophage community.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {119},
pmid = {41239428},
issn = {2524-4671},
}
@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
}
@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration &amp; dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.<br><br>DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}
@article {pmid41239026,
year = {2025},
author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H},
title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {211},
pmid = {41239026},
issn = {1896-1851},
support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; },
abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.},
}
@article {pmid41238915,
year = {2025},
author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA},
title = {Microbial signals in primary and metastatic brain tumors.},
journal = {Nature medicine},
volume = {31},
number = {11},
pages = {3675-3688},
pmid = {41238915},
issn = {1546-170X},
support = {R21 NS130323/NS/NINDS NIH HHS/United States ; F32 CA260769/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA221703/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; },
abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.},
}
@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}
@article {pmid41238615,
year = {2025},
author = {Wang, R and Wang, H and Jiang, J and Xu, S and Dong, M},
title = {Diagnostic value of metagenomic next-generation sequencing in the etiological diagnosis of lower respiratory tract infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39987},
pmid = {41238615},
issn = {2045-2322},
support = {GXLIRMMKL-201916//Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has been widely used in infectious diseases. However, reports on mNGS for lower respiratory tract infection (LRTI) diagnosis remain limited, potentially offering significant value for improving pathogen identification. This study evaluates the diagnostic performance and clinical value of mNGS compared to traditional methods in LRTI. We analyzed traditional and mNGS detection results from 165 patients with suspected LRTI using different specimens including bronchoalveolar lavage fluid (BALF), blood, tissue samples, and pleural effusion. We compared diagnostic differences and characteristics between mNGS and traditional methods, and evaluated the effect of mNGS results on antibiotic treatment.Among 165 cases, 146 (88.48%) patients with LRTI had microbial etiology finally identified. Compared with traditional diagnostic methods, mNGS showed significantly higher positive rate (143/165, 86.7% vs 69/165, 41.8%, P < 0.05). The diagnostic performance of mNGS was not affected by sample types. mNGS demonstrated significant advantage in detecting poly-microbial infections and rare pathogens. Twenty-nine kinds of pathogens were detected only by mNGS, including non-tuberculous mycobacteria (NTM), Prevotella, anaerobic bacteria, Legionella gresilensis, Orientia tsugamushi, and viruses. The pathogen spectrum differed between immunocompetent and immunocompromised individuals. mNGS resulted in treatment changes in 119 patients (72.13%), with 54 patients (32.73%) having reduced antibiotics. mNGS has obvious advantages over traditional detection methods with results unaffected by sample types. mNGS demonstrates significant value for pathogen detection and may provide guidance in clinical practice.},
}
@article {pmid41238538,
year = {2025},
author = {Bilcke, G and Campese, L and Annunziata, R and Amadei Martínez, L and Borgonuovo, C and Rijsdijk, N and Chaerle, P and Van den Berge, K and D'hondt, S and Iudicone, D and Montresor, M and Ferrante, MI and Vandepoele, K and Vyverman, W},
title = {Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10029},
pmid = {41238538},
issn = {2041-1723},
support = {1228423N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L2323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; MARCO-BOLO (101082021)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; AtlantECO (862923)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Diatoms/genetics/physiology ; Reproduction/genetics ; Genetic Markers/genetics ; Oceans and Seas ; Transcriptome ; Phytoplankton/genetics ; Gene Expression Profiling ; Salinity ; Metagenome ; Seawater ; },
abstract = {Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms' evolutionary success.},
}
@article {pmid41238046,
year = {2025},
author = {Oliveira, RDS and Oliveira Alves Filho, NC and Gomes Netto, WB and Silva, DC and Oliveira, MS and Oliveira, ACFM and Baraúna, RA and Graças, DAD and Silva, A and Oliveira Veras, AA},
title = {ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes.},
journal = {Gene},
volume = {},
number = {},
pages = {149893},
doi = {10.1016/j.gene.2025.149893},
pmid = {41238046},
issn = {1879-0038},
abstract = {To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: https://github.com/allanverasce/contigpolishing.},
}
@article {pmid41237940,
year = {2025},
author = {Borroni, D and Lo Monaco, F and Silvia, F and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C},
title = {Ocular Surface Microbiota in Primary Open Angle Glaucoma.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110734},
doi = {10.1016/j.exer.2025.110734},
pmid = {41237940},
issn = {1096-0007},
abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1×10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.},
}
@article {pmid41237902,
year = {2025},
author = {Pitarch, A and Arribas, V and Gil, C},
title = {Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {},
number = {},
pages = {101463},
doi = {10.1016/j.mcpro.2025.101463},
pmid = {41237902},
issn = {1535-9484},
abstract = {Invasive candidiasis (IC) is a serious, life-threatening, and costly fungal infection if not diagnosed early and treated appropriately. However, this healthcare-associated mycosis caused by Candida spp. is difficult to diagnose because of its nonspecific clinical signs and symptoms, and the lack of early and accurate detection methods. IC is also difficult to treat due to its late diagnosis, the limited antifungal arsenal, and the rapid emergence and spread of (multi)drug-resistant Candida strains. Therefore, early and accurate innovative methods for species and resistance identification in IC (candidemia and deep-seated candidiasis) are urgently needed to initiate timely and appropriate antifungal therapy, and reduce its high morbidity, mortality, and healthcare costs in hospitalized patients (in particular, severely immunocompromised or critically ill patients). The availability of the complete genome sequences of the most clinically relevant Candida species coupled with recent advances in high-throughput omics technologies have spurred an unprecedented era in the discovery and development of IC diagnostics at different levels of molecular complexity. Here we review the contribution of current and emerging omics technologies, including genomics, transcriptomics, proteomics, peptidomics, metabolomics, lipidomics, glycomics, immunomics (immunoproteomics, immunopeptidomics, and immunoglycomics), imiomics (imaging-omics), and microbiomics (metagenomics, metatranscriptomics, metaproteomics, and metabonomics), to the process of biomarker development for early diagnosis, antifungal susceptibility, prognosis, follow-up, and therapeutic monitoring in IC. We highlight the potential of integrating multiple omic data (through integromics, multiomics or panomics, together with systems biology and artificial intelligence) for the discovery of multidimensional biomarker signatures and computational algorithms for IC diagnosis. Finally, we discuss future challenges and prospects for their clinical implementation. These next-generation IC diagnostics promise to revolutionize medical practice by unraveling the complexity of biological systems at multiple levels. In addition, these could help clinicians make more precise and personalized clinical decisions through multiomics or panomics-based precision medicine approaches, rather than traditional one-size-fits-all approaches.},
}
@article {pmid41237728,
year = {2025},
author = {Meng, Q and Wang, J and Li, K and Zhang, Y and Hu, Z and Wang, F and Pan, F and Fu, J and Dang, C},
title = {Low-dose chlorine disinfection poses a greater potential risk of antibiotic resistance genes and their pathogenic hosts.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124895},
doi = {10.1016/j.watres.2025.124895},
pmid = {41237728},
issn = {1879-2448},
abstract = {Identifying the responses of antibiotic resistance genes (ARGs) and their hosts to chlorine disinfection is necessary because it has been paradoxically reported to both amplify and suppress antibiotic resistance in water treatment processes. In this study, our integrated metagenomic and metatranscriptomic analysis of sequencing batch reactors under different chlorine disinfection conditions (0, 2, 6, and 10 mg/L) in activated sludge reveals that low-dose chlorine obviously increases ARG abundance, diversity, and transcriptional activity, particularly for multidrug, β-lactam, and tetracycline types, while higher doses reduce transcriptional diversity and activity. Acinetobacter johnsonii, a pathogen abundant and active under chlorine-addition conditions, poses a high risk of ARG transmission due to its multiple mobile genetic elements and potential involvement in horizontal gene transfer with non-pathogens. Notably, chlorine disinfection may simultaneously promote the co-transfer of chlorine resistance and antibiotic resistance genes, such as the qacE gene, with the involvement of plasmids and integrons. Overall, this study demonstrates that low-dose chlorine may promote greater ARG enrichment, mobility, and pathogenic potential in activated sludge. The findings highlight overlooked risks of low-concentration residual chlorine, urging reconsideration of disinfection strategies to protect public health.},
}
@article {pmid41237727,
year = {2025},
author = {Zhao, Z and Zhao, Y and Hua, M and Yao, X and Hu, B},
title = {Deep metagenomic insights into the formation characteristics of the resistome in Pristine Saline Lakes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124937},
doi = {10.1016/j.watres.2025.124937},
pmid = {41237727},
issn = {1879-2448},
abstract = {Pristine and isolated ecosystems remain underexplored in resistome research, leaving a major gap in understanding how antibiotic resistance genes (ARGs) persist and spread outside human influence. To address this, we performed the first long-term, systematic, ultra-deep metagenomic survey of four high-altitude pristine saline lakes in the Altun Shan National Nature Reserve-an uninhabited region of the Qinghai-Tibet Plateau-generating 1.8 terabases of sequencing data. We identified a total of 756 ARG subtypes spanning 28 ARG types in all sampled lakes, with the clinically relevant polymyxin resistance gene, ugd, accounting for 30.5 % of the total ARG abundance. Moreover, ugd showed high mobility potential, with 183 horizontal gene transfer (HGT) events identified across 18 genera, and was widely associated with mobile genetic elements (MGEs). Similarity analyses revealed that the ARG profiles of pristine saline lakes were most comparable to those of marine environments, suggesting that salinity is a key ecological driver shaping the prevalence of polymyxin resistance genes. These findings indicate that pristine saline lakes can act as previously underexplored reservoirs and exchange hubs for clinically important resistance genes. Our results reveal the abundance and dissemination potential of ugd in isolated ecosystems and provide new insights into how natural environmental factors independently shape the resistome, with implications for One Health antimicrobial resistance surveillance.},
}
@article {pmid41237724,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Enhance H2 production by regulating acetyl-CoA supply and reducing equivalent diversion in an enriched purple phototrophic bacteria culture.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124910},
doi = {10.1016/j.watres.2025.124910},
pmid = {41237724},
issn = {1879-2448},
abstract = {Short-chain volatile fatty acids (VFAs) are promising carbon sources for biohydrogen production by purple phototrophic bacteria (PPB), given their high hydrogen conversion potential and low cost. However, most existing studies used a single VFA as the carbon source, providing only partial insights for practical applications, as VFAs in waste streams typically exist in mixtures. Furthermore, the metabolic responses of PPB to VFA mixtures, which determine H2 yield, and the metabolic mechanisms, remain largely unexplored. This study investigated the effects of co-feeding propionate with acetate or butyrate on PPB's hydrogen production and explored the associated metabolic responses through metagenomic and metatranscriptomic analyses. Results show that co-feeding butyrate with propionate (1:1 COD ratio) increased substrate conversion efficiency to 61 %, compared to 54 % from sole propionate. This improvement is linked to increased acetyl-CoA (Ac-CoA) availability, which, on one hand, activates the tricarboxylic acid (TCA) cycle and generates more electrons during carbon assimilation, and on the other hand, reduces the competitiveness of other electron sinks, thereby enhancing electron flow toward hydrogen. In contrast, co-feeding acetate with propionate results in a comparable conversion efficiency (∼50 %), where the increased Ac-CoA availability promotes carbon assimilation through the glyoxylate shunt instead. These findings reveal a synergistic metabolic impact from mixed VFAs and highlight the role of Ac-CoA in regulating carbon assimilation and electron dissipation. Understanding these interactions can guide the selection of waste streams and pretreatment processes to provide PPB with favorable VFA compositions, enabling more efficient and sustainable hydrogen production in practice.},
}
@article {pmid41237630,
year = {2025},
author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L},
title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140469},
doi = {10.1016/j.jhazmat.2025.140469},
pmid = {41237630},
issn = {1873-3336},
abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.},
}
@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}
@article {pmid41236809,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY},
title = {Characterization of Gut Microbiota of Honey Bees in Korea.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-025},
pmid = {41236809},
issn = {2544-4646},
abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.},
}
@article {pmid41236788,
year = {2025},
author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C},
title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e72950},
doi = {10.2196/72950},
pmid = {41236788},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists &amp; inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; },
abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.<br><br>OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.<br><br>METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.<br><br>RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.<br><br>CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.<br><br>TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.<br><br>DERR1-10.2196/72950.},
}
@article {pmid41236769,
year = {2025},
author = {Lima Filho, CM and Santos, AA and Lima, DVN and Silva, LO and Paranhos, RR and Branco, S and Pacheco, ABF and Azevedo, SMFO},
title = {Combining Ludwigia leptocarpa with the dried biomass of Pontederia crassipes for mitigating cyanobacteria: a sustainable way to use macrophyte waste.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/15226514.2025.2579148},
pmid = {41236769},
issn = {1549-7879},
abstract = {Constructed Floating Wetlands (CFWs) with emergent macrophytes offer a low-cost, sustainable strategy to mitigate eutrophication. We evaluated the combined use of Ludwigia leptocarpa, a native macrophyte from the Americas, and dried biomass of Pontederia crassipes (DB Pc) as substrate in small-scale CFWs to suppress a natural cyanobacterial bloom. Ex-situ mesocosm experiments (40 L) were conducted over 16 days with treatments: L. leptocarpa with DB Pc (S+), L. leptocarpa alone (S-), DB Pc alone, and living P. crassipes as positive control. L. leptocarpa (S-) and P. crassipes reduced Soluble Reactive Phosphorus by >85%, but L. leptocarpa produced 10 times less biomass. Treatments with DB Pc increased nutrient and phenol concentrations. All treatments led to reduced chlorophyll-a and phytoplankton density, especially cyanobacteria, along with pH reduction. 16S rRNA sequencing revealed higher bacterial diversity in the L. leptocarpa rhizosphere than in the water, suggesting a role in phytoremediation. The combination of L. leptocarpa and DB Pc in CFWs shows potential for cyanobacterial control through nutrient uptake, allelopathy, and pH modulation. This method supports sustainable water management by utilizing a native, slow-growing macrophyte and repurposing waste biomass that would otherwise harm aquatic ecosystems.},
}
@article {pmid41236031,
year = {2025},
author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ},
title = {Altered oral microbiome diversity in patients with oral candidiasis.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106430},
doi = {10.1016/j.archoralbio.2025.106430},
pmid = {41236031},
issn = {1879-1506},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.<br><br>DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.<br><br>RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.<br><br>CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.},
}
@article {pmid41235937,
year = {2025},
author = {Mills, S and Collins, G and Ijaz, UZ and Lens, PNL},
title = {Metagenome-assembled genomes from microbial communities in lab-scale anaerobic bioreactors treating simulated dairy wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048725},
doi = {10.1128/mra.00487-25},
pmid = {41235937},
issn = {2576-098X},
abstract = {This dataset describes metagenome-assembled genomes from three lab-scale (4L) expanded granular sludge bed bioreactors treating synthetic dairy wastewater. The resulting MAGs encompass 60 phyla with average genome completeness of 78.68% and average contamination of 2.29%. These genomes represent a valuable resource for studying anaerobic bioreactors used in wastewater treatment.},
}
@article {pmid41235136,
year = {2025},
author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y},
title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {9993-10010},
pmid = {41235136},
issn = {1177-8881},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; },
abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.<br><br>METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.<br><br>RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.<br><br>CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.},
}
@article {pmid41234773,
year = {2025},
author = {Levé, M and Manghi, P and Bredon, M and Lefevre, A and Manara, S and Armanini, F and Emond, P and Planchais, J and Rolhion, N and Segata, N and Sokol, H},
title = {Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113751},
pmid = {41234773},
issn = {2589-0042},
abstract = {Tryptophan metabolism plays a key role in host-microbiota interactions, producing a wide array of bioactive metabolites. However, our understanding of the interactions between tryptophan metabolites and the gut microbiota is still limited. Using targeted quantitative metabolomics and metagenomics in mice across various compartments, we showed that the cecal microbiota massively impacts tryptophan metabolism both in the gut and systemically. Grouping bacterial taxa in co-abundance guilds better reflected the links between gut microbes and tryptophan metabolites than single taxa taken individually and suggested the involvement of complex microbial interactions in tryptophan metabolism regulation. Finally, analyzing functional data, we shed light on the potential links between tryptophan metabolism and bacterial enzymes or metabolic pathways.},
}
@article {pmid41234739,
year = {2025},
author = {Jin, L and Chen, S and Kang, R and Li, C and Yang, S and Yang, Q and Zhao, K and Zou, L},
title = {Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683394},
pmid = {41234739},
issn = {1664-302X},
abstract = {BACKGROUND: Application of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion's (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.<br><br>METHODS: We employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.<br><br>RESULTS: Anaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.<br><br>CONCLUSION: This study demonstrates AD's limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.},
}
@article {pmid41234344,
year = {2025},
author = {Yang, L and Zeng, J and Zhang, Y and Li, L},
title = {Purulent Meningitis Due to Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis and Streptococcus constellatus from Oral and Maxillofacial Space Infection: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5843-5851},
pmid = {41234344},
issn = {1178-6973},
abstract = {BACKGROUND: Purulent meningitis caused by polymicrobial oral anaerobes represents a rare but life-threatening clinical challenge, with Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus being pfastidious organisms. Traditional diagnostic methods often fail to identify these fastidious organisms, leading to delayed or inappropriate therapy.<br><br>CASE PRESENTATION: We report a rare case of purulent meningitis resulting from a polymicrobial infection involving Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus in a 76-year-old male patient who presented with a 40-day history of left facial pain. This case represents the first documented instance of these four oral anaerobes concurrently causing an infection of the central nervous system.<br><br>CONCLUSION: To the best of our knowledge, this case represents the first documented evidence of polymicrobial purulent meningitis caused by oral anaerobes, specifically Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus. Our findings not only provide direct evidence for the oral-central nervous system (CNS) infection pathway but also validate that the valuable approach based on metagenomic next-generation sequencing (mNGS) offers significant clinical insights for diagnostic and therapeutic strategies.},
}
@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}
@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}
@article {pmid41233919,
year = {2025},
author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB},
title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {232},
pmid = {41233919},
issn = {2049-2618},
support = {ECOGIG//Gulf of Mexico Research Initiative/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.<br><br>RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.<br><br>CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.},
}
@article {pmid41233799,
year = {2025},
author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA},
title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1276},
pmid = {41233799},
issn = {1479-5876},
abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.<br><br>METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.<br><br>RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.<br><br>CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.},
}
@article {pmid41233543,
year = {2025},
author = {Aroney, STN and Newell, RJP and Tyson, GW and Woodcroft, BJ},
title = {Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41233543},
issn = {1548-7105},
support = {DP230101171//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; },
abstract = {The recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low-abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm that substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritized, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.},
}
@article {pmid41233523,
year = {2025},
author = {Dell, M and Kogawa, M and Streiff, AB and Shiraishi, T and Lotti, A and Meier, CM and Schorn, MA and Field, C and Cahn, JKB and Yokoyama, H and Yamada, Y and Peters, E and Egami, Y and Nakashima, Y and Tan, KC and Rückert, C and Alanjary, M and Kalinowski, J and Kuzuyama, T and Cardenas, P and Pomponi, S and Sipkema, D and Wright, A and Takada, K and Abe, I and Wakimoto, T and Takeyama, H and Piel, J},
title = {Chemical richness and diversity of uncultivated 'Entotheonella' symbionts in marine sponges.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41233523},
issn = {1552-4469},
support = {22H05120//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H02635//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H05128//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, 'Candidatus Entotheonella' members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 'Entotheonella' candidate species and a member of a sister lineage named 'Candidatus Proxinella'. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.},
}
@article {pmid41233350,
year = {2025},
author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW},
title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1782},
pmid = {41233350},
issn = {2052-4463},
support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; },
mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; },
abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.},
}
@article {pmid41233343,
year = {2025},
author = {Lu, JN and Chao, Y and Tian, L and Zhong, X and Chen, Z and He, H and Huang, B and Li, M and Feng, Z and Feng, H and Hu, C and Zhou, S and Zhang, L and Yang, Y and Ruan, Z and Ding, K and Yang, Y and Yuan, K and Liu, W and Qi, H and Cao, Y and Fei, YH and Ling, N and Wang, S and Tang, YT and Luan, T and Xu, Z and Qiu, R},
title = {DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9984},
pmid = {41233343},
issn = {2041-1723},
mesh = {*Carbon Cycle/genetics ; *Soil Microbiology ; Carbon/metabolism ; Soil/chemistry ; China ; *DNA Viruses/genetics/metabolism ; Metagenomics ; *Soil Pollutants/metabolism ; *DNA, Viral/genetics ; Metagenome ; Mining ; },
abstract = {Soil is the largest organic matter repository on land and the virosphere is an essential component of soil carbon cycling. While a few carbon-related auxiliary metabolic genes (AMGs) in viruses are reported to potentially influence the hosts, the effects of virus-host interactions on soil carbon fixation, particularly in carbon-deficient contaminated soils, need further validation. Here, we explore the impact of viruses on carbon fixation in contaminated soils from 58 metal mining areas across eastern China. Eleven different functional categories of carbon fixation AMGs are identified via metagenomic analysis in 323 contaminated soil samples. Enzymatic activities of three key AMGs (i.e., rbcL, ppdK and TKT) are experimentally characterized, indicating the positive role of these genes in carbon fixation. Furthermore, transcriptomic sequencing reveals that after active virus inoculation the carbon fixation genes significantly up-regulate (~73%, p < 0.05). In mesocosms with stable isotope labeling, the accumulation of [13]C-labeled organic carbon significantly increases (~10%, p < 0.01). Our results provide theoretical and experimental evidence for incorporating viral contributions into the assessments of carbon fixation, and improve the understanding of viral roles within the processes of carbon cycling.},
}
@article {pmid41233306,
year = {2025},
author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X},
title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9980},
pmid = {41233306},
issn = {2041-1723},
support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; },
abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.},
}
@article {pmid41232906,
year = {2025},
author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M},
title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123287},
doi = {10.1016/j.envres.2025.123287},
pmid = {41232906},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13% of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49%), macrolide-lincosamide-streptogramin (15.84%), beta-lactam (7.95%), and tetracycline (6.52%). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.},
}
@article {pmid41232839,
year = {2025},
author = {Fang, L and Jiaqi, L and Zhenwei, Z and Jingang, Z and Xiao, L and Yongdong, C},
title = {Remediation of soil contaminated by waste drilling slurry in oilfield with mixed bacteria immobilized by fly ash modified biochar.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133644},
doi = {10.1016/j.biortech.2025.133644},
pmid = {41232839},
issn = {1873-2976},
abstract = {Organic and heavy metal combined pollution from large-scale landfill of waste drilling slurry in oilfields poses a significant remediation challenge. This study innovatively combined fly ash doping with physicochemical modification to regulate the morphology and functionalize the surface of reed straw biochar, developing a low-cost modified biochar-based carrier material. This material, validated through leachate adsorption experiments and characterization (SEM, FT-IR, BET, XRD, TEM-EDS), exhibited both high-efficiency organic pollutant adsorption capacity and strong microbial immobilization performance. To simulate practical conditions, pot experiments were conducted, with ICP-OES and metagenomic analyses used to investigate pollutant transformation and fate. Key findings showed that unmodified biochar and fly ash formed a "glass phase-carbon matrix" structure, and under optimal conditions (biochar-fly ash mass ratio 5:1, NaOH-H2O2-assisted ultrasonic modification, 700℃ calcination), the specific surface area of modified material increased by 158.60 % compared to unmodified biochar, with an organic pollutant adsorption capacity of 32.56 mg·g[-1]. When immobilized with specific degrading bacteria, this material achieved 80.54 % COD removal in contaminated soil over 63 days, a rate significantly higher than that of free bacterial or biochar-based material groups, thereby demonstrating stable degradation advantages. Mechanistically, the synergistic integration of high-efficiency adsorption and biodegradation leveraging local oilfield wastes highlights this as an engineerable, efficient, and low-cost strategy for remediating waste drilling slurry-contaminated sites, with broad implications for addressing legacy composite pollution in energy industries.},
}
@article {pmid41232286,
year = {2025},
author = {Romero-Arguelles, R and Gómez-Govea, MA and Adame-Martinez, AE and Guzman-Velazco, A and Gonzalez-Rojas, JI and Ham-Dueñas, JG and Amezquita-Garcia, HJ and Rios-Del Toro, EE},
title = {Sulfammox in sediments of a natural wetland in northeastern Mexico: a sustainable approach to nitrogen and sulfur removal.},
journal = {The Science of the total environment},
volume = {1006},
number = {},
pages = {180920},
doi = {10.1016/j.scitotenv.2025.180920},
pmid = {41232286},
issn = {1879-1026},
abstract = {The simultaneous removal of nitrogenous and sulfate compounds in natural environments represents a major environmental challenge. The sulfammox process, a microbial pathway that couples anaerobic ammonium oxidation with sulfate reduction, has recently been proposed as a sustainable alternative for the removal of these pollutants. In this study, we evaluated for the first time the presence and activity of sulfammox microbial communities in sediments from a natural wetland in northeastern Mexico under controlled microcosm conditions. Physicochemical parameters, sediment composition, and ammonium dynamics were analyzed in two natural wetlands: Cachorritos pond (CHP) and Azul turqueza pond (AZP), during a four-week incubation period under controlled conditions. A decrease in ammonium concentration (up to 41.38 mM) was observed only in the CHP, with a stoichiometric NH4[+]/SO4[2-] ratio of 2.45 (92 %), confirming the activity of the sulfammox process. Metagenomic analysis revealed an enrichment of bacterial phylum associated with the sulfammox process, such as Chloroflexi, Chlorobi and Proteobacteria, which increased markedly in sulfate and ammonium treatments. This study represents the first report of sulfammox activity in a natural wetland in Mexico, highlighting the ecological potential of these ecosystems as natural treatment systems and supporting their consideration in sustainable bioremediation strategies.},
}
@article {pmid41232227,
year = {2025},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}
@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth &amp; development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}
@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148025},
doi = {10.1128/aem.01480-25},
pmid = {41231970},
issn = {1098-5336},
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.<br><br>IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}
@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}
@article {pmid41231233,
year = {2025},
author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE},
title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001510},
pmid = {41231233},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; },
abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.},
}
@article {pmid41231016,
year = {2025},
author = {Wang, YL and Aghdam, SA and Brown, AMV and Deonarine, A},
title = {Global Survey of Mercury Methylation and Demethylation Microbial Communities in Wastewater and Activated Sludge.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11448},
pmid = {41231016},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.},
}
@article {pmid41230645,
year = {2025},
author = {El-Mayet, FS and Moharam, I and El-Nahas, EM and El-Habbaa, AS and Najar, FZ and Stayton, E and El Nagar, EMS and Radi, M and Khalil, NW and Abaza, MA},
title = {First identification of concurrent infections with novel emerging duck astrovirus and duck hepatitis A virus type 3 (DHAV-3) in ducklings in Egypt using metagenomic next-generation sequencing (m-NGS).},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/03079457.2025.2581279},
pmid = {41230645},
issn = {1465-3338},
abstract = {First complete genome sequencing of a DHAV-3 strain from Egypt using m-NGS.Discovery of a novel duck astrovirus co-infecting with DHAV-3.Phylogenetic analysis reveals cross-border transmission links with Asian strains of both DHAV-3 and DAstV-5.},
}
@article {pmid41230492,
year = {2025},
author = {Rodriguez-Fernandez, IA and Santiago-Rodriguez, TM and Figueroa-Pratts, PG and Cintrón-Berríos, K and Rodriguez-Cornier, ND and Toranzos, GA},
title = {Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1676003},
pmid = {41230492},
issn = {2673-8600},
abstract = {Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the presence of a muscular, sclerotized gizzard. Colorimetric analysis revealed a mildly acidic gut environment (approximately pH 4-5, based on qualitative ranges), consistent across sexes and regions. Shotgun metagenomic sequencing of dissected guts from males and females revealed microbial communities distinct from the leaf samples microbiota. While alpha and beta diversity did not differ significantly between sexes, co-occurrence analyses identified sex-specific correlation patterns among bacterial taxa. Notably, Enterobacter cloacae, Pantoea vagans, Lactococcus lactis, and Pseudomonas monteilii were repeatedly detected across individuals and generated metagenomic datasets, and some were localized to the hindgut, suggesting possible niche specialization. The presence of taxa, such as Enterobacter cloacae, previously reported as symbionts in other phytophagous insects further supports the hypothesis that certain bacteria may contribute to host digestion or adaptation. These findings establish a framework for understanding the gut environment and microbial community of D. abbreviatus, and highlight candidate taxa for future functional studies. More broadly, this work supports further research into the potential roles of gut microbiota in the ecology and management of this pest.},
}
@article {pmid41230491,
year = {2025},
author = {Juhász, J and Ligeti-Nagy, N and Bodnár, B and Juhász, J and Pongor, S and Ligeti, B},
title = {ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf188},
pmid = {41230491},
issn = {2635-0041},
abstract = {MOTIVATION: Phage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or virome assemblies are often fragmented, and the diversity of environmental phages is not well known. Current computational approaches often rely on database comparisons that require significant effort and expertise to update. We propose using genomic language models (LMs) for phage lifestyle classification, allowing efficient direct analysis from nucleotide sequences without the need for sophisticated preprocessing pipelines or manually curated databases. We trained three genomic LMs (DNABERT-2, Nucleotide Transformer, and ProkBERT) on datasets of short, fragmented sequences. These models were then compared with dedicated phage lifestyle prediction methods in terms of accuracy, prediction speed, and generalization capability.<br><br>RESULTS: ProkBERT PhaStyle achieves accuracy comparable to, and in many cases higher than, state-of-the-art models across various scenarios. It demonstrates the ability to generalize to unseen data in our benchmarks, accurately classifies phages from extreme environments, and also demonstrates high inference speed.<br><br>Genomic LMs offer a simple and computationally efficient alternative for solving complex classification tasks, such as phage lifestyle prediction. ProkBERT PhaStyle's simplicity, speed, and performance suggest its utility in various ecological and clinical applications.},
}
@article {pmid41230489,
year = {2025},
author = {Scherz, V and Nassirnia, S and Chaabane, F and Castelo-Szekely, V and Greub, G and Pillonel, T and Bertelli, C},
title = {zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf255},
pmid = {41230489},
issn = {2635-0041},
abstract = {SUMMARY: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling.<br><br>Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.},
}
@article {pmid41230409,
year = {2025},
author = {Tian, Y and Xu, N and Chen, Y and Xu, Z and Zhou, JX and Zhang, L},
title = {Cost-effectiveness analysis of metagenomic next-generation sequencing versus traditional bacterial cultures for postoperative central nervous system infections in critical care settings: a prospective pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1710412},
pmid = {41230409},
issn = {2235-2988},
mesh = {Humans ; *Cost-Benefit Analysis ; Pilot Projects ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/economics/methods ; Female ; Male ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology/economics ; *Metagenomics/economics/methods ; *Critical Care/economics ; Aged ; *Bacteria/genetics/isolation &amp; purification/classification ; Adult ; *Postoperative Complications/microbiology/diagnosis ; Intensive Care Units ; China ; *Bacteriological Techniques/economics/methods ; Cost-Effectiveness Analysis ; },
abstract = {BACKGROUND: Early and accurate pathogen identification is crucial for managing central nervous system infections (CNSIs). While Metagenomic Next-Generation Sequencing (mNGS) offers rapid and sensitive pathogen detection, its cost-effectiveness in postoperative neurosurgical patients in critical care settings remains underexplored. Our study aims to investigate the clinical health economic value of mNGS in detecting pathogens of CNSIs after neurosurgery.<br><br>METHODS: In this prospective pilot study, 60 patients with CNSIs at Beijing Tiantan Hospital ICU (March 2023-January 2024) were randomized 1:1 to mNGS or conventional pathogen culture groups. A decision-tree model compared cost-effectiveness using incremental cost-effectiveness ratios (ICERs). A decision-tree model was used to compare the cost-effectiveness between mNGS and traditional pathogen culture methods using incremental cost-effectiveness ratios (ICERs).<br><br>RESULTS: From March 2023 to January 2024, 60 patients were included. mNGS demonstrated superior diagnostic efficiency with shorter turnaround time (1 vs 5 days; _P_<0.001) and lower anti-infective costs (&#xa5;18,000 vs &#xa5;23,000; _P_=0.02). Despite higher detection costs (&#xa5;4,000 vs &#xa5;2,000; _P_<0.001), the ICER of &#xa5;36,700 per additional timely diagnosis suggested cost-effectiveness at China's GDP-based WTP threshold. No significant differences in hospitalization duration or total costs were observed (_P_>0.05).<br><br>CONCLUSION: mNGS improves diagnostic efficiency and reduces antimicrobial expenditure for postoperative CNSIs in critical care, demonstrating favorable cost-effectiveness when considering clinical outcome gains.},
}
@article {pmid41230408,
year = {2025},
author = {Lin, L and Li, X and Li, J and Wu, B and Lin, Y and Li, W and Li, H and Guo, Y and Huang, C and Huang, Z and Zhang, W and Fang, X},
title = {Microbial culture vs. mNGS: diagnostic variations in periprosthetic joint infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1611332},
pmid = {41230408},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; *Metagenomics/methods ; *Microbiological Techniques/methods ; Retrospective Studies ; },
abstract = {OBJECTIVE: This study aimed to compare the diagnostic performance of conventional microbial culture and metagenomic next-generation sequencing (mNGS) in detecting pathogens in periprosthetic joint infection (PJI) and to identify factors contributing to discrepancies between these two methods.<br><br>METHODS: A total of 167 patients with suspected PJI (including PJI patients and aseptic failure patients) who underwent revision joint replacement at our center from September 2017 to April 2024 were enrolled. Demographic data, prior antibiotic use, and results of microbial culture and mNGS were documented. Joint fluid, periprosthetic tissue, or prosthetic ultrasonic fluid samples were collected, and at least one sample from each patient underwent both microbial culture and mNGS testing. In the light of the concordance between culture and mNGS results, patients were divided into the detection consistent and detection inconsistent groups. The differences in pathogen detection between the two models were compared, and factors contributing to discordant results were analyzed.<br><br>RESULTS: The prior antibiotic use (OR = 2.137, 95% CI = 1.069-4.272, P = 0.032), polymicrobial infections (OR = 3.245, 95% CI = 1.278-8.243, P = 0.013), infection caused by rare pathogens (OR = 2.735, 95% CI = 1.129-6.627, P = 0.026), and intraoperative tissue specimens (OR = 2.837, 95% CI = 1.007-7.994, P = 0.049) were identified as risk factors for discordance between microbial culture and&#xa0;mNGS results, particularly in cases with negative microbial culture but positive mNGS findings. Conversely, consistency in specimen type (OR = 0.471, 95%CI=0.254-0.875, P = 0.017) was identified as a protective factor against discordance.<br><br>CONCLUSION: Clinicians should optimize diagnostic strategies by tailoring microbial culture methods to the patient's clinical condition and integrating mNGS testing where appropriate. It is recommended to use tissue specimens from the same anatomical site across multiple tests while sampling from different regions when necessary. Although this approach may increase costs, it significantly enhances the accuracy of pathogen identification and facilitates more effective treatment.},
}
@article {pmid41229791,
year = {2025},
author = {Wang, W and Mo, Q and Yu, Q and Ding, X},
title = {Clinical characteristics of Pneumocystis jirovecii pneumonia in 20 non-HIV-infected patients.},
journal = {Journal of thoracic disease},
volume = {17},
number = {10},
pages = {8904-8914},
pmid = {41229791},
issn = {2072-1439},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PCP) is a life-threatening disease in clinics, commonly associated with human immunodeficiency virus (HIV) infected patients. Nowadays, with the increasing use of immunosuppressants, the incidence of PCP in non-HIV-infected patients is also on the rise. This study aimed to investigate the clinical diagnosis and treatment of PCP in non-HIV-infected patients.<br><br>METHODS: We collected and retrospectively analyzed 20 cases of PCP diagnosed in HIV-negative patients at Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University.<br><br>RESULTS: All cases were diagnosed using metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL). Of all 20 patients, 11 were men and nine were women. The median age was 66.5 (range, 18-83) years old. Three out of 20 patients had no immunosuppressive background, while 17 were exposed to immunosuppressants due to different diseases. Among them, four had solid malignancies, four had kidney disease, three had hematological malignancies, two had skin diseases, one had thrombocytopenia, one had rheumatoid arthritis, one had anaphylactoid purpura and one had knee arthritis. All patients had not received prophylactic drugs for PCP. All patients underwent antimicrobial treatment, 16 cases received glucocorticoid treatment, and seven underwent mechanical ventilation. A total of six out of 20 patients died. Bivariate Pearson's test revealed a negative correlation between patients' oxygenation index and age (r=-0.493, P=0.03). Serum lactate dehydrogenase (LDH) levels were positively correlated with serum creatinine levels (r=0.557, P=0.01). LDH levels were positively correlated with the time between symptom onset and oral administration of compound sulfamethoxazole (SMZ-TMP) (r=0.477, P=0.03). There was also a positive correlation between creatinine levels and the time to oral SMZ-TMP administration (r=0.607, P=0.005).<br><br>CONCLUSIONS: HIV-negative patients with PCP have atypical clinical symptoms and a high mortality rate. mNGS technology may facilitate early diagnosis based on its rapid turnaround time. To reduce mortality, SMZ-TMP drug treatment should be initiated promptly once PCP is considered clinically.},
}
@article {pmid41229688,
year = {2025},
author = {Zhao, J and Zeng, R and Zhang, C and He, B and Zhang, Q and Zhou, Q and Gong, Z and Liu, H and Liu, S},
title = {Comparative analysis of soil properties before and after Morchella sextelata cultivation across various soil types.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1700246},
pmid = {41229688},
issn = {1664-302X},
abstract = {Morchella, a highly nutritious edible fungus, has been successfully cultivated through artificial means. However, as cultivation areas have expanded, declining yield have emerged more prominently. Soil physicochemical characteristics and microbial communities were critical to production on cultivating morels. In this study, our results reveals that cultivation significantly alters soil properties and microbial communities in a soil type-dependent manner. In sandy soil, pH and key nutrients (total nitrogen, total phosphorus, available phosphorus) increased, while potassium and calcium levels decreased. Microbial diversity decreased in sandy soil but increased in paddy soil, with the overall community structure in sandy soil being more drastically reshaped. Metagenomic profiling identified distinct differential taxa and functional shifts, showing that sandy soil exhibited greater enrichment of microbial genes, including soil-borne diseases. These findings demonstrate that M. sextelata cultivation induces considerable and contrasting changes in soil nutrient profiles and microbiome composition, with sandy soil being more susceptible to microbial restructuring and potential pathogen enrichment.},
}
@article {pmid41229344,
year = {2025},
author = {Sures, K and Esser, SP and Bornemann, TLV and Moore, CJ and Soares, AR and Plewka, J and Figueroa-Gonzalez, PA and Ruff, SE and Moraru, C and Probst, AJ},
title = {Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf201},
pmid = {41229344},
issn = {1759-6653},
mesh = {*CRISPR-Cas Systems ; *Genome, Archaeal ; *Archaea/genetics ; Genome, Bacterial ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Bacteria/genetics ; Metagenome ; Evolution, Molecular ; *DNA, Intergenic/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in CRISPR-Cas systems from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.},
}
@article {pmid41229166,
year = {2025},
author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K},
title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70128},
doi = {10.1002/mbo3.70128},
pmid = {41229166},
issn = {2045-8827},
support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, P&#xe4;ivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Waist-Hip Ratio ; },
abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.},
}
@article {pmid41228422,
year = {2025},
author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S},
title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213350},
pmid = {41228422},
issn = {2072-6643},
support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; },
abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.},
}
@article {pmid41228409,
year = {2025},
author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X},
title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213335},
pmid = {41228409},
issn = {2072-6643},
support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; },
mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; },
abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.},
}
@article {pmid41227654,
year = {2025},
author = {Liscano, Y and Caicedo, N and Oñate-Garzón, J},
title = {Unlocking New Bioactive Peptides from Coffee Pulp: A Metagenomics and AI-Driven Discovery Paradigm.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227654},
issn = {2304-8158},
support = {call No. DGI-01-2025//Universidad Santiago de Cali/ ; },
abstract = {This perspective reframes Colombian coffee pulp from an environmental liability into a strategic asset by proposing a new discovery paradigm. We argue that the pulp's challenging chemical environment is not a barrier but its key advantage, having acted as a natural evolutionary filter that has sculpted a unique, highly resilient microbiome. Our vision is a technology pipeline that harnesses this natural pre-selection. By converging deep metagenomic data from the pulp's microbiome with generative artificial intelligence, we can create and validate novel, high-performance bioactive peptides and enzymes that are already pre-optimized for industrial robustness. This approach transcends traditional waste valorization, establishing a new framework for "biointelligence" in action. It offers a strategic roadmap for Colombia to generate knowledge-intensive value chains from its most iconic agricultural product, turning a national challenge into a global opportunity in the bioeconomy.},
}
@article {pmid41227630,
year = {2025},
author = {Luo, Q and Li, X and Li, J and Lu, Y and Chen, J and Su, J and Zhao, D and Hu, J and Zhang, X and Zhao, P and Zhang, Z and Zhang, Q and Lei, X and Bai, J and Zheng, J and Zhao, X},
title = {Multi-Metaomics Unveils the Development Process of Microbial Communities During the Fermentation of Baobaoqu.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227630},
issn = {2304-8158},
support = {JUSRP202504012//Fundamental Research Funds for the Central Universities/ ; BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; 32021005//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
abstract = {In order to understand the dynamic interaction process among species, enzymes, and metabolites during the fermentation process of Baobaoqu, which is a representative Daqu starter for Chinese baijiu, the intimate connection between the progression of microbial communities and the diversities and activities of enzymes was examined by metagenomics, metatranscriptomics and metaproteomics. It was found that while 5211 species of microorganisms were detected by metagenomics, only 1774 active species were detected by metatranscriptomics, which indicated that only a small proportion (34.04%) were active. The metabolic routes associated with the breakdown of substrates and synthesis of metabolites were redesigned, and the special functional microorganisms for lactate, pyrazines and phenylethyl alcohol production were isolated. It was found that the progression of the microbial community was highly coupled with the components of enzymes and flavor substrates, precisely corresponding to the three stages of the Baobaoqu fermentation process, and were regulated by multiple physical factors. During the Baobaoqu-making process of the fermentation, microorganisms with different functions work together to complete metabolism in different stages. These findings will aid us in gaining a deeper and clearer understanding of the "species-enzyme-metabolite" system within the Daqu starter culture, thus offering valuable perspectives for developing artificial synthetic communities and the production of high-quality Baobaoqu.},
}
@article {pmid41227601,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Li, B and Zhu, J},
title = {The Presence of Stone Moroko (Pseudorasbora parva) Drives Divergent Sediment Resistome Profiles in Chinese Mitten Crab (Eriocheir sinensis) Polyculture Pond.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227601},
issn = {2304-8158},
support = {CARS-45//China Agriculture Research System of MOF and MARA/ ; 31802302//National Natural Science Foundation of China/ ; 2023TD64//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; BK20231140//Jiangsu Provincial Natural Science Foundation of China/ ; 2019YFD0900305//National Key R&amp;D Program of China/ ; },
abstract = {The propagation of antibiotic resistance genes (ARGs) in aquatic environments poses a significant threat to global health. This study compared sediment resistome profiles in river crab (Eriocheir sinensis) polyculture systems with and without stone moroko (Pseudorasbora parva). The results showed that, compared to the control group (MC group), the sediment from the polyculture system containing stone moroko (PC group) exhibited significant reductions in the total abundances of ARGs, metal resistance genes (MRGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Crucially, the total abundance and composition of MGEs in pond sediment were substantially correlated with ARGs, MRGs, and BRGs, respectively. Co-occurrence network analysis revealed that there was only one edge between ARGs and MGEs in the PC group, whereas the MC group had eight edges. Additionally, the proportion of mobile ARGs in the PC group was significantly lower than that in the MC group. Alterations in resistome profiles were markedly associated with decreased levels of total carbon (TC) and phosphate in the sediment. All of the findings demonstrated that the introduction of stone moroko in the river crab polyculture system effectively mitigated the sediment resistome primarily by altering environmental factors and suppressing MGEs, thereby disrupting the horizontal transfer network of resistance genes. This study highlights the potential of leveraging aquatic biota as a novel biological strategy for the in situ management of environmental antimicrobial resistance.},
}
@article {pmid41227457,
year = {2025},
author = {Soto-López, JD and Fernández-Soto, P and Muro, A},
title = {Bacterial Composition Across Bat Species: A Human Health Perspective.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227457},
issn = {2076-2615},
abstract = {Bats are widely recognized as reservoirs of diverse bacterial pathogens with important implications for human health. Recent zoonotic disease outbreaks have intensified interest in bat microbiomes, with high-throughput sequencing increasingly used to assess microbial diversity. In this article, we review literature from the past five years on bacterial species associated with bats and their potential clinical relevance. Using automated searches and manual filtering, we extracted data from 47 peer-reviewed studies. Most research has focused on guano samples, though interest in skin microbiomes is rising, particularly in relation to Pseudogymnoascus destructans, the agent of white-nose syndrome. China leads in the number of publications, followed by the United States, and amplicon sequencing remains the predominant metagenomic method. Across studies, 4700 bacterial species were reported, including several known human pathogens capable of aerosol transmission or opportunistic infections in immunocompromised individuals. Many of these taxa are classified as global priority targets for antimicrobial drug development by the World Health Organization and the U.S. Centers for Disease Control and Prevention. Given the clinical severity of diseases linked to some species, bats should be integrated into epidemiological surveillance systems. However, the lack of standardized reporting practices significantly limits the comparability and utility of bat microbiome data for robust ecological and epidemiological analyses.},
}
@article {pmid41227433,
year = {2025},
author = {Yang, B and Shen, P and Xu, Z and Yang, J and Song, B and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y},
title = {Functional and Compositional Changes in Ileal Microbiota in Piglets During the Nursing Period Revealed by 16s rRNA Gene and Metagenomics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227433},
issn = {2076-2615},
support = {2023YFE0124400//the National Key Research and Development Program of China/ ; 2023B10564001//the Specific University Discipline Construction Project/ ; 2022A1515110819//Youth Project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; No. 32202715//the National Natural Science Foundation of China/ ; },
abstract = {In piglets, the gut microbiota matures in a segment-specific manner during the nursing period, while fecal-based studies provide limited functional resolution across intestinal sites. We profiled the ileum using 16s rRNA gene sequencing and assessed segmental functions by shotgun metagenomics at selected ages. Ileal species richness and diversity were relatively stable across days. Lactobacillus were prominent from day 7, with stage-associated taxa including Lactobacillus johnsonii, Lactobacillus delbrueckii, Ligilactobacillus salivarius, and Limosilactobacillus pontis. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and Limosilactobacillus pontis as a potential probiotic played an important role in it. At day 28, metagenomic analysis indicated higher relative abundance in the ileum of pathways linked to cysteine and methionine metabolism and lysine biosynthesis, largely carried by Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These data describe the composition and function of the ileum in the intestines of piglets and indicate a differentiation period around day 21 to day 28.},
}
@article {pmid41227430,
year = {2025},
author = {Deng, L and Yao, Y and Li, H and Lu, Q and Wu, R},
title = {Effects of Antimicrobial Peptides on the Growth Performance of Squabs Were Investigated Based on Microbiomics and Non-Targeted Metabolomics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227430},
issn = {2076-2615},
support = {2023B02036//Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; XJARS-12-01//Xinjiang Uygur Autonomous Region Modern Agricultural Industrial Technology System/ ; 2025XJJQ-z-01//Xinjiang Uygur Autonomous Region Modern Livestock and Poultry Breeding Industry Promotion Project/ ; },
abstract = {This study aims to investigate the effects of dietary supplementation with AMPs on the growth performance, antioxidant capacity, and intestinal health of squabs. Furthermore, metagenomic and metabolomic approaches were employed to identify key differential bacterial species and metabolites associated with growth performance, and thereby the potential mechanisms underlying the enhancement of squab growth and development by AMPs being elucidated. One hundred and twenty pairs of healthy adult White Carneau pigeons (2 years old) were randomly divided into two groups, the control group (CK, fed with basal diet) and antimicrobial peptide group (AP, fed with basal diet +200 mg/kg antimicrobial peptide), with 10 replicates per group and 6 pairs of breeding pigeons per replicate. The experiment lasted for 53 days, including 7 days of prefeeding, 18 days of incubation and 28 days of feeding. In this study, squabs were weighed at 0 and 28 days of age to evaluate growth performance. At 28 days of age, duodenal contents were collected to assess digestive enzyme activities, while jejunal and liver tissues were harvested to determine antioxidant capacity. Intestinal morphology was examined using tissue samples from the duodenum, jejunum, and ileum. Finally, ileal contents were collected for a comprehensive analysis of microbial composition and metabolite profiles in the two experimental groups, employing high-throughput sequencing and LC-MS/MS techniques. The results showed that body weight, liver total antioxidant capacity (T-AOC), jejunal malondialdehyde (MDA) content, jejunum and ileum villus height-to-crypt depth ratio (VH/CD) were significantly increased, and jejunal crypt depth (CD) was significantly decreased in the AP group at 28 days of age (p < 0.05). In addition, the microbiome data showed that Lactobacillus in the AP group was a biomarker with significant differences (p < 0.05). Metabolomics analysis showed that the steroid hormone biosynthesis pathway was significantly different between the two groups (p < 0.01). In addition, the content of potentially beneficial metabolites (Biotin, beta-Tocotrienol, 7-Chloro-L-tryptophan and Dihydrozeatin) was significantly increased in the AP group (p < 0.05). These results indicate that dietary AMPs can significantly improve the body weights, liver antioxidant capacity and jejunum and ileum VH/CD of squabs.},
}
@article {pmid41227427,
year = {2025},
author = {Lu, H and Wang, H and Li, B and Lv, Z and Li, S and Xia, Y and Wang, L},
title = {Effects of Soybean Meal Replacement on Growth Performance, Rumen Fermentation, Rumen Microorganisms, and Metabolites in Dumont Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227427},
issn = {2076-2615},
support = {BR231520//Basic Research Operating Funds of Universities under the Direct Administration of the Inner Mongolia Autonomous Region/ ; project No. BR22-13-13//Basic Research Fund for Universities in Inner Mongolia Autonomous Region/ ; YLXKZX-NND-007//Inner Mongolia Education Department Special Research Project For First Class Disciplines/ ; },
abstract = {This study investigated the effects of replacing part of the soybean meal in the diet of Dumont lambs with urea, rapeseed meal, and cottonseed meal on their growth performance and rumen fermentation and combined rumen microbial metagenomics and metabolomics to explain the reasons for the changes in phenotypic data. Twenty-four healthy male Dumont lambs were divided into four groups: soybean meal group (T1, control group), group with 1.5% urea replacing 6.4% soybean meal (T2), group with 1% urea replacing 4.3% soybean meal (T3), and group with 1% urea + 6.6% cottonseed meal +5% rapeseed meal replacing all soybean meal (19%) (T4), following the principle of equal energy and nitrogen. Urea, rapeseed meal, and cottonseed meal have different degradation rates in the rumen, primarily stimulating arginine biosynthesis, sulphur metabolism, and carbon fixation in photosynthetic organisms through Prevotella genus mediation, thereby influencing the accumulation of metabolites such as 9,10-DiHOME, DG (PGJ2/a-15:0/0:0), isonicotinate and taxifolin, affecting rumen fermentation. Compared with the T1 group, the T2 group showed significantly increased ammonia nitrogen (NH3-N) and microbial protein (MCP) content (p < 0.01) and improved fructose and mannose metabolic capacity (p < 0.05). The T3 group showed a significant increase in total volatile fatty acids (TVFA) and MCP content (p < 0.01), which facilitated the absorption of subsequent nutrients. In the T4 group, different degradation rates of nitrogen resources and rapeseed meal + cottonseed meal contained abundant and complementary amino acids, which improved rumen fermentation, enhanced rumen microbial and metabolite diversity, and optimized the synergistic metabolic efficiency of carbon, nitrogen and sulphur. However, the specific mechanisms of post-rumen metabolism and absorption require further investigation.},
}
@article {pmid41227163,
year = {2025},
author = {Armbruster, J and Thomas, B and Stengel, D and Spranger, N and Gruetzner, PA and Hackl, S},
title = {Managing Nonunions and Fracture-Related Infections-A Quarter Century of Knowledge, and Still Curious: A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {21},
pages = {},
pmid = {41227163},
issn = {2077-0383},
abstract = {Nonunions and fracture-related infections represent a significant complication in orthopedic and trauma care, with their incidence rising due to an aging, more comorbid global population and the escalating threat of multi-resistant pathogens. This narrative review highlights pivotal advancements in diagnostics and therapeutic approaches, while also providing an outlook on future directions. Diagnostic methodologies have significantly evolved from traditional cultures to sophisticated molecular techniques like metagenomic next-generation sequencing and advanced imaging. Simultaneously, therapeutic strategies have undergone substantial refinement, encompassing orthoplastic management for infected open fractures and the innovative application of antibiotic-loaded bone substitutes for local drug delivery. The effective integration of these possibilities into daily patient care critically depends on specialized centers. These institutions play an indispensable role in managing complex cases and fostering innovation. Despite considerable progress over the past 25 years, ongoing research, interdisciplinary collaboration, and a steadfast commitment to evidence-based practice remain crucial to transforming management for the future.},
}
@article {pmid41226831,
year = {2025},
author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E},
title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110796},
pmid = {41226831},
issn = {1422-0067},
support = {&#x41a;&#x41f;-06-&#x41d;83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; },
mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; },
abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.},
}
@article {pmid41226812,
year = {2025},
author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T},
title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110775},
pmid = {41226812},
issn = {1422-0067},
support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; },
abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.},
}
@article {pmid41226502,
year = {2025},
author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110463},
pmid = {41226502},
issn = {1422-0067},
support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; },
abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.},
}
@article {pmid41225603,
year = {2025},
author = {Rong, H and Wu, Z and Zhao, K and Ding, Y and Ning, S and Tian, Y and Wang, X and Qiao, Q and Zhu, X and Wu, T and Ge, Y and Chu, H and Cui, L},
title = {Identification and characterization of Jingmen tick virus in Jiangsu, China.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {372},
pmid = {41225603},
issn = {1743-422X},
support = {BK20231374//Natural Science Foundation of Jiangsu Province/ ; 2023YFC2605100, 2023YFC2605104//National Key Research and Development Program of China/ ; },
mesh = {China ; Phylogeny ; Animals ; Genome, Viral ; *Flaviviridae/isolation &amp; purification/genetics/classification ; Genetic Variation ; Sequence Analysis, DNA ; *Ticks/virology ; *Ixodidae/virology ; },
abstract = {Jingmen virus (JMV) is a group of viruses that belong to the Flaviviridae family. These viruses have been shown to cause widespread infections in various hosts and can lead to febrile illnesses in humans. Jingmen tick virus (JMTV) as an important member of the JMV group, has been detected in multiple countries worldwide and poses a significant threat to public health. This study utilized metagenomic sequencing technology to detect JMV in tick samples collected in Jiangsu Province. The results demonstrated the presence of JMTV in Jiangsu and identified two complete genomes (ZJ-7-4-2 and ZJ-7-9) from Haemaphysalis campanulate ticks. These gene sequences exhibited the highest sequence similarity to the known Japanese isolate of JMTV. Phylogenetic analysis showed that the JMTV identified in this study clustered within the same clade as the Japanese JMTV. In summary, this study reported for the first time that JMTV is prevalent in Jiangsu Province, China. These findings expand the known geographic distribution and genetic diversity of JMTV, providing new insights into its epidemiology and viral evolution.},
}
@article {pmid41225454,
year = {2025},
author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T},
title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {1198},
pmid = {41225454},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; },
abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).<br><br>METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n&#x2009;=&#x2009;31) and those with normal thyroid function (Control group, n&#x2009;=&#x2009;30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16&#xa0;S rRNA metagenomic sequencing.<br><br>RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p&#x2009;=&#x2009;0.034; Shannon index, p&#x2009;=&#x2009;0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p&#x2009;=&#x2009;0.002, p&#x2009;=&#x2009;0.049, and p&#x2009;=&#x2009;0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.<br><br>CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.},
}
@article {pmid41225248,
year = {2025},
author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F},
title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41225248},
issn = {1867-1314},
support = {28740//Horizon 2020/ ; },
abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.},
}
@article {pmid41225104,
year = {2026},
author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA},
title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {291-313},
pmid = {41225104},
issn = {0065-2598},
mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; },
abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.},
}
@article {pmid41225090,
year = {2026},
author = {Ziaei, H and Rezaei, N},
title = {Introduction to Oral Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {3-21},
pmid = {41225090},
issn = {0065-2598},
abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.},
}
@article {pmid41224996,
year = {2025},
author = {Nadel, O and Hanna, R and Rozenberg, A and Shitrit, D and Tahan, R and Pekarsky, I and Béjà, O and Kleifeld, O and Lindell, D},
title = {Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41224996},
issn = {1476-4687},
abstract = {Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages-viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phage's benefit[1-5]. One such gene is nblA, which is present in multiple cyanophage families[2,6-8]. Under nutrient deprivation cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome[9-11], the large cyanobacterial photosynthetic light-harvesting complex. This increases the pool of amino acids available for essential tasks[11], serving as a survival mechanism[12]. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation[6,8,13]. However, the benefit of the virus-encoded NblA for cyanophages and the broader impact on the host are unclear. Here, using a recently developed genetic manipulation system for marine cyanophages[14], we reveal that viral NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and comprise 35% and 65% of oceanic T7-like cyanophages in surface and deep photic zones, respectively. Our results show a large benefit of NblA to the cyanophage, while it exerts a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage NblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.},
}
@article {pmid41224779,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9943},
pmid = {41224779},
issn = {2041-1723},
support = {RFGA2023-008-15//ADHS | Arizona Biomedical Research Commission (ABRC)/ ; },
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes representing major microbial phyla, covering only a small fraction of gene families. However, most microbial diversity resides in metagenome-assembled genomes, which exhibit taxonomic imbalance and harbor gene families that do not fit the criteria for universal orthologs. To address these limitations, we introduce TMarSel, a software tool for automated, free-from-expert opinion, and tailored marker selection for deep microbial phylogenomics. TMarSel allows users to select a variable number of markers and copies based on KEGG and EggNOG gene family annotations, enabling a systematic evaluation of the phylogenetic signal from the entire gene family pool. We show that an expanded marker selection tailored to the input genomes improves the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes compared to previous markers, even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. TMarSel provides flexibility in the number of markers, copies, and annotation databases while remaining robust against taxonomic imbalance and incomplete genomic data.},
}
@article {pmid41224755,
year = {2025},
author = {Gupta, S and Almeida, A},
title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9959},
pmid = {41224755},
issn = {2041-1723},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.},
}
@article {pmid41224035,
year = {2025},
author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F},
title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133630},
doi = {10.1016/j.biortech.2025.133630},
pmid = {41224035},
issn = {1873-2976},
abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane (CH4) yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.},
}
@article {pmid41223797,
year = {2025},
author = {Xu, YY and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, NQ and Wu, YN and Xie, GJ},
title = {Thermophilic Sulfide-Driven autotrophic Denitrification: High-Rate nitrogen removal and metagenomic insights into microbial cooperation.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109918},
doi = {10.1016/j.envint.2025.109918},
pmid = {41223797},
issn = {1873-6750},
abstract = {Sulfide-driven autotrophic denitrification (SDAD) plays a pivotal role in linking nitrogen and sulfur cycles, particularly in thermophilic environments. However, the performance and metabolic mechanisms of thermophilic SDAD systems remain underexplored. This study successfully enriched thermophilic sulfide-oxidizing denitrifiers from hot spring sediments (60 °C) in an expanded granular sludge bed (EGSB) reactor, achieving a stable nitrate removal rate of 250 mg N L[-][1] d[-][1]. This thermal system demonstrated a higher tolerance threshold for sulfides (250 mg TDS L[-1]) than mesophilic processes. The influent sulfide-to-nitrate (S/N) molar ratio critically influenced nitrogen removal efficiency with nitrite accumulation at low S/N ratios (1:1), whereas higher ratios (2:1) restored complete nitrate reduction. Microbial community analysis demonstrated Thermus (52.89 %) as the predominant genus in the SDAD system, marking the first report of its dominance in thermophilic nitrogen-sulfur coupling, alongside uc_Aquificales (21.78 %). Metagenomic insights further revealed two high-quality genomes: Thermus scotoductus exclusively executed complete sulfide-to-sulfate oxidation via the Sox system and partially catalyzed denitrification (narGHI); while Aquificaeae_UBA11096 adopted Sox-independent enzyme system and complete denitrification. Strikingly, Thermus scotoductus encoded nrfH, and it might be the overlooked " nitrogen retainer" in geothermal ecosystems. This work elucidates the cooperative and competitive interactions between thermophilic denitrifiers, and establishes a multi-level thermal adaptability analysis. These findings advance understanding of their biogeochemical roles in geothermal ecosystems, and provide a sustainable strategy for nitrogen removal in high-temperature wastewater treatment.},
}
@article {pmid41223750,
year = {2025},
author = {Yao, S and Luo, Y and Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H},
title = {Microbial functional shifts in a paradigmatic petrochemical brownfield: Mechanisms of adaptation in soil and groundwater.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119380},
doi = {10.1016/j.ecoenv.2025.119380},
pmid = {41223750},
issn = {1090-2414},
abstract = {The long-term presence of pollutants from the petrochemical industry, including benzene, nitro compounds, and amine-based aromatics, poses a significant threat to soil and groundwater, resulting in shifts in microbial community structures. In this study, 48 soil and groundwater samples from contaminated environments were analyzed using metagenomic technology and gas chromatography-mass spectrometry to examine the metabolic strategies employed by microorganisms in response to these pollutants. The results revealed that microbial community composition was significantly influenced by varying contamination levels, primarily determined by the distance from contamination sources and the diffusion characteristics of the environmental media. In highly contaminated areas, specific bacterial genera, including Pseudomonas and Stutzerimonas, became dominant, suggesting an adaptation toward pollutant degradation. Soil and groundwater microorganisms exhibited distinct adaptive mechanisms: in soils, enhanced motility, metabolism, and toxicant transport were associated with the expression of genes such as mcp, tktA, and pleD, while in groundwater, pollutant degradation and the maintenance of cellular function were driven by genes including xylA, dmpB, nfnB, and glnA. These findings emphasise the capacity of microbes to adapt to pollutants from petrochemical industry environments, thus providing valuable insights into microbial remediation strategies for environmental pollution management.},
}
@article {pmid41223625,
year = {2025},
author = {Yang, B and Wang, H and Yan, Y and Bao, P and Feng, Q and Chen, B and Jia, Y and Shu, WS and Lu, H},
title = {Coupling Microalgae-based Biochar with MBGS Enhances Microbial Synergy and Multi-Pollutant Removal from Saline Aquaculture Wastewater.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124881},
doi = {10.1016/j.watres.2025.124881},
pmid = {41223625},
issn = {1879-2448},
abstract = {The microalgal-bacterial granular sludge (MBGS) system has gained attention as an energy-efficient, multifunctional approach for wastewater treatment, yet its stability and pollutant removal under combined salinity and antibiotic stress remain unclear. In this study, we developed an MBGS system integrated with nitrogen-rich microalgae-derived biochar to enhance removal of organic matter, nutrients, and enrofloxacin (ENR) from saline aquaculture wastewater. The biochar-coupled MBGS achieved high removal efficiencies: 94.2±4.8% COD, 87.1±3.6% NH4[+]-N, 60.3±4.6% PO4[3-]-P, and 60.1±3.5% ENR. Microbial community analysis revealed enrichment of ammonia-oxidizing bacteria (Nitrosomonas, 3.3-9.7%), nitrite-oxidizing bacteria (Nitrospira, 2.3-6.4%), denitrifiers (Thauera, 14.9-27.6%), phosphate-accumulating organisms (Acinetobacter, 0.8-7.7%), and photosynthetic microalgae (Chlorophyceae, 1.4-23.6%). Fluorescence in situ hybridization (FISH) confirmed that biochar enhanced the spatial organization of these functional microbes within MBGS. Metagenomics revealed increased abundance of genes associated with carbon (porCD, CS, korD), nitrogen (amoAB, narGHI, norBC), phosphorus (ppk, phaA, acs), and photosynthesis-related (petABCD, psaA) genes, indicating improved metabolic capacity and synergy. Genome-resolved metagenomics further identified Nitrosomonas europaea, Acinetobacter sp002296655, Thauera aminoaromatica, and Chlorobium sp013334435 as core taxa driving carbon, nitrogen, and phosphorus cycling and energy flow, promoting synergistic interactions and enhancing pollutant removal under stress. Coupling MBGS with microalgae-based biochar improves resilience and multi-pollutant removal, offering a robust, sustainable strategy for advanced aquaculture wastewater treatment.},
}
@article {pmid41223471,
year = {2025},
author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X},
title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140406},
doi = {10.1016/j.jhazmat.2025.140406},
pmid = {41223471},
issn = {1873-3336},
abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.},
}
@article {pmid41222958,
year = {2025},
author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Zhang, Y and Zhang, W and Lei, N and Pei, X and Xie, Y},
title = {Elucidating the Mechanism of PFOA Regulation of Biofilms in Aquatic Systems at Gene and Metabolic Levels.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06467},
pmid = {41222958},
issn = {1520-5851},
abstract = {Perfluorooctanoic acid (PFOA) is prevalent in aquatic ecosystems and exhibits significant toxicity to aquatic organisms. Microorganisms can adhere to the surfaces of submerged plants, forming complex extracellular structures referred to as attached biofilms. However, the mechanisms underlying the regulation of biofilm formation by PFOA remain unclear. This study cultured plant-attached biofilms under PFOA stress to investigate the mechanisms by which PFOA regulates biofilm formation, utilizing metagenomics and metabolomics. Results show that the biofilm structure was significantly altered under PFOA exposure, characterized by an increase in polysaccharide and protein content. Furthermore, PFOA bound to proteins within extracellular polymeric substances contributes to a reduction in PFOA toxicity. PFOA regulates biofilm formation by modifying the content of signaling molecules and the abundance of genes (bapA and ABC.PE.S) associated with quorum sensing, establishing a natural barrier against the toxic effects of PFOA. In addition, PFOA was found to inhibit the metabolism of linoleic and linolenic acids, thus indirectly promoting the formation of biofilms, which allowed microbial aggregation and coresistance to the toxic effects of exogenous pollutants. This study provides a comprehensive understanding on the mechanisms by which PFOA regulates biofilm formation, which is crucial for enhancing our understanding of microbial processes in aquatic ecosystems.},
}
@article {pmid41222645,
year = {2025},
author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D},
title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {16},
pmid = {41222645},
issn = {1432-0991},
abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.},
}
@article {pmid41222234,
year = {2025},
author = {Sinno, A and Baghdadi, R and Narch, R and El Rayes, S and Tokajian, S and Al Khoury, C},
title = {Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0155425},
doi = {10.1128/jvi.01554-25},
pmid = {41222234},
issn = {1098-5514},
abstract = {The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of artificial intelligence (AI) into viromics has transformed this landscape, introducing machine learning and deep learning models-including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and transformers-that extend viral discovery beyond sequence similarity constraints. Structure-based frameworks such as AlphaFold, ESMFold, and Foldseek further enable annotation of divergent viral proteins through conserved 3D folds, while graph neural networks (GNNs) model host-virus interaction and explainable AI enhances interpretability of prediction. Despite their high sensitivity and scalability, AI-driven approaches face notable challenges: computational burden, data set bias, limited explainability, and elevated false discovery rates. This review traces the evolution of computational virology from traditional methods to AI-based and hybrid frameworks. We examine landmark AI tools while underscoring the continuing importance of phylogenetics and functional annotation in contextualizing AI predictions. We propose an integrated workflow that combines AI pattern recognition with classical bioinformatics to enhance both scalability and interpretability. By addressing the limitations of solely AI-driven or traditional approaches, this review presents a unified computational strategy to accelerate viral discovery, enhance evolutionary insights, and strengthen global preparedness for emerging infectious diseases.},
}
@article {pmid41222171,
year = {2025},
author = {Lazov, CM and Larsen, LE and Johnston, CM and Rasmussen, TB and Hjulsager, CK},
title = {Announcement of two complete coding genomes of mink coronavirus and one partial coding genome of mink enteric calicivirus from mink in Denmark.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0045925},
doi = {10.1128/mra.00459-25},
pmid = {41222171},
issn = {2576-098X},
abstract = {Two complete coding genomes of mink coronavirus and one partial coding genome of the sapovirus mink enteric calicivirus were assembled from metagenomic sequencing data from mink on different farms with diarrhea outbreaks in 2015 in Denmark.},
}
@article {pmid41222160,
year = {2025},
author = {Liu, W and Nagasaka, K and Wu, J and Ban, H and Mimick, E and Meng, L and Neches, RY and Moniruzzaman, M and Yoshida, T and Nishimura, Y and Endo, H and Okazaki, Y and Ogata, H},
title = {Giant viruses specific to deep oceans show persistent presence and activity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093225},
doi = {10.1128/msystems.00932-25},
pmid = {41222160},
issn = {2379-5077},
abstract = {Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate mesopelagic GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To further investigate the distribution and phylogenomic features of GVs at a global scale across broader depths, we compiled 4,473 species-level GV genomes from the OceanDNA MAG project and other resources and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included a GV genome identified in our Muroto data, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat.IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the mesopelagic water. Using a global marine data set, we further uncovered geographically widespread and vertically extensive groups of deep-sea-specific giant viruses and characterized their distinctive gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.},
}
@article {pmid41222147,
year = {2025},
author = {Vogel, H and Weiss, B and Rama, F and Rinklef, A and Engl, T and Kaltenpoth, M and Vilcinskas, A},
title = {A multi-partner symbiotic community inhabits the emerging insect pest Pentastiridius leporinus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0310325},
doi = {10.1128/mbio.03103-25},
pmid = {41222147},
issn = {2150-7511},
abstract = {The planthopper Pentastiridius leporinus has emerged as a severe crop pest, rapidly expanding both its host plant range and the affected areas in central Europe. Originating as a monophagous herbivore of reed grass, P. leporinus recently adopted polyphagous feeding and is now a pest of sugar beet, potato, carrot, and onion, suggesting rapid ecological niche expansion. P. leporinus vectors two bacterial pathogens: the γ-proteobacterium Candidatus Arsenophonus phytopathogenicus (CAP) and the stolbur phytoplasma Candidatus Phytoplasma solani (CPS), which are responsible for a range of disease syndromes, including syndrome basses richesses in sugar beet. We used long-read metagenomic sequencing to characterize the genomes of microbes associated with P. leporinus, resulting in the complete sequences of CAP and CPS, as well as obligate symbionts of the genera Purcelliella, Karelsulcia, and Vidania, and facultative symbionts Rickettsia and Wolbachia. The obligate symbionts are inferred to provide or contribute to the biosynthesis of 10 essential amino acids and to B vitamin. The genomes of CPS and CAP encode numerous pathogenicity factors, enabling the colonization of different hosts. Bacterial fluorescence in situ hybridization revealed the tissue distribution, cellular localization, relative abundance, and transmission patterns of these bacteria. The intracellular presence of all obligate symbionts in bacteriomes, the intracellular presence of Wolbachia, and the intranuclear localization of Rickettsia suggest vertical transmission. CPS was restricted to salivary glands, suggesting strict horizontal, plant-mediated transmission, whereas CAP colonized all tissue types, allowing for horizontal and vertical transmission. Our data suggest that P. leporinus hosts an exceptionally broad range of symbionts, encompassing mutualistic, commensal, and pathogenic interactions.IMPORTANCEThe planthopper Pentastiridius leporinus has recently expanded its host plant range and emerged as a severe pest of sugar beet and potato crops in central Europe, which is exacerbated by its capacity to vector bacterial pathogens to its host plants. Because microbial symbionts may play an important role for both the host plant shifts and the transmission of pathogens, we used metagenomic sequencing and fluorescence in situ hybridization to characterize the microbial community associated with P. leporinus. We detected three bacteriome-localized obligate symbionts that together provision all essential amino acids and several B-vitamins to the host, as well as two intracellular bacteria with a broader tissue distribution. In addition, we infer localization, transmission, and putative pathogenicity factors for the two major phytopathogens that are vectored by P. leporinus. Our results reveal a complex community of symbiotic bacteria that likely shapes the interaction of this emerging pest with its host plants.},
}
@article {pmid41222145,
year = {2025},
author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE},
title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234125},
doi = {10.1128/mbio.02341-25},
pmid = {41222145},
issn = {2150-7511},
abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.<br><br>IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.},
}
@article {pmid41222144,
year = {2025},
author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL},
title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0111225},
doi = {10.1128/msystems.01112-25},
pmid = {41222144},
issn = {2379-5077},
abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.},
}
@article {pmid41222143,
year = {2025},
author = {Liu, P and Zhang, R and Meng, F and Zhang, C and Roberts, AP and Wang, Y and Zhu, K and Cao, Z and Pan, Y and Li, J},
title = {Deep-branching magnetotactic bacteria form intracellular carbonates enriched in trace metals.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113125},
doi = {10.1128/msystems.01131-25},
pmid = {41222143},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation.<br><br>IMPORTANCE: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba&#xb2;&#x207a; and Ni&#xb2;&#x207a;, and biologically essential Mg&#xb2;&#x207a;. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba&#xb2;&#x207a; and Ni&#xb2;&#x207a;) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.},
}
@article {pmid41221535,
year = {2025},
author = {Xie, K and Zhang, Y and Tan, S and Luo, J and Ou, X and Tan, S},
title = {Gut microbiota involvement in the alteration of inflammatory cell infiltration and gut barrier integrity in liver cirrhosis.},
journal = {Biomedical reports},
volume = {23},
number = {6},
pages = {193},
pmid = {41221535},
issn = {2049-9442},
abstract = {The gut microbiota is essential for the development and regulation of the immune and intestinal homeostasis of the host. The present study aimed to investigate the composition, diversity and functional features of the microbiota in patients with liver cirrhosis. and healthy volunteers using high-throughput sequencing of the 16S rRNA gene, and evaluated inflammatory cell infiltration and the gut barrier in both the colonic mucosa and liver sections using histological analysis. Diversity and metagenome function of the gut microbiota significantly differed between healthy volunteers and patients with liver cirrhosis. Patients with cirrhosis showed decreased microbial richness, evenness, and diversity, with functional prediction indicating enrichment of phosphotransferase and membrane transport pathways, while amino acid and energy metabolism pathways were predominant in healthy controls. Furthermore, gut microbial dysbiosis associated with liver cirrhosis augmented inflammatory cell infiltration in the colonic mucosa and liver sections, impaired gut barrier function and enhanced intestinal permeability and bacterial translocation. The gut microbiota contributes to the pathophysiology of liver cirrhosis, which may impact prevention and treatment strategies for patients with liver cirrhosis.},
}
@article {pmid41221508,
year = {2025},
author = {Siljanen, HMP and Manoharan, L and Hilts, AS and Bagnoud, A and Alves, RJE and Jones, CM and Kerou, M and Sousa, FL and Hallin, S and Biasi, C and Schleper, C},
title = {Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf183},
pmid = {41221508},
issn = {2730-6151},
abstract = {Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.},
}
@article {pmid41221507,
year = {2025},
author = {Clinton, CK and Jackson, FLC},
title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf181},
pmid = {41221507},
issn = {2730-6151},
abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.},
}
@article {pmid41221399,
year = {2025},
author = {Huang, Y and Zhou, Q and Gui, M and Guo, D and Cheng, J and Ma, W and Shu, P and Liu, X},
title = {Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host-microbiome metabolic interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668712},
pmid = {41221399},
issn = {1664-302X},
abstract = {BACKGROUND: Retinol remains an essential component in anti-aging skincare; however, a subset of users develop intolerance, characterized by compromised barrier integrity and inflammation. The temporal dynamics of how skin microbiota and host metabolism co-evolve during retinol tolerance establishment remain poorly understood.<br><br>METHODS: We conducted a prospective 28-day longitudinal study with 18 Chinese women (aged 25-40): 9 retinol-intolerant subjects monitored at baseline, adverse reaction phase, and tolerance establishment, while baseline data from 9 retinol-tolerant individuals served as controls. We integrated cutaneous phenotypic measurements, metagenomic sequencing, and untargeted metabolomics.<br><br>RESULTS: In the intolerant group, skin phenotype assessment revealed a distinct biphasic response-an acute phase marked by increased stratum corneum hydration, reduced sebum secretion, lower skin pH, and improved wrinkle metrics, followed by a re-equilibration phase characterized by sustained barrier restoration. Metagenomic profiling of 969 microbial species demonstrated that, although overall microbial &#x3b1;-diversity remained stable across time points in both groups, key taxa in the intolerant group exhibited transient "rise-and-fall" dynamics. At baseline, the intolerant group exhibited overrepresentation of Cutibacterium acnes, whereas the tolerant group was enriched in potentially protective species, including Sphingomonas hankookensis and Acinetobacter johnsonii. Untargeted metabolomics showed marked temporal fluctuations with an initial phase of metabolic turbulence, followed by partial recovery. During the early adverse reaction phase in intolerant subjects, lipid and fatty acid metabolic pathways-specifically, glycerophospholipid, linoleic acid, &#x3b1;-linolenic acid, and ether lipid metabolism-were significantly upregulated, concomitant with the suppression of TCA cycle and sphingolipid activity. Conversely, as tolerance was established, enhanced activity in the TCA cycle, sphingolipid, ascorbate, and pentose metabolism pathways-coupled with a reduction in pro-inflammatory arachidonic acid derivatives-indicated metabolic reconstitution and restoration of barrier integrity.<br><br>DISCUSSION: Integrated multi-omics correlation analyses further underscored the tightly interconnected regulation of host-microbe energy metabolism, antioxidant defenses, and membrane repair in response to retinol-induced stress. These findings elucidate the temporal interplay between host and microbial processes underpinning retinol tolerance and highlight baseline biomarkers that may facilitate personalized skincare interventions.},
}
@article {pmid41221168,
year = {2025},
author = {Yu, X and Cheng, J and He, J and Wu, X and Wang, W and Chen, M and Zhuo, B and Ge, Y},
title = {First Documented Case of Pneumonia with Nocardia africana and SARS-CoV-2 Co-Detection in Mainland China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5721-5730},
pmid = {41221168},
issn = {1178-6973},
abstract = {Nocardia spp. are zoonotic pathogens that can cause infections ranging from localized lesions to systemic dissemination, primarily via pulmonary inhalation or percutaneous inoculation. We report the first confirmed case of Nocardia africana pneumonia with SARS-CoV-2 co-detection in mainland China, diagnosed through bronchoalveolar lavage fluid (BALF) analysis using metagenomic next-generation sequencing (mNGS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A 76-year-old male presented with persistent cough and fever, accompanied by radiographic evidence of progressive pneumonia. Targeted antimicrobial therapy with trimethoprim-sulfamethoxazole and amoxicillin-clavulanate resulted in clinical resolution within 12 days. This case underscores three critical implications for post-COVID-19 pandemic medicine: the requirement for heightened vigilance for opportunistic pathogens (eg, Nocardia species) in pneumonia patients with recurrent fever, the essential role of advanced diagnostics (eg, mNGS and MALDI-TOF MS) in identifying fastidious organisms like actinomycetes, and the potential for antimicrobial resistance in N. africana, which necessitates susceptibility-guided therapy.},
}
@article {pmid41220843,
year = {2025},
author = {Kwon, K and Kim, M and Jung, Y and Yoon, MY and Lee, JY and Yoon, SS and Rho, M and Chung, YW and Ryu, JH},
title = {Intestinal Dysbiosis Caused by Epithelial Fabp6 Gene Disruption Exacerbates Gut Inflammatory Disease.},
journal = {Immune network},
volume = {25},
number = {5},
pages = {e35},
pmid = {41220843},
issn = {1598-2629},
abstract = {Ileal lipid binding protein (Ilbp), encoded by Fabp6 gene, plays a critical role in intracellular transport of bile acids (BAs) from apical to basolateral side of ileal enterocytes, maintaining BA homeostasis within enterohepatic circulation. However, pathophysiological consequences of Ilbp deficiency remain largely unexplored. Here, we demonstrate that disruption of BA balance, caused by intestinal epithelial cell (IEC)-specific Fabp6 gene knockout (Fabp6 [ΔIEC]), exacerbates dextran sulfate sodium (DSS)-induced gut inflammation. Fecal microbiota transplantation from Fabp6 [ΔIEC] mice to germ free recipient mice replicated the adverse effects observed in Fabp6 [ΔIEC] mice, which were mitigated when these mice were co-housed with control (Fabp6 [f/f]) mice. Metagenomic analysis identified Ligilactobacillus murinus as a primarily diminished strain in Fabp6 [ΔIEC] mice. Oral administration of L. murinus isolated from feces of Fabp6 [f/f] mice ameliorated DSS-induced colitis in Fabp6 [ΔIEC] mice by restoring epithelial barrier integrity and lowering pro-inflammatory cytokines IL-1β, IL-6 and TNF-α. Furthermore, daily administration of taurodeoxycholic acid-one of the BAs reduced in Fabp6 [ΔIEC] mice and that promotes the growth of L. murinus in an in vitro growth assay-also exhibited a protective effect against DSS-induced colitis through a similar mechanism. These findings suggest that deficiency of specific BAs due to epithelial Fabp6 deletion leads to gut dysbiosis, predisposing the host to inflammatory disease.},
}
@article {pmid41220286,
year = {2025},
author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK},
title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl250360},
pmid = {41220286},
issn = {2005-1212},
abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.},
}
@article {pmid41219964,
year = {2025},
author = {George, NA and Zhou, Z and Anantharaman, K and Hug, LA},
title = {Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {370},
pmid = {41219964},
issn = {1743-422X},
support = {R35GM143024/GM/NIGMS NIH HHS/United States ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; Tier II chair//Canada Research Chairs/ ; },
abstract = {BACKGROUND: Viruses are the most abundant microbial entities on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering bacteria and archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of bacteria and archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America.<br><br>RESULTS: We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~&#x2009;678 kbp), and noted a large diversity of viruses in landfills that has limited overlap across landfills and is distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect hosts across multiple phyla. Auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in the literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector-like proteins appear distinct relative to previously reported Cas effectors and are interesting targets for potential genome editing tools.<br><br>CONCLUSIONS: Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.},
}
@article {pmid41219190,
year = {2025},
author = {Chung, D and Brask, N and Matar, S and Gallot-Lavallée, L and Pringle, ES and Duguay, BA and Blais, C and Latimer, J and Haro, R and Slamovits, CH and Leyland, B and Rest, JS and Collier, JL and McCormick, C and Archibald, JM},
title = {Persistent mirusvirus infection in the marine protist Aurantiochytrium.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9922},
pmid = {41219190},
issn = {2041-1723},
support = {GBMF5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {Mirusviruses are abundant and broadly distributed double-stranded (ds) DNA viruses recently discovered in marine metagenomic data. Their host range and ecological impact are unclear. The protist Aurantiochytrium limacinum possesses two mirusvirus-like genomic elements, one a circular episome (AurliV-1) and the other (AurliV-2) a chromosomal integrant. Here we show that genes in both genomes are expressed and viral particles containing mainly AurliV-1 DNA are produced under starvation conditions and when cells are cultured in standard growth medium. We detected viral particles of ~140 nm in the nucleus, in cytoplasmic vesicles, between the plasma membrane and cell wall, and in the extracellular environment. Of 67 AurliV-1-encoded proteins detected using proteomics, 45 are enriched under starvation conditions, including the structurally important major capsid and triplex proteins. Our results establish Aurantiochytrium as a model system for elucidating mirusvirus-host interactions and demonstrate persistent viral infection in a microbial eukaryote.},
}
@article {pmid41218604,
year = {2025},
author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O},
title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102426},
doi = {10.1016/j.xcrm.2025.102426},
pmid = {41218604},
issn = {2666-3791},
abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).},
}
@article {pmid41214576,
year = {2025},
author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W},
title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {460},
pmid = {41214576},
issn = {1471-2377},
support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear.<br><br>METHODS: The aim of this study was to investigate this relationship in Parkinson&#x2019;s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography&#x2012;tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing.<br><br>RESULTS: A total of 12 PD patients (age: 58.00&#x2009;&#xb1;&#x2009;8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0&#x2013;3.0) and a disease duration of 8.46&#x2009;&#xb1;&#x2009;4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%&#xb1;17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics.<br><br>CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12883-025-04428-6.},
}
@article {pmid41206538,
year = {2025},
author = {Hall, MB and Zhou, C and Coin, LJM},
title = {Genome size estimation from long read overlaps.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf593},
pmid = {41206538},
issn = {1367-4811},
support = {FSPGN000045//Australian Government Medical Research Future Fund (MRFF) Genomics Health Futures Mission (GHFM) Flagships-Pathogen Genomics/ ; //META-GP/ ; //DELIVERING A CLINICAL METAGENOMICS PLATFORM FOR AUSTRALIA/ ; },
abstract = {MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data.<br><br>RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources.<br><br>Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.},
}
@article {pmid41218490,
year = {2025},
author = {Qingrui, L and Hongyang, L and Guijun, W and Yiqiao, Z and Yue, C and Changqun, D and Chang'e, L},
title = {Synergistic ecotoxicity of nanoscale zero-valent iron and cadmium in soil: Insights from Eisenia fetida.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119381},
doi = {10.1016/j.ecoenv.2025.119381},
pmid = {41218490},
issn = {1090-2414},
abstract = {Nano-zero-valent iron (nZVI) has been extensively applied as a soil conditioner in remediation practices. However, studies have suggested that excessive doses of nZVI can adversely affect soil organisms and even exacerbate the toxicity of contaminants such as cadmium (Cd) in earthworms. This study investigated whether nZVI induces stress and exacerbates Cd toxicity in Eisenia fetida under controlled laboratory conditions. Four treatments were established: control (no nZVI or Cd), nZVI (10 g∙kg[-1]), Cd (30 mg∙kg[-1]), and Cd-nZVI (30 mg∙kg[-1] Cd + 10 g∙kg[-1] nZVI). Survival rate, biomass, Cd bioaccumulation, enzyme activity, and other indicators were measured. On day 7 of exposure, reactive oxygen species (ROS) levels in the nZVI, Cd, and Cd-nZVI groups were 1.4-, 1.5-, and 1.6-fold higher than those in the control group, respectively (P < 0.05). Over time, both survival rate and biomass declined, with the lowest survival rate and greatest biomass loss observed in the Cd-nZVI group on day 28. Histological staining revealed that under Cd or nZVI stress, the circular muscle layer of the earthworms was loosened, intestinal tissue was partially detached, and the number of villi decreased. Metagenomic sequencing indicated significant alterations in the community structure of the earthworm intestinal microbiota under different treatments. Both 30 mg∙kg[-1] Cd and 10 g∙kg[-1] nZVI disrupted gut microbial balance, which was further exacerbated by combined exposure.},
}
@article {pmid41218435,
year = {2025},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}
@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
doi = {10.1371/journal.pone.0336700},
pmid = {41218045},
issn = {1932-6203},
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}
@article {pmid41217732,
year = {2025},
author = {Boutin, S and Klein, S and Untergasser, G and Loka, TP and Jakob, S and Caf, Y and Khatamzas, E and Knabl, L and Wrettos, G and Knobloch, H and Nurjadi, D},
title = {Evaluating Seqstant LiveGene Analysis in real-time assessment of metagenomic next-generation sequencing (mNGS) data from respiratory samples.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41217732},
issn = {1439-0973},
abstract = {BACKGROUND: The detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples.<br><br>METHOD: We used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results.<br><br>RESULTS: We observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant (&#x3b4;&#x2009;=&#x2009;10, &#x3b1;&#x2009;=&#x2009;0.05, 1&#x2009;-&#x2009;&#x3b2;&#x2009;=&#x2009;0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable, timely results, as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%.<br><br>CONCLUSION: Overall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detecting Aspergillus spp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.},
}
@article {pmid41217690,
year = {2025},
author = {Nguyen, HN and Kim, OTP and Tran, TT},
title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {11},
pages = {445},
pmid = {41217690},
issn = {1573-0972},
support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; },
abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.},
}
@article {pmid41217278,
year = {2025},
author = {Zhang, C and Chang, N and Yin, G and Shen, W and Lu, L and Bao, M and Guan, D and Zhang, S and Wang, R and Zhang, H},
title = {Drivers of Metal Resistance-Virulence Co-Selection in Landfill Leachates.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf275},
pmid = {41217278},
issn = {1365-2672},
abstract = {AIMS: Metal resistance genes (MRGs) and virulence factor genes (VFGs) are driven by environmental factors and host immunity, respectively, and they are traditionally considered to evolve independently. However, their co-selection dynamics in landfill leachates remain poorly characterized. In this study, a multi-regional metagenomic assessment integrating environmental gradients was first presented to reveal how heavy metals shape MRG-VFG interactions and associated ecological risks in landfill leachates.<br><br>METHODS AND RESULTS: Landfill leachates were collected from 13 landfills spanning six regions in China. Multi-regional metagenomic sequencing combined with co-occurrence network analysis was applied to examine pathogen-gene relationships. The results revealed pronounced regional disparities in pathogen, MRG, and VFG distribution, alongside shared features. Staphylococcus aureus and Pseudomonas aeruginosa were identified as dominant pathogens. tufA and gyrA emerged as conserved VFGs, whereas arsB and copA represented dominant MRGs. Network analysis revealed Escherichia coli, Salmonella enterica, and Acinetobacter baumannii as central nodes carrying overlapping functional genes, forming a "metal resistance-virulence" synergy module. Redundancy analysis revealed that specific heavy metals (Cu, Zn, Cr, and As) were crucial for the formation and stability of "pathogen-MRG-VFG" functional assemblies.<br><br>CONCLUSIONS: This study addresses a critical knowledge gap by integrating multi-regional metagenomic evidence with environmental selection pressures. MRGs conferred survival advantages and synergized with VFGs to enhance pathogen infectivity. These findings provide insight into MRG-VFG co-selection mechanisms in landfill leachates and guide targeted monitoring to mitigate environmental and health risks.},
}
@article {pmid41217198,
year = {2025},
author = {Valade, M and Le Bideau, M and Grimaldier, C and Boschi, C and Colson, P and La Scola, B},
title = {Development of cell combos micromethod to isolate respiratory viruses not detected by molecular techniques.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0257125},
doi = {10.1128/spectrum.02571-25},
pmid = {41217198},
issn = {2165-0497},
abstract = {Virological diagnosis of respiratory infections relies mainly on molecular methods but can be overlooked in cases of unexpected or unknown emerging viruses. In this case, modern approaches use mainly metagenomics without a priori. The other approach to detecting new viruses is based on their isolation in cell culture using virus-specific cells and culture conditions. Unfortunately, inoculation on several lines and metagenomics requires a large volume of clinical sample, while the initial sample has already been largely used to carry out multiplexed RT-PCR. Herein, we aimed to develop micro-methods to inoculate combos of cell lines to isolate respiratory viruses missed by molecular techniques. Ten cell lines were selected, and then five cell combos of two cell lines each were developed. Strains of 15 respiratory virus species were inoculated, and viral growth was assessed by cytopathic effect detection and RT-PCR assays. Among these, all grew on at least one combo. The Caco-2/MRC5 combo was the most promising. As proof-of-concept, 859 human respiratory samples found negative by multiplex RT-PCR panels were inoculated into these five cell combos and monitored for the appearance of cytopathic effects. The efficiency of this approach was evidenced by isolating 12 herpes simplex or varicella-zoster viruses not detected by respiratory multiplex PCR assays. In conclusion, this updated approach can detect known but, most importantly, likely emerging respiratory viruses. It could be used to investigate undiagnosed respiratory infection outbreaks especially if optimized with an approach allowing for the detection of viral multiplications with minor or no cytopathic effects.IMPORTANCEThe detection of respiratory viruses relies on a range of laboratory methods each of which has distinct advantages in terms of speed, practicality, and sensitivity. Current molecular methods for respiratory virus detection, such as multiplex PCR, may fail to identify unexpected, genetically divergent, or emerging viruses. This study presents an innovative approach using micromethods inoculating combinations of cell lines (cell combos) to enhance the isolation of a broad panel of respiratory viruses, including those undetected by standard molecular techniques. This strategy revives and modernizes classical virology techniques for use in contemporary diagnostics, particularly during unexplained respiratory outbreaks. It opens up new possibilities for detecting both known and unknown viruses across different sample types.},
}
@article {pmid41217051,
year = {2025},
author = {Alam, SS and Mehdi, A and Zafar, A and Ali, S and Rehman, AU and Liaqat, I and Peng, L and Kanwal, F and Afzal, S and Haq, IU and Aftab, MN},
title = {Advances in microbial biofuel production by metabolic and enzyme engineering, synthetic biology, metagenomics, and genome editing applications.},
journal = {Emerging topics in life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1042/ETLS20240002},
pmid = {41217051},
issn = {2397-8554},
abstract = {Microorganisms are the primary source of genetic diversity on earth due to their unparalleled metabolic and functional variability. With the depletion of fossil fuels, a sustainable alternative approach is the use of biofuels, where plant biomass as feedstock is essentially degraded to sugars with the aid of microbe-derived enzymes, followed by the conversion of those sugars to biofuels. Several cellulolytic and non-cellulolytic enzymes are involved in biofuel synthesis. Molecular cloning, along with the advancements in genetic and metabolic engineering in microbial cells, plays a significant contribution to biofuel overproduction. Advanced molecular technologies such as metagenomics and synthetic biology approaches are also being used to construct effective microorganisms for biofuel manufacturing. Obtaining novel enzymes from undiscovered microbial consortia and functional gene analysis is possible through a metagenomics approach. While synthetic biology provides engineered biological systems to generate required biofuel productivity, the CRISPR-Cas genome editing tool is another revolutionary tool being utilized for efficient biofuel production. This article provides a brief overview of different methods of biofuel production using microorganisms.},
}
@article {pmid41216332,
year = {2025},
author = {Facciotti, F and Di Stefano, G and Maragno, P and Ferraro, C and Dridi, D and Somigliana, E and Viganò, P and Vercellini, P and Casalechi, M},
title = {Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.},
journal = {Human reproduction open},
volume = {2025},
number = {4},
pages = {hoaf061},
pmid = {41216332},
issn = {2399-3529},
abstract = {STUDY QUESTION: What is the evidence available concerning gut and reproductive tract microbiomes in patients with endometriosis and what are the methodological approaches employed in microbiome studies on endometriosis?<br><br>SUMMARY ANSWER: The taxonomic profiles exhibited pronounced heterogeneity within women with and also within women without endometriosis across reviewed studies for all the anatomical districts evaluated.<br><br>WHAT IS KNOWN ALREADY: Both human and animal studies support differences in the microbiome composition of individuals with and without endometriosis. Endometriosis onset occurs with variable symptoms and manifestations. The microbiome composition at different sites may contribute to this variability.<br><br>STUDY DESIGN SIZE DURATION: We used the scoping review methodology. Systematic searches of studies from the PubMed, EMBASE, and Web of Science databases published between 1 January 2016 and 1 November 2024 addressing endometriosis microbiome characterization in: (i) gut, (ii) vaginal fluid, (iii) cervical fluid, (iv) peritoneal fluid, (v) uterine fluid, (vi) ovarian cyst fluid, (vii) oropharyngeal fluid, and (viii) eutopic and (ix) ectopic tissues were performed using a combination of MeSH terms. References from relevant publications were systematically screened.<br><br>Results were reported in accordance with the PRISMA-ScR guidelines. Studies that did not report original data, not written in English or providing a review of the field were excluded. From the 2182 publications retrieved, 36 papers were selected and analyzed, focusing on sample characterization (patients, controls, tissues, and fluids) and methodologies used.<br><br>Sound evidence is lacking to support a specific gut dysbiosis profile in women with endometriosis. The largest metagenome study performed using shotgun sequencing and controlling for multiple hypotheses testing did not detect significant differences between women with and without the disease. For eutopic and ectopic tissue microbiomes, the literature is too scant to draw any conclusion. Some data suggest a possible enrichment of Streptococcus sp. in cervical fluid and of Pseudomonas sp. in peritoneal fluid and a depletion of Lachnospira sp. in stool/anal fluid of endometriosis patients. However, these findings may be explained by confounders or by intrinsic patient or population characteristics. We appraised the limitations of the studies and proposed suggestions for optimizing sequencing techniques and experimental designs.<br><br>The number of participants per study greatly varied and, with few exceptions, was typically low. Incomplete information on methodological approaches was broadly observed. The impact of participants' menstrual cycle phase, diet, and drug assumption was frequently not considered.<br><br>Standardization of research protocols to allow reproducibility is required, as well as collaborations to harmonize data analysis, interpretation, and, more importantly, health outcome prediction or improvement.<br><br>The review was funded by the Italian Ministry of Health: RF-2019-12369460, and Current Research IRCCS. P.Vi. serves as co-editor in Chief of Journal of Endometriosis and Uterine Disorders. E.S. serves as Editor in Chief of Human Reproduction Open and discloses research grants from Ferring, Ibsa, Gedeon Richter, and Theramex, and honoraria from Ibsa and Gedeon Richter. P.Ve. serves as Associate Editor for Human Reproduction Open; is a member of the Editorial Board of the Journal of Obstetrics and Gynaecology Canada, of the Italian Journal of Obstetrics and Gynaecology, and of the International Editorial Board of Acta Obstetricia et Gynecologica Scandinavica; has received royalties from Wolters Kluwer for chapters on endometriosis management in the clinical decision support resource UpToDate; and maintains both a public and private gynecological practice. All other authors declare they have no conflict of interest.<br><br>REGISTRATION NUMBER: 10.17605/OSF.IO/X6HBT at https://osf.io/registries.},
}
@article {pmid41216322,
year = {2025},
author = {Li, C and Hou, J and Datry, T and Adyel, TM and Zhou, W and Wu, J and You, G and Jin, T and Deng, Y and Miao, L},
title = {How river drying influences greenhouse gas emissions: insights from species and gene shifts.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf187},
pmid = {41216322},
issn = {2730-6151},
abstract = {Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This mesocosm study investigated the greenhouse gas emissions fluxes and underlying mechanisms from benthic habitats prone to 20-100 days of drying. Results show that CO2 and N2O emissions from biofilms did not increase when drying increased, due to the changes in functional communities and genes. Notable is the transformation of biofilm from carbon source to sink following prolonged drying (mean emission fluxes ranged from 804.78 to -305.55 mg m[2] h[2]). This was mainly due to strong increases in the abundance of genes involved in the Calvin-Benson-Bassham cycle (2.82 × 10[-5] to 7.12 × 10[-5]), and functional taxa such as gemmatimonadota and pseudomonadota. These findings reveal a potential mitigation effect of drying on greenhouse gas emissions from rivers and streams, which could be relevant in the face of climate change.},
}
@article {pmid41216321,
year = {2025},
author = {Hawthorne, SEG and Tsola, SL and Carrión, O and Todd, JD and Eyice, &#xd6;},
title = {Active microorganisms and potential metabolic pathways mediating anaerobic degradation of DMSP in anoxic saltmarsh sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf180},
pmid = {41216321},
issn = {2730-6151},
abstract = {Dimethylsulfoniopropionate (DMSP) is a globally abundant organosulfur compound produced by marine organisms, where it plays key physiological roles in stress protection and serves as a major source of carbon, sulfur, and energy for microbial communities. Importantly, DMSP degradation contributes to the formation of the climate-active gas dimethyl sulfide (DMS), which can drive the production of potent greenhouse gases, methane and carbon dioxide, in anoxic environments. While aerobic DMSP degradation is well studied, its fate under anoxic conditions remains poorly understood, and the microbial populations and metabolic pathways underlying these biotransformations are virtually unknown. Here, we present the first detailed investigation of microbial DMSP cycling in anoxic saltmarsh sediments. Our sediment samples had high in situ DMSP concentrations (up to 7.7 μmol/g) and the conversion efficiencies of DMSP to DMS under anoxic conditions (~68%) were comparable to those in oxic environments. Furthermore, using [13]C-labelled DMSP in stable isotope probing (SIP) experiments, combined with 16S rRNA gene sequencing and metagenomics, we identified Amphritea (Oceanospirillales) as a key active DMSP degrader, likely operating via the dddD-encoded lysis pathway. Additional taxa, including Geopsychrobacter, were implicated as potential secondary consumers, while Arcobacteraceae may contribute to sulfur cycling rather than direct DMSP catabolism. This study uncovers a previously overlooked route for DMSP transformation via anaerobic metabolism, expands the known metabolic roles of saltmarsh microorganisms and highlights the potential for DMSP to drive climate-active gas production in anoxic coastal ecosystems.},
}
@article {pmid41216320,
year = {2025},
author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M},
title = {A global deep terrestrial biosphere core microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf176},
pmid = {41216320},
issn = {2730-6151},
abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.},
}
@article {pmid41216181,
year = {2025},
author = {Song, Z and Huang, T and Jiang, X and Hu, M and Wu, H and Wang, J},
title = {A case report of Staphylococcus saccharolyticus bloodstream infection in a non-implanted host diagnosed by mNGS: Mechanism and pathogenesis analysis.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02408},
pmid = {41216181},
issn = {2214-2509},
abstract = {BACKGROUND: Staphylococcus saccharolyticus is an obligate anaerobic skin commensal that is rarely implicated in bloodstream infections, particularly in immunocompetent individuals without implanted medical devices. Due to its low virulence and fastidious growth requirements, it is often overlooked or dismissed as a contaminant. This report describes a rare case of S. saccharolyticus bacteremia and explores the underlying pathogenic mechanism.<br><br>CASE PRESENTATION: A 50-year-old immunocompetent female presented with recurrent low-grade fever and oral mucosal ulceration. Pathogen detection was performed using plasma-based metagenomic next-generation sequencing (mNGS), which identified S. saccharolyticus at a relative abundance of 15&#x202f;% (seven species-specific reads). The result was corroborated by anaerobic blood culture. Laboratory assessment revealed severe vitamin D deficiency (25-hydroxyvitamin D: 11.6&#x202f;ng/mL). Initial treatment with ceftriaxone was ineffective. Following the initiation of intravenous moxifloxacin and oral vitamin D supplementation (cholecalciferol 2000 IU/day), the patient's fever resolved within five days, and high-sensitivity C-reactive protein (hsCRP) levels decreased markedly from 88.3&#x202f;mg/L to 12.0&#x202f;mg/L. Mechanistically, the combination of mucosal barrier disruption due to oral ulceration and vitamin D deficiency may have facilitated translocation of the anaerobic pathogen into the bloodstream.<br><br>CONCLUSIONS: This case underscores the diagnostic value of mNGS in detecting low-biomass anaerobic infections and proposes a synergistic "mucosal barrier disruption-pathogen translocation" model. It also highlights the potential role of host-directed adjunctive therapy in managing bloodstream infections not associated with prosthetic material.},
}
@article {pmid41215794,
year = {2025},
author = {Onile-Ere, O and Name, PE and Tibiri, EB and Tiendrébéogo, F and Pita, J and Mohammed, IU and Nkere, CK and Oranusi, S and Eni, A},
title = {Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112204},
pmid = {41215794},
issn = {2352-3409},
abstract = {The dataset presented here was obtained by sequencing selected historic herbarium cassava samples collected across Nigeria. Total DNA was extracted from the samples using the CTAB method, after which the samples were enriched by Rolling Circle Amplification (RCA) and then sequenced on the MinION. The dataset consists of raw sequencing data in FASTQ format reflecting microbial diversity in cassava leaf samples. Taxonomic classification of the samples using the Kraken2 PlusPFP-16 database revealed 12 kingdoms, 36 phyla, 67 classes, 154 orders, 273 families, 524 genera, and 895 species across the dataset, with a substantial proportion (77.9%) of reads remaining unclassified following host removal. The data is beneficial for exploring the microbiome diversity of cassava leaves across Nigeria, as well as serving as a reference for future microbial discovery, given the large number of unidentified reads in the dataset.},
}
@article {pmid41214992,
year = {2025},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Aldehyde metabolism in Maotai-flavor Baijiu: insights from integrated metagenomic and metaproteomic analyses.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117518},
doi = {10.1016/j.foodres.2025.117518},
pmid = {41214992},
issn = {1873-7145},
abstract = {Acetaldehyde and acetal are crucial to the flavor of Maotai-flavor Baijiu, affecting aroma release and sauce-aroma traits. Targeted control of acetaldehyde metabolic flux is critical for stabilizing base liquor quality. However, the diversity of acetaldehyde-metabolizing enzymes and their microbial drivers remain uncharacterized, critically impeding precision control. This study selected the third production round to systematically investigate acetaldehyde accumulation dynamics and metabolic mechanisms. Time-resolved profiling showed that acetaldehyde and acetal concentrations display an initial rise, followed by a decline and stabilization. By integrated metagenomic and metaproteomic analyses, we confirmed that the metabolic network comprised two biosynthetic and three conversion pathways. The dominant biosynthetic pathway featured pyruvate decarboxylase (PDC)-catalyzed decarboxylation, while ethanolamine ammonia-lyase contributed minimally. Among conversion pathways, NADH-dependent alcohol dehydrogenase (NADH-ADH) reduction to ethanol predominated, with lower-flux oxidation to acetate and acetyl-CoA. Dynamic enzyme profiling revealed that PDC activity preceded the activation of NADH-ADH during stacking fermentation, resulting in a temporal mismatch between aldehyde production and consumption, which led to metabolic retention. During pit fermentation, acetaldehyde was more efficiently converted to ethanol through upregulation of NADH-ADH and NADH/NAD[+] ratio. As main contributors of PDC and NADH-ADH, Schizosaccharomyces pombe and Saccharomyces cerevisiae exhibited dual regulatory roles in acetaldehyde metabolism, with their metabolic mode shifts governed by dissolved oxygen and the NADH/NAD[+] ratio. Microbial interaction analysis and simulated fermentation confirmed that Pichia kudriavzevii synergized with Saccharomyces cerevisiae and Schizosaccharomyces pombe, driving rapid acetaldehyde accumulation during the stacking fermentation. These findings establish a theoretical framework for optimizing brewing processes and enhancing base liquor quality.},
}
@article {pmid41214941,
year = {2025},
author = {Kahraman Ilıkkan, &#xd6; and Cerit, ZG and Baloglu, MC and Yılmaz, R},
title = {Microbial monitoring and Resistome analysis in white cheese production at a dairy plant: MALDI-TOF MS and shotgun metagenomics approaches.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117432},
doi = {10.1016/j.foodres.2025.117432},
pmid = {41214941},
issn = {1873-7145},
abstract = {This study presents a comprehensive microbiological evaluation of white cheese production in a small-scale dairy facility in northern Türkiye, integrating culture-dependent and culture-independent methods. Ten samples, including raw milk, milk with starter culture added, curd, clot, final cheese product, and environmental samples such as milk truck, cheese vessel, stirrer, cutting wire, and cheesecloth, were analyzed. Pathogenic bacteria were identified using MALDI-TOF MS, while shotgun metagenomics enabled a detailed investigation of microbial communities, antibiotic resistance genes (ARGs), and functional properties. The analysis using MALDI-TOF MS revealed ten pathogenic species, among which Staphylococcus aureus and Escherichia coli were the most dominant. Shotgun metagenomics corroborated the prevalence of S. aureus in dairy samples and Salmonella spp. on equipment surfaces, particularly the cheese vessel, stirrer, and cutting wire. The highest E. coli contamination was detected on cheesecloth, underscoring a critical point of concern. Across 15 antibiotic classes, 974 ARGs were identified, with equipment samples harboring significantly higher ARG loads than dairy products. Resistance mechanisms included β-lactamase enzymes, RND efflux pumps, and ribosomal protection proteins. Equipment samples showed an enrichment of carbohydrate-active enzymes (CAZymes), notably glycoside hydrolases and glycosyl transferases, suggesting microbial biofilm development and increased spoilage potential. Functional gene profiling revealed distinct metabolic signatures between dairy and equipment samples, with enriched pathways related to virulence and antimicrobial resistance in environmental samples. These findings underscore the limitations of conventional thermal treatment and the necessity of stringent sanitation practices, particularly for reusable equipment such as cheesecloth. The combined use of MALDI-TOF MS and shotgun metagenomics offers an effective strategy for microbial risk assessment in traditional cheese production systems.},
}
@article {pmid41214546,
year = {2025},
author = {Su, YS and Tsai, WH and Wu, HC and Chiu, YT and Jiang, NR and Lee, CY and Cheng, SH and Huang, CT and Chi, CY and Lin, EJ and Kuo, YP and Tsai, WT and Tien, CF and Liao, YC and Lee, KL and Chen, FJ and Yu, GY},
title = {Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1531},
pmid = {41214546},
issn = {1471-2334},
abstract = {BACKGROUND: Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are constrained by predefined targets, limiting their ability to detect novel or unexpected viral strains.<br><br>METHODS: We applied Oxford Nanopore Technology sequencing (ONT-Seq), a long-read, real-time, and multiplex metagenomic platform, to 85 clinical specimens using a sequence-independent, single-primer amplification (SISPA) workflow. Sequencing results were compared with routine clinical diagnostics for concordance and for identification of co-infections RESULTS: ONT-Seq achieved 80% concordance with clinical diagnostics and identified co-infections in 7% of cases missed by routine testing, including influenza C virus (ICV), and Sapporovirus. Among 58 adenovirus-positive cases, 31 samples with over 80% genome coverage at 20&#xd7; depth were used for phylogenetic analysis, revealing adenovirus B3 as the predominant circulating strain.<br><br>CONCLUSIONS: ONT-based metagenomic sequencing enhances the detection of both known and emerging viruses in clinical specimens. Its ability to provide real-time, unbiased data supports its utility in improving diagnostic accuracy and viral surveillance.<br><br>CLINICAL TRIAL: Not applicable.},
}
@article {pmid41212644,
year = {2025},
author = {Acosta, DJ and Barth, DR and Bondy, J and Appler, KE and De Anda, V and Ngo, PHT and Alper, HS and Baker, BJ and Marcotte, EM and Ellington, AD},
title = {Plastic degradation by enzymes from uncultured deep sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41212644},
issn = {1751-7370},
abstract = {Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are commonly identified in bacteria; however, pipelines for discovery are often biased to recover highly similar enzymes. Here, we searched metagenomic data from hydrothermally impacted deep sea sediments in the Guaymas Basin (Gulf of California) for PETases. A broad diversity of potential proteins were identified and 22 were selected based on their potential thermal stability and phylogenetic novelty. Heterologous expression and functional analysis of these candidate PETases revealed three candidates capable of depolymerizing PET or its byproducts. One is a PETase from a Bathyarchaeia archaeon (dubbed GuaPA, for Guaymas PETase Archaeal) and two bishydroxyethylene terephthalate-hydrolyzing enzymes (BHETases) from uncultured bacteria, Poribacteria, and Thermotogota. GuaPA is the first archaeal PETase discovered that is able to depolymerize PET films and originates from a specific enzyme class which has endowed it with predicted novel structural features. Within 48 h, GuaPA released ~3-5 mM of terephthalic acid and mono-(2-hydroxyethyl) terephthalate from low crystallinity PET. PET co-hydrolysis containing GuaPA and one of the newly discovered BHETases further improves the hydrolysis of untreated PET film by 68%. Genomic analysis of the PETase- and BHETase-encoding microorganisms reveals that they likely metabolize the products of enzymatic PET depolymerization, suggesting an ecological role in utilizing anthropogenic carbon sources. Our analysis reveals a previously uncharacterized ability of these uncultured microorganisms to catabolize PET, suggesting that the deep ocean is a potential reservoir of biocatalysts for the depolymerization of plastic waste.},
}
@article {pmid41212311,
year = {2025},
author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY},
title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {42},
pmid = {41212311},
issn = {1433-4909},
abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.},
}
@article {pmid41211992,
year = {2025},
author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y},
title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0163724},
doi = {10.1128/jvi.01637-24},
pmid = {41211992},
issn = {1098-5514},
abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.},
}
@article {pmid41211985,
year = {2025},
author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O},
title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/msystems.01247-25},
pmid = {41211985},
issn = {2379-5077},
abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.},
}
@article {pmid41211947,
year = {2025},
author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A},
title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054325},
doi = {10.1128/msphere.00543-25},
pmid = {41211947},
issn = {2379-5042},
abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.},
}
@article {pmid41211940,
year = {2025},
author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ},
title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70101},
pmid = {41211940},
issn = {1529-8817},
support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; },
abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.},
}
@article {pmid41211921,
year = {2025},
author = {Wang, Q and Bao, H},
title = {Integrated metagenomics and metabolomics reveal the dynamic mechanism in the rhizosphere soil of Morus alba L. and Fraxinus mandshurica Rupr. with Inonotus hispidus.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0125125},
doi = {10.1128/aem.01251-25},
pmid = {41211921},
issn = {1098-5336},
abstract = {Inonotus hispidus is a medicinal fungus that grows on Morus alba L., Fraxinus mandshurica Rupr., and Ziziphus jujuba Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in the rhizosphere soil of different tree species, specifically M. alba and F. mandshurica, growing with I. hispidus. Therefore, this study conducts a multi-omics joint analysis utilizing metagenomics and metabolomics to explore the differences in the synergistic mechanisms between different hosts of I. hispidus. Using metagenomics technology, a total of 177 phyla and 2,651 genera were identified as significantly different. At both the phylum and genus levels, Actinomycetota and Pseudomonadota as well as Solirubrobacter and Bradyrhizobium emerged as the predominant phyla and genera, respectively. In the Kyoto Encyclopedia of Genes and Genomes database, carbohydrate and amino acid metabolisms were identified as the primary metabolic pathways. Differential analysis of these metabolic pathways revealed that glucokinase and pyruvate kinase were downregulated. Additionally, metabolomics analysis identified 558 differential metabolites, with tyrosine metabolism being the foremost metabolic pathway involved. This pathway included five differential metabolites, among which salidroside, 3,4-dihydroxyphenylpropanoate, rosmarinate, and homovanillate were significantly upregulated in M. alba in association with I. hispidus. Furthermore, correlation analysis indicated that Enhydrobacter was positively correlated with 10 differential metabolites, while Gaiella, Haladaptatus, Jiangella, and Prauserella showed negative correlations. This study lays a solid foundation for elucidating the interactions between I. hispidus and its hosts, as well as for the effective utilization of I. hispidus resources across different tree species.IMPORTANCEInonotus hispidus, which is traditionally recognized as the authentic source of the medicinal fungus, primarily grows on Morus alba L. It is commonly found in ancient regions along the Yellow River, including Linqing, Xiajin, and Wudi in Shandong, as well as Chengde in Hebei Province and Aksu in Xinjiang. In traditional Chinese medicine, it is known as "Sanghuang" and has a long history of medicinal use. In addition to M. alba, I. hispidus also grows on other broad-leaved species, such as Ulmus macrocarpa, Acer truncatum, and Fraxinus mandshurica. The lack of fundamental research on its multi-host and -source diversity has hindered its industrial development and medicinal value. Consequently, this study employs metagenomics and metabolomics to investigate the rhizosphere soil microbial diversity and differential metabolites associated with the different host plants of I. hispidus, specifically M. alba and F. mandshurica, with the aim of providing a reference for its resource conservation and development.},
}
@article {pmid41211880,
year = {2025},
author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ},
title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf592},
pmid = {41211880},
issn = {1477-4054},
support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China/ ; WU2022A009//National Natural Science Foundation of China/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //InnoHK program and Ant Group through CAAI-Ant Research Fund/ ; },
abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.},
}
@article {pmid41211879,
year = {2025},
author = {},
title = {Retraction and replacement of: FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf591},
pmid = {41211879},
issn = {1477-4054},
}
@article {pmid41210936,
year = {2025},
author = {Xu, Y and Miao, J and Chen, J and Ye, L and Yang, K and Wang, H},
title = {Metagenomic next-generation sequencing facilitates precision treatment and prognostic improvement in pulmonary cryptococcosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638215},
pmid = {41210936},
issn = {2235-2988},
abstract = {BACKGROUND: The early diagnosis of pulmonary cryptococcosis (PC) remains challenging due to the low sensitivity and prolonged turnaround time of conventional diagnostic methods. Despite the broad-spectrum pathogen detection capability of metagenomic next-generation sequencing (mNGS), its clinical utility in the diagnosis and therapeutic management of pulmonary cryptococcosis remains underexplored.<br><br>METHODS: In this retrospective study, 31 patients diagnosed with Cryptococcus infection through mNGS at The First Affiliated Hospital of Zhengzhou University between July 2023 to March 2025 were included. data on clinical characteristics, treatment regimens, and patient prognosis were systematically collected.<br><br>RESULTS: Compared to conventional pathogen detection methods, mNGS demonstrated superior sensitivity, shorter turnaround time (1.00 d vs. 4.50 d, p = 0.002), and significantly reduced interval from admission to clinical decision-making (3.50 d vs. 9.00 d, p = 0.002). Among 31 patients with mNGS-identified cryptococcal infection, only 12 underwent fungal culture, with merely 1 case yielding positive results (positivity rate: 8.33%). Antimicrobial therapy was optimized for all patients based on mNGS findings. During post-discharge follow-up of 27 cases, 1 patient experienced disease recurrence, 1 died from tumor metastasis, and 1 was lost to follow-up.<br><br>CONCLUSION: Our retrospective analysis revealed that mNGS facilitated treatment optimization, improved clinical outcomes, and provided crucial evidence supporting the precision management of pulmonary cryptococcosis.},
}
@article {pmid41210414,
year = {2025},
author = {Hu, L and Li, S and Gao, F and Diao, S and Liu, X and Qiu, J},
title = {Silent Threat: Multi-Organ Failure in Neonatal Scrub Typhus Without Traditional Markers.},
journal = {Clinical case reports},
volume = {13},
number = {11},
pages = {e71352},
pmid = {41210414},
issn = {2050-0904},
abstract = {Scrub typhus, an acute zoonotic disease from Orientia tsutsugamushi, is uncommon in newborns and presents atypical symptoms. Untimely diagnosis and treatment can lead to a prolonged and potentially fatal course. Early diagnosis and treatment are essential for better patient outcomes. Metagenomic next-generation sequencing can rapidly and accurately diagnose pathogens, aiding precise treatment.},
}
@article {pmid41210074,
year = {2025},
author = {Lin, L and You, W and Liao, Y and Wu, B and Lin, H and Huang, Z and Zeng, J and Zhang, Z and Huang, C and Li, W and Fang, X},
title = {Impact of Antibiotic Exposure Duration on Pathogen Detection in Periprosthetic Joint Infection.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5661-5670},
pmid = {41210074},
issn = {1178-6973},
abstract = {OBJECTIVE: Antibiotic exposure affects pathogen detection in periprosthetic joint infection (PJI). This study evaluated the impact of antibiotic duration before sampling on the diagnostic performance of microbiological cultures and metagenomic next-generation sequencing (mNGS).<br><br>METHODS: We conducted a retrospective analysis of 153 patients with PJI treated at our center between January 2013 and March 2024. Patients who had discontinued antibiotics for at least 7 days before sampling and those with no history of antibiotic use were classified into the antibiotic-withdrawal group (AWD group). Based on the duration of antibiotic exposure, those who received antibiotics for &#x2264;7 days before sampling was assigned to the short-term antibiotic group (STA group), while those with >7 days of continuous antibiotic use were included in the long-term antibiotic group (LTA group). By comparing microbiological culture and mNGS results across these groups, we analyzed how antibiotic duration before sampling affects etiological diagnosis in PJI patients.<br><br>RESULTS: In the AWD group, microbial culture positivity (86.3%, 44/51) was comparable to mNGS (92.2%, 47/51; P=0.338). However, mNGS demonstrated superior positivity rates in both the STA (86.7% vs 70.0%, P=0.027) and LTA groups (76.2% vs 54.8%, P=0.039). Prolonged antibiotic use (>7 days) markedly reduced culture positivity (86.3% to 54.8%, P=0.001), whereas the decline in mNGS sensitivity was smaller (92.2% to 76.2%, P=0.032), indicating its greater resistance to antibiotic effects. Among culture-negative PJI cases, mNGS maintained robust diagnostic performance across all groups (CN-AWD: 57.1%; CN-STA: 66.7%; CN-LTA: 57.9%), with no significant differences observed.<br><br>CONCLUSION: Antibiotic use before sampling significantly impacts PJI pathogen detection. We recommend either: (1) sampling after &#x2265;7 days without antibiotics, or (2) for patients on prolonged antibiotics (>7 days), combining microbial culture with routine mNGS to improve diagnostic accuracy.},
}
@article {pmid41209715,
year = {2025},
author = {Yadav, P and Kumar, A and Ram, K and Kumar, A and Gupta, RK and Dufossé, L},
title = {Microbial degradation of microplastics: Effectiveness, challenges, and sustainable solutions.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100495},
pmid = {41209715},
issn = {2666-5174},
abstract = {Microplastics (MPs), defined as plastic particles ranging from 1 µm to 5 mm, have emerged as pervasive contaminants in both terrestrial and aquatic environments, posing significant ecological and human health risks. Their sources are broadly categorized as primary, such as microbeads, microfibres, paints and pharmaceutical additives, and secondary, which result from the degradation of larger plastic products. This growing concern of MPs led to development of different mitigation techniques but the recent advancements in microbial biodegradation present a promising approach to mitigating MPs pollution. Thus, microbial biodegradation could play a crucial role in developing sustainable solutions to tackle global MPs pollution. This review explores the potential of various microorganisms, including bacteria, fungi, and algae, in degrading MPs through enzymatic processes, thereby shortening the half-life of these pollutants. A detailed examination of the degradation mechanisms of commonly used polymers such as polyethylene, polystyrene, and polyvinyl chloride highlights the efficacy and limitations of microbial biodegradation. Despite the promising capabilities of certain strains, the overall weight loss rate of MPs remains quite low, typically ranging from 0 to 15%, necessitating further investigation into optimizing enzymatic activity and environmental conditions. Advancements in metagenomics and enzyme engineering offer pathways to enhance degradation efficiency, potentially achieving up to 90% degradation within 10 hrs under optimized conditions. This review underscores the need for comprehensive research to identify key microbial strains and enzymes involved, understand their degradation pathways, and investigate the influence of different environmental matrices on biodegradation processes.},
}
@article {pmid41208101,
year = {2025},
author = {Paul, JK and Akter, A and Jewel, NA and Rolin, MH and Karim, D and Niloy, RK and Mondal, SI},
title = {Exploration of Human Skin Phageome to Reveal Endolysins and Novel Antimicrobial Peptides for Therapeutic Applications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70115},
doi = {10.1002/mbo3.70115},
pmid = {41208101},
issn = {2045-8827},
support = {//The study was supported by the SUST Research Center (Grant number: LS/2023/1/05)./ ; },
abstract = {The global rise of antibiotic-resistant pathogens has intensified the search for alternative therapeutics. Bacteriophage-derived endolysins are emerging as promising candidates. They exhibit strong potential due to their target specificity, rapid bactericidal action, and low tendency to induce bacterial resistance. This study presents a comprehensive metagenomic analysis of the human skin phageome using 1564 samples from 10 metagenomic projects. Our analysis led to the classification of 696 phage genomes into clusters and singletons. These genomes displayed considerable variation in size, GC content (average 56%), and coding efficiency (72%). A total of 968 endolysins were identified, including 75 SAR variants, with diverse domain architectures such as CHAP, Amidase, and SH3, suggesting host-specific adaptations. Notably, we identified 37 previously unreported endolysin-derived antimicrobial peptides (AMPs), several of which exhibited nontoxic, antifungal, and antiviral properties. Molecular dynamics and docking studies revealed strong binding affinity and stability of peptides EP-464 and EP-519 to key virulence factors, including Staphylococcus epidermidis autolysin (PDB: 4EPC), beta-lactamase VIM-2 (PDB: 5O7N), and AHL synthase LasI (PDB: 1RO5). These interactions suggest potential for disrupting bacterial virulence, resistance mechanisms, and quorum sensing. This study provides the first large-scale functional characterization of the human skin phageome focused on therapeutic endolysins and their novel AMP derivatives, offering promising candidates for the development of next-generation antimicrobial agents. However, further experimental validation is essential to assess their clinical efficacy in treating skin-related infections.},
}
@article {pmid41207803,
year = {2025},
author = {You, TY and Chen, YW and Chen, SY and Jan, HE and Lee, NY and Ko, WC},
title = {Etiological identification of Rickettsia typhi and Coxiella burnetii by metagenomic next-generation sequencing among adults with acute febrile illness in southern Taiwan.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2025.11.012},
pmid = {41207803},
issn = {0929-6646},
}
@article {pmid41207298,
year = {2025},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1152},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}
@article {pmid41207243,
year = {2025},
author = {Kumalo, PC and Amoah, ID and Pierneef, RE and Ismail, A and Bux, F and Kumari, S},
title = {Unveiling the role of aeration systems in the bioaerosol emission rate, particle size and microbial composition from wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140394},
doi = {10.1016/j.jhazmat.2025.140394},
pmid = {41207243},
issn = {1873-3336},
abstract = {Wastewater treatment plants (WWTPs) are important sources of bioaerosols; however, the influence of aeration on emission characteristics, particle size distribution, and microbial composition remains poorly studied. This study investigates how surface aeration (SA) and diffused aeration (DA) systems affect bioaerosol emission rates, particle size distribution, and microbial diversity using an 8-stage Andersen cascade impactor and shotgun metagenomics. Bioaerosol emission rates were estimated by combining measured particle concentrations with system-specific airflow rates. Abiotic factors were analysed through redundancy analysis to determine their influence on community structure. SA consistently generated higher emission rates, particularly in respirable particles (0.43-2.1 µm), which are capable of deep respiratory deposition. Dominant taxa included Rhodococcus, Pseudomonas, Bacillus, Meyerozyma, and Siphoviridae, with SA showing higher relative abundance of opportunistic pathogens even in smaller particle sizes. In contrast, DA systems exhibited a lower emission rate but broader microbial diversity, reflecting more stable aeration conditions. The study indicated that activated sludge was the main source of microbial populations, with a larger bioaerosol -activated sludge overlap in SA than DA. Redundancy analysis revealed that wind speed (WS) and relative humidity (RH) significantly influenced bacterial and viral populations, while WS and air temperature (AT) affected eukaryotes. Notably, SA emissions decreased with distance (100 m), while DA emissions increased. By quantifying emission rates rather than concentrations and integrating high-throughput metagenomics, this study provides a comprehensive framework for characterising bioaerosol hazards in WWTPs. These findings highlight the need for mitigation strategies in WWTPs, especially near SA systems.},
}
@article {pmid41207031,
year = {2025},
author = {Ren, Y and Li, Y and Lei, Y and He, R and Fu, J and Ma, D and Zhong, G},
title = {Deciphering microbial and metabolite dynamics in rice noodle fermentation: A metagenomic and untargeted metabolomic approach.},
journal = {Food chemistry},
volume = {497},
number = {},
pages = {147011},
doi = {10.1016/j.foodchem.2025.147011},
pmid = {41207031},
issn = {1873-7072},
abstract = {Inoculated fermentation accelerates rice noodle production and improves quality, but the underlying microbe-metabolite dynamics remain unclear. This study employed metagenomic and non-targeted metabolomic profiling to investigate microbial succession and metabolic transformations during fermentation. Lacticaseibacillus rhamnosus, Lactococcus cremoris, and Saccharomyces cerevisiae were identified as dominant strains, with Lacticaseibacillus rhamnosus rapidly outcompeting other microbes and suppressing Klebsiella pneumoniae and Salmonella enterica by over 70 %. At 6 h, rice noodle hardness and springiness improved markedly, driven by microbial shifts and metabolic outputs. Metabolomic analysis identified 1405 metabolites, of which 57 showed significant changes: aspartic and citric acid levels declined by 14.99 % and 33.16 %, while citrulline, γ-aminobutyric acid, lactate, and Cinnamic acid increased by 16.38 %, 8.96 %, 70.69 %, and 63.90 %, respectively. Enzyme annotation indicated α-amylase and glycogen synthase regulate starch degradation and amylose synthesis. These findings provide insights into the microbial and metabolic mechanisms that enhance the quality of fermented rice noodles.},
}
@article {pmid41206939,
year = {2025},
author = {Yu, H and Xu, Y and Chen, D and Gong, M and Sun, W and Liu, M and Zhang, T and Xue, J},
title = {The application of mNGS of bronchoalveolar lavage fluid in dissecting pulmonary infections in patients with CTD-ILD.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf571},
pmid = {41206939},
issn = {1462-0332},
abstract = {OBJECTIVES: To evaluate the application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of pulmonary infection in patients with connective tissue disease-associated interstitial lung disease (CTD-ILD).<br><br>METHODS: Patients with CTD-ILD who had been evaluated for suspected pulmonary infection by mNGS of BALF were identified, and were then categorized either as pulmonary infection or non-infectious disease progression of CTD-ILD based on clinical composite assessment. The performance of mNGS in the diagnosis of pulmonary infection was compared with that of conventional microbiological tests (CMTs).<br><br>RESULTS: In the 48 patients with CTD-ILD who had been evaluated for pulmonary infection by mNGS of BALF, the majority (66.67%) were patients with idopathic inflammatory myopathy-associated ILD (IIM-ILD). According to the clinical composite assessment, 36 patients were classified as pulmonary infection and 12 as non-infectious disease progression. Cytomegalovirus (CMV), pneumocystis jirovecii, and aspergillus were among the most common causative pathogens. While mNGS was superior in identifying bacteria, viruses, and pneumocystis jirovecii, CMTs identified more aspergillus and cryptococcus. Decreased albumin, reduced immunoglobulin M, and increased lactate dehydrogenase (LDH) were predictors for pulmonary infections in CTD-ILD. Short disease duration, decreased lymphocytes, and reduced immunoglobulins were predictive of infection with pneumocystis jirovecii. Older age and increased serum ferritin were more common in patients with aspergillus infection.<br><br>CONCLUSION: Pulmonary infections are common in patients with CTD-ILD. mNGS has the advantages of rapidly detecting more bacteria, viruses, and pneumocystis jirovecii. However, infection with aspergillus should be more rigorously evaluated in combination with CMTs.},
}
@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.<br><br>HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.<br><br>SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}
@article {pmid41206740,
year = {2025},
author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP},
title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf056},
pmid = {41206740},
issn = {1574-6976},
abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.},
}
@article {pmid41206659,
year = {2025},
author = {Siddiqui, R and Maciver, SK and Khan, NA},
title = {Beyond Predation: Potential Metabolic Roles of Intracellular Bacteria in Acanthamoeba Ecology.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf124},
pmid = {41206659},
issn = {1574-6968},
abstract = {Although Acanthamoeba is well known as a reservoir and "Trojan horse" for other microbes, its relationship with intracellular organisms may extend beyond protection. Here, we discuss that certain bacteria contribute metabolically to the host, breaking down complex substrates and providing nutrients that expand its ecological adaptability. The proposed model reframes amoebae not only as predators and shelters, but also as metabolic consortia, with implications for environmental microbiology, protist ecology, and the evolution of opportunistic pathogens. Further studies using integrated multi-omics and co-culture approaches, combining metagenomic and metabolomic profiling of Acanthamoeba-bacteria interactions and transcriptomic analyses will help identify bidirectional metabolic exchange and functional gene expression within the symbiosis.},
}
@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}
@article {pmid41205488,
year = {2025},
author = {Lv, AP and Ying-Han, and Fang, BZ and Wang, GZ and Liu, MC and Bian, BR and Zheng, ZH and Li, K and Li, BY and Jiao, JY and Liu, L and Dong, L and Chen, LQ and Yang, F and Li, WJ},
title = {Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {6},
pages = {126667},
doi = {10.1016/j.syapm.2025.126667},
pmid = {41205488},
issn = {1618-0984},
abstract = {Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus Pseudogracilibacillus. Phylogenomic analysis demonstrated that three MAGs (A3-12A_bin_9[TS], M2-6-2A_bin_27 and M2-7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus Pseudogracilibacillus. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name Pseudogracilibacillus amylolyticus sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family Bacillaceae in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.},
}
@article {pmid41205408,
year = {2025},
author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J},
title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.},
journal = {Journal of neuroradiology = Journal de neuroradiologie},
volume = {53},
number = {1},
pages = {101402},
doi = {10.1016/j.neurad.2025.101402},
pmid = {41205408},
issn = {0150-9861},
abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.<br><br>MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.<br><br>RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (&#x3b2; =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (&#x3b2; =-0.003), CRP (&#x3b2; =-0.035), SII (&#x3b2; =-0.062), INFLA (&#x3b2; =-0.010), and SIRI (&#x3b2; =-0.058). We also observed significant correlations between DKI ALPS index and ESR (&#x3b2; =-0.006), CRP (&#x3b2; =-0.051), SII (&#x3b2; =-0.130), INFLA (&#x3b2; =-0.017), SIRI (&#x3b2; =-0.095), IL-6 (&#x3b2; =-0.081) and NLR (&#x3b2; =-0.108).<br><br>CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.},
}
@article {pmid41205292,
year = {2025},
author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA},
title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118904},
doi = {10.1016/j.marpolbul.2025.118904},
pmid = {41205292},
issn = {1879-3363},
abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.},
}
@article {pmid41205042,
year = {2025},
author = {Zolkefli, N and Shui, X and Ma, K and Mustapha, NA and Maeda, T},
title = {Unveiling the Impact of Indole Derivatives on Methanogenic Archaea and Microbial Functions in Anaerobic Digestion of Waste Sewage Sludge.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41205042},
issn = {1559-0291},
abstract = {As an interspecies-signaling molecule, indole that is also regulating the microbial community quorum sensing (QS) can be an indispensable factor in influencing the performance of an anaerobic digestion process. Mainly released by Gram-negative bacteria, the impact of indole regulation on methane production in such a system is hardly exposed. This research intends to analyze the methane production affected by the microbial community fluctuations in the waste sewage sludge (WSS) in response to QS repression by indole and its analogs: 4-fluoroindole (4-FI), 5-fluoroindole (5-FI), 6-fluoroindole (6-FI), 3-indoleacetic acid (3-IAA), and 3-indoleacrylic acid (3-IARA). Illumina MiSeq platform was utilized to delve into the active microbes, with ribonucleic acid (RNA) used as the template to generate the 16S metagenomic library. As results, all of them inhibit methane generation even with substrates (acetic acid) availability, and this phenomenon can be led by the slight imbalance of Gram-positive/negative bacterial composition and the inactivation of the viable core fermenters: Firmicutes, Proteobacteria, and Chloroflexi. Plus, the following compounds, indole, 3-IAA, and 6-FI directly disrupted methane production by both acetoclastic and hydrogenotrophic methanogenic archaea. Methanosarcina acetivorans C2A, as a prominent methane synthesizer, was also characterized in terms of its viability and methane synthesis activity against them. Notably, Methanosarcina acetivorans C2A was non-viable in the presence of indole and 6-FI, thus lowering methane production. From here, the affirmation of the direct and indirect inhibitions of methanogenic archaea by indole and its derivatives will pave the way for a valuable future exploration of QS mechanism mapping in archaea during methanogenesis.},
}
@article {pmid41204634,
year = {2025},
author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q},
title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.},
journal = {Journal of food science},
volume = {90},
number = {11},
pages = {e70654},
doi = {10.1111/1750-3841.70654},
pmid = {41204634},
issn = {1750-3841},
support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; },
abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.},
}
@article {pmid41204581,
year = {2025},
author = {Zhuang, Q and Xu, R and Sun, X and Pan, X and Wan, L and Li, S and Chen, H and Yu, X and Zheng, L and Yu, Y and Deng, Z and Zheng, X and Chen, Z},
title = {Performance of metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen detection in patients with acute exacerbations of bronchiectasis.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45606},
doi = {10.1097/MD.0000000000045606},
pmid = {41204581},
issn = {1536-5964},
support = {FYQM-LC-202003//The Affiliated Hospital of Medical School of Ningbo University Youth Talent Cultivation Program/ ; 2021Y13//Ningbo Medical Science and Technology Program/ ; 2015C50012//Ningbo Social and Scientific Development Fund/ ; 2020SWSQNGG-05//Ningbo Health Youth Technical Key Talents Training Special Project/ ; 2018A610271&#xe3;&#x20ac;2017A610250//the Natural Science Foundation of Ningbo/ ; 2022ZYC-Z31//Clinical Medicine Special Fund Project of Zhejiang Medical Association/ ; Normal project No.6//Special Project on Scientific and Technological Research of COVID-19 Infection Diseases/ ; 2016KYB268//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; },
mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Pseudomonas aeruginosa/isolation &amp; purification ; Sensitivity and Specificity ; },
abstract = {This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in detecting pathogens among bronchiectasis patients with acute exacerbations. A retrospective analysis was conducted on 89 bronchiectasis patients who were treated for acute exacerbations at the First Affiliated Hospital of Ningbo University from April 1, 2021, to September 30, 2023. Among the 89 patients, 88 were diagnosed with pulmonary infection, of which 15.9% (14/88) were cases of mixed infections. The sensitivity of BALF-mNGS for detecting pathogens in bronchiectasis patients during acute exacerbations was significantly higher than that of BALF culture (93.2% vs 28.4%; P < .001). All cases of mixed infection were fully identified by BALF-mNGS. The most common pathogens in patients with bronchiectasis were Pseudomonas aeruginosa, nontuberculous mycobacteria, Haemophilus influenzae, and Aspergillus. In conclusion, compared with the traditional microbial culture method, BALF-mNGS significantly improves the accuracy of diagnosis for detecting pathogens associated with bronchiectasis infections.},
}
@article {pmid41204496,
year = {2025},
author = {Tian, J and Dong, J and Yu, G and Guan, W},
title = {Bronchoscopy-associated dissemination of pulmonary nocardiosis caused by Nocardia terpenica in an immunocompetent patient with bronchiectasis: A case report.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45875},
doi = {10.1097/MD.0000000000045875},
pmid = {41204496},
issn = {1536-5964},
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/etiology/microbiology ; Middle Aged ; *Bronchoscopy/adverse effects ; *Bronchiectasis/complications ; *Nocardia/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Bronchoalveolar Lavage/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration &amp; dosage ; Bronchoalveolar Lavage Fluid/microbiology ; Immunocompetence ; },
abstract = {RATIONALE: Bronchoscopy with bronchoalveolar lavage (BAL) is essential for diagnosing pulmonary infections; however, its potential to iatrogenically disseminate a localized Nocardia infection represents a severe and unreported risk. This case aims to alert clinicians to this danger and underscore essential therapeutic lessons for disseminated disease.<br><br>PATIENT CONCERNS: A 51-year-old immunocompetent woman with longstanding bronchiectasis presented with 1-day of hemoptysis and a 40-year history of chronic cough and sputum production. These symptoms had worsened over the preceding 2 months despite broad-spectrum antibiotic therapy.<br><br>DIAGNOSES: Bronchiectasis was diagnosed based on chronic respiratory symptoms and characteristic computed tomography findings. Nocardia terpenica infection was confirmed by BAL fluid culture and metagenomic next-generation sequencing. Within 24 hours post-BAL, the patient developed fever, respiratory failure, and new bilateral consolidations on computed tomography, indicating procedure-related disseminated nocardiosis.<br><br>INTERVENTIONS: Diagnostic bronchoscopy with BAL was performed. Therapeutically, the patient received a total of 24 days of intensive combination therapy with intravenous imipenem/cilastatin and oral trimethoprim-sulfamethoxazole (TMP-SMX), followed by sequential long-term oral TMP-SMX monotherapy.<br><br>OUTCOMES: The initial 10-day course of combination therapy led to rapid clinical improvement, with resolution of fever and respiratory failure within 3 days, and normalization of C-reactive protein levels by day 10. Radiographic improvement was also evident. However, relapse (recurrent fever and malaise) occurred promptly within 3 days after de-escalation to TMP-SMX monotherapy. After reinstitution of imipenem/cilastatin plus TMP-SMX for an additional 14 days (totaling 24 days of intensive therapy), the patient achieved sustained clinical and radiographic remission. She was successfully discharged on long-term TMP-SMX monotherapy and remained well at the 2-month follow-up.<br><br>LESSONS: This is the first report suggesting that bronchoscopy, particularly BAL, can disseminate a localized airway Nocardia infection, causing acute disseminated pulmonary nocardiosis. Extreme caution is warranted when performing bronchoscopy in bronchiectasis patients with suspected or confirmed nocardiosis. For disseminated pulmonary nocardiosis, intensive combination therapy for at least 3 weeks is mandatory to prevent relapse, regardless of a rapid initial response.},
}
@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}
@article {pmid41203352,
year = {2025},
author = {Tonoli, A and Dalby, PA and Hailes, HC and Jeffries, JWE},
title = {Transketolase enzyme discovery and engineering.},
journal = {Methods in enzymology},
volume = {722},
number = {},
pages = {343-368},
doi = {10.1016/bs.mie.2025.07.002},
pmid = {41203352},
issn = {1557-7988},
mesh = {*Transketolase/genetics/metabolism/chemistry/isolation &amp; purification ; Substrate Specificity ; *Protein Engineering/methods ; Directed Molecular Evolution/methods ; Ribosemonophosphates/metabolism ; Metagenomics/methods ; Pyruvates ; },
abstract = {Transketolases (TKs) are important C-C bond forming enzymes that in vivo transfer a two carbon ketol unit to the acceptors d-ribose-5-phosphate or d-erythrose-4-phosphate. There is significant interest in biocatalytic applications where frequently the donor β-hydroxypyruvic acid is used. In recent years there has been interest in the discovery of new TKs with unique or robust properties that are an excellent starting point for mutagenesis, or that are able to accept new acceptors or donors. Similarly, TK mutagenesis has led to TKs with alternative substrate profiles. In this chapter, firstly an overview of the substrates accepted by TKs is briefly summarized. Then, metagenomic strategies for the discovery of unique TKs and how this approach has developed with an early example, and a more recent study on the discovery of 'split'-TKs, are described with methods. Finally, enzyme evolution methods and approaches to develop a wide range of TKs with modified substrate acceptance and improved stabilities are detailed.},
}
@article {pmid41203168,
year = {2025},
author = {Vangah, SJ and Kermani, AA and Vali, H and Noghabi, KA and Zahiri, HS},
title = {Engineering Saccharomyces cerevisiae for the secretion of an acidic, halotolerant, and cold-adapted xylanase derived from the camel rumen metagenome: Enzyme characterization and strain assessment.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148805},
doi = {10.1016/j.ijbiomac.2025.148805},
pmid = {41203168},
issn = {1879-0003},
abstract = {This study reports the development of a recombinant Saccharomyces cerevisiae strain engineered to produce and secrete a novel xylanase (rXylM) derived from the camel rumen metagenome. The recombinant enzyme exhibited optimal activity at 35 °C, pH 5.0, and retained 58 % of its activity even at 5 °C. The enzyme activity was not significantly affected by high sodium chloride (NaCl) concentrations up to 5 M. These properties characterize rXylM as an acidic, halotolerant, and cold-adapted xylanase. The combination of these adaptive traits in a single enzyme offers substantial advantages for industrial applications. Enzyme kinetic analysis was performed at 35 °C and pH 5.0 using beechwood xylan, wheat bran, and high-extraction wheat flour as substrates, yielding specific activities of 1190 U/mg, 1029 U/mg, and 383 U/mg respectively. Scanning electron microscopy (SEM) revealed noticeable morphological alterations indicating substantial degradation of the substrates following treatment with rXylM. The engineered strain, CEN.PK-Xyl, was assessed as a leavening agent for baking applications. Rheological analysis of the dough demonstrated a significant reduction in elasticity and viscous resistance, improving dough handling and kneading properties. Correspondingly, the resulting bread exhibited a significant decrease in hardness, gumminess, and chewiness, indicating an improvement in texture and overall quality. Cytotoxicity evaluation using the MTT assay showed that rXylM did not affect the viability of L929 mouse fibroblast cells under the tested conditions. The favorable biochemical properties and non-toxicity of rXylM, together with the established safety of S. cerevisiae, highlight CEN.PK-Xyl as a promising platform for applications in food, feed, bioprocessing, and fermentation.},
}
@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}
@article {pmid41202935,
year = {2025},
author = {Wu, B and Cheng, Y and Gu, J and Yuan, H and Murphy, JD},
title = {Toward sustained and efficient n-caproate production: Insights into magnetite-encapsulated biochar mediated microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133617},
doi = {10.1016/j.biortech.2025.133617},
pmid = {41202935},
issn = {1873-2976},
abstract = {Decarbonization of the chemical sector may be facilitated by microbial chain elongation, through conversion of organic waste into chemical products. Challenges in efficient interspecies electron transfer is a barrier to this technology. Here we introduce a magnetite-encapsulated biochar (Fe@biochar) amendment strategically integrated with chain elongation to facilitate sustained and efficient n-caproate production. This strategy increased n-caproate yields to 13.92 g COD/L, 199 % and 71 % higher than the control (4.66 g COD/L) and biochar (8.13 g COD/L) groups, respectively. Most importantly, Fe@biochar consistently enhanced n-caproate production after recycle, a continuity not observed with biochar. This difference may be attributed to the inhibitory effects of high concentrations of undissociated n-caproic acid (up to 9.06 mM or 2.32 g COD/L) on functional microbes in the biochar group. Microbial community analysis identified Clostridium_sensu_stricto as the key genus involved in n-caproate production. Comparative metagenomic and microbial activity analyses revealed the energy metabolism, where Fe@biochar promoted extracellular iron-based electron transfer, and further accelerated intracellular electron sinks. This is substantiated by a 3.6 fold increase in electron transfer system activity and evaluated relative abundances of key genes encoding acetyl-CoA synthetase (15.0 % increase), cytochrome c biosynthesis (28.7 % increase) and NADH dehydrogenase (48.0 % increase). This study offers a new paradigm for sustained n-caproate production.},
}
@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}
@article {pmid41202381,
year = {2025},
author = {Jiang, CH and Zhang, SJ and Li, P and Miao, H and Zhao, YY},
title = {Natural products targeting TGF-β/Smad signaling in renal fibrosis: Multiomics-based novel molecular mechanisms and therapeutic strategies.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157496},
doi = {10.1016/j.phymed.2025.157496},
pmid = {41202381},
issn = {1618-095X},
abstract = {BACKGROUND: Renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) have become one of the major global public health challenges. Regardless of the underlying aetiology, renal fibrosis is a common pathological endpoint in the progression of diverse kidney diseases to end-stage renal disease. Increasing studies have highlighted that emerging multi-omics techniques (metagenomics, transcriptomics, proteomics and metabolomics) have been used for elucidating the pathogenesis of kidney disease and underlying molecular mechanism of renal fibrosis. However, few reviews provide a comprehensive and systematic presentation of multi-omics signaling-mediated TGF-β/Smad pathway in both AKI and CKD as well as therapeutic strategies for targeting signaling cascades by natural products.<br><br>PURPOSE AND STUDY DESIGN: This review summarizes multi-omics signaling-mediated TGF-&#x3b2;/Smad pathway and therapeutic strategies of natural products by targeting this signaling axis in patients and animal models with kidney disease.<br><br>METHODS: All the available information is searched by several electronic database such as Web of Science, Pubmed, ScienceDirect, Splinker, Google Scholar, etc., that covered approximately 1000 publications from 2015 to 2025.<br><br>RESULTS: Ample evidence has indicated that transforming growth factor-&#x3b2; (TGF-&#x3b2;)/suppressor of mothers against decapentaplegic (Smad) signaling pathway plays a central role in renal fibrosis. Based on the multi-omics techniques, a variety of novel mediators are identified and affects kidney diseases by regulating TGF-&#x3b2;/Smad pathway. Therefore, targeting TGF-&#x3b2;/Smad pathway is an important and promising antifibrotic therapy. This review summarizes TGF-&#x3b2;/Smad pathway in both AKI and CKD, elaborate on the multidimensional regulatory mechanisms in renal fibrosis by crosstalk between TGF-&#x3b2;/Smad pathway and novel multi-omics signaling-associated mechanisms including microbial dysbiosis, dysregulating non-coding ribonucleic acids including long non-coding RNAs and microRNAs and metabolite disorder and shed light on the latest therapeutic effects of natural products such as terpenoids, anthraquinones, xanthones and flavonoids as well as natural polysaccharides by targeting multi-omics signaling-mediated TGF-&#x3b2;/Smad pathway.<br><br>CONCLUSION: This review presents a multiomics-driven therapeutic strategy for the development of effective and precise antifibrotic therapies.},
}
@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}
@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001541},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation &amp; purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}
@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}
@article {pmid41201496,
year = {2025},
author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C},
title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.10.048},
pmid = {41201496},
issn = {2090-1224},
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.<br><br>OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.<br><br>METHODS: PPE was extracted using 50&#xa0;% ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.<br><br>RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.<br><br>CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.},
}
@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&amp;D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration &amp; dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.<br><br>METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.<br><br>RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 &#xb1; 0.76 kg; LDG: -2.40 &#xb1; 0.67 kg), body fat percentage (HDG: -1.87 &#xb1; 0.69; LDG: -1.49 &#xb1; 0.45), cortisol (HDG: -6.79 &#xb1; 4.26 &#x3bc;g/dL; LDG: -4.5 &#xb1; 4.84 &#x3bc;g/dL), maximum power (HDG: 27.16 &#xb1; 9.77 W; LDG: 14.50 &#xb1; 9.43 W), maximal oxygen uptake (HDG: 8.78 &#xb1; 0.97; LDG: 6.90 &#xb1; 1.37), and half-court triangle run times (HDG: -0.48 &#xb1; 0.36 s; LDG: -0.25 &#xb1; 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 &#xb1; 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.<br><br>CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}
@article {pmid41200800,
year = {2025},
author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Chen, CH and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E},
title = {Metagenomics in the diagnosis of pneumonia: a systematic review.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/23744235.2025.2580954},
pmid = {41200800},
issn = {2374-4243},
abstract = {BACKGROUND: Pneumonia is a major cause of morbidity and mortality, yet causative organisms are rarely identified. Metagenomic next-generation sequencing (mNGS) may improve this, however the impact on outcomes is uncertain and the relative utility in pneumonia subtypes or different clinical samples is unclear.<br><br>METHODS: This systematic review compared mNGS with conventional microbiology, assessing pathogen identification, turnaround time and clinical impact. It also reviewed&#xa0;difference related to the pneumonia subtype, or sample used. We searched EMBASE, MEDLINE, Scopus, and the Cochrane Central Register of Controlled Trials (CENTRAL) for studies comparing mNGS with conventional microbiology, in patients with pneumonia. All study types were included (excluding case reports of <10 people). Eligibility assessment and data extraction was performed by two independent reviewers, and risk of bias assessed using the QUADAS-2.<br><br>RESULTS: We identified 74 studies including 10,566 people, with all studies having high risk of bias or applicability concerns in at least one domain. Conventional tests identified a pathogen in 43.2% of cases (3559/8229) compared to 78.9% for mNGS (6242/7980). mNGS had faster turnaround times than conventional microbiology (MD -73.6h, CI-111.36 - -35.73&#x2009;hrs) but meta-analysis was not possible for other outcomes. Most studies did not specify the pneumonia subtype. 92%of studies used exclusively or predominantly bronchoalveolar lavage fluid (BALF), and the utility of other sample types could not be established.<br><br>CONCLUSIONS: mNGS may identify possible pathogens with greater frequency than standard techniques although bias in study design limits definite conclusions, and the clinical relevance of this remains unresolved. There is a need for studies assessing&#xa0;clinical outcomes, and the differential impact in pneumonia subtypes and in samples other than BALF.},
}
@article {pmid41200470,
year = {2025},
author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {535},
pmid = {41200470},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).},
}
@article {pmid41200317,
year = {2025},
author = {Kazemzadeh, S and Korneeva, O and Shabunin, S and Syromyatnikov, M},
title = {Antibiotic resistance in mastitis-causing bacteria: Exploring antibiotic-resistance genes, underlying mechanisms, and their implications for dairy animal and public health.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {3980-4006},
pmid = {41200317},
issn = {2218-6050},
mesh = {Animals ; *Mastitis, Bovine/microbiology/drug therapy ; Female ; Cattle ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Public Health ; *Bacteria/drug effects/genetics ; Dairying ; Humans ; Milk/microbiology ; },
abstract = {The development and spread of superbugs, which are bacterial strains resistant to several types of antibiotics, threatening the lives of myriad people and animals worldwide, is one of the most concerning issues facing both global and animal health. Dairy animals are considered to be key reservoirs of antibiotic-resistant bacteria, which are closely correlated with the widespread and inappropriate application of antibiotics in agriculture and veterinary medicine, particularly for mastitis treatment. Although antimicrobial agents are administered in dairy farming for various conditions beyond mastitis, such as respiratory infections and digestive disorders, as well as prophylaxis and growth promotion, the most common reason for antimicrobial use in this industry is mastitis treatment. Since raw milk can be contaminated with opportunistic pathogens carrying antimicrobial resistance genes, these pathogens increase the gene pool from which pathogenic bacteria can acquire resistance traits. Indeed, these resistance genes may be horizontally transferred from livestock to human pathogens through mobile genetic elements through the consumption of raw milk. This phenomenon poses a global health threat, emphasizing the necessity of applying the "One Health" approach in global health and medicine to safeguard animal health and public health. Given the high prevalence and economic impact of mastitis and the evidence supporting mastitis as a major driver of antimicrobial use in dairy farming, this review summarizes recent genomic and metagenomic studies on major mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, Streptococcus spp., and Pseudomonas spp.) in dairy animals, detailing their primary resistance mechanisms. We highlight advanced surveillance tools, such as metagenomics, whole-genome sequencing, and quantitative polymerase chain reaction, for the rapid detection of resistance genes and mobile elements in the dairy chain.},
}
@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.<br><br>METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.<br><br>RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-&#x3b1; and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.<br><br>DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}
@article {pmid41199948,
year = {2025},
author = {Vasanthrao, R and Nidhin, IK and Taj, Z and Chattopadhyay, I},
title = {Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649872},
pmid = {41199948},
issn = {1664-302X},
abstract = {INTRODUCTION: Environmental contamination by heavy metals and hydrocarbons significantly impacts microbial diversity and soil functionality.<br><br>METHODS: This study employs whole-genome metagenome sequencing to analyse microbial compositions, antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRs), and virulence genes (VGs) in soil samples from diverse locations, including gardens, poultry farms, cattle sheds, markets, hospitals, thermal power plants, paper industries, and waste disposal sites.<br><br>RESULTS: The findings indicate that heavy metal concentrations (Pb, Cr, Cd, and Cu) and hydrocarbons (heptadecane, triacontane, docosane, and heneicosane) were positively correlated with several microbial phyla with relatively high abundances in these contaminated sites, such as Actinobacteria, Proteobacteria, Basidiomycota, Ascomycota, Euryarchaeota, and Apicomplexa. The prevalence of multidrug resistance genes, including MexD, MexC, MexE, MexF, MexT, CmeB, MdtB, MdtC, and OprN, was significant, facilitating antibiotic resistance primarily via efflux pump mechanisms (42%), followed by antibiotic inactivation (23%) and changes in antibiotic targets (18%). Virulence genes such as espR, regX3, sigA/rpoV, bap, and sugB were significantly prevalent in contaminated locations, indicating microbial pathogenic potential in polluted ecosystems. The functional gene analysis revealed significant metabolic pathways related to protein metabolism, carbohydrates, amino acids and their derivatives, metabolism, and DNA metabolism, highlighting the microbial adaptation processes engaged in pollution degradation and resource utilisation.<br><br>DISCUSSION: This study establishes a clear link between environmental pollution, microbial adaptations, and functional resilience, emphasizing the ecological significance of microbial bio-remediation in shaping targeted remediation strategies and long-term ecological recovery. Understanding these microbial interactions is essential for developing targeted remediation techniques and assessing long-term ecological recovery in contaminated regions.},
}
@article {pmid41199944,
year = {2025},
author = {Dai, L and Guo, XR and Chen, XR and Ma, MH and Liu, ZH and Lai, J and Lu, J and Feng, M and Liu, XX and Yang, SH},
title = {A review of the mechanism, diagnosis, and treatment of Naegleria fowleri infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1686695},
pmid = {41199944},
issn = {1664-302X},
abstract = {Naegleria fowleri is a rare pathogen responsible for primary amoebic meningoencephalitis (PAM), a fatal central nervous system infection characterized by rapid clinical progression and an extremely high mortality rate. The existing diagnostic methods are insufficiently sensitive, and therapeutic options are minimal, making early recognition and intervention extremely challenging. This review systematically examines the biological characteristics and pathogenic mechanisms of this pathogen, as well as current diagnostic and treatment strategies, with a particular focus on the groundbreaking applications of emerging technologies such as metagenomic next-generation sequencing (mNGS) in the diagnosis of difficult-to-treat infections. The aim is to provide theoretical support and practical guidance for rapid identification, accurate diagnosis, and timely intervention in clinical practice, serving as a reference for the prevention and treatment of N. fowleri infections.},
}
@article {pmid41199943,
year = {2025},
author = {Zhang, M and Di, H and Wang, S and Ning, Z},
title = {Column experiment reveals high natural attenuation potential for toluene in iron-rich aquifers but significant concomitant secondary Fe pollution risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687219},
pmid = {41199943},
issn = {1664-302X},
abstract = {INTRODUCTION: Iron mineral reduction mediated by indigenous microbes represents a crucial natural attenuation mechanism for organic contaminants like toluene in anaerobic aquifers, yet the partitioning of generated Fe(II) species and associated secondary pollution risks remain poorly constrained.<br><br>METHODS: This study employed controlled column experiments simulating an iron-rich aquifer (ferrihydrite-amended quartz sand) to track the biogeochemical dynamics of toluene degradation coupled with iron transformation. Over 43 days, we quantified spatiotemporal changes in toluene concentrations, dissolved/solid-phase iron species, and microbial community structure through high-frequency hydrochemical monitoring and metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Results demonstrated that iron-reducing consortia (notably Thiobacillus and Pseudomonas) drove > 99% toluene degradation within 10 cm flow distance, effectively containing plume migration. However, Fe(III) reduction generated Fe(II) predominantly (98%) as immobile solid-phase minerals, with only 1%-2% manifesting as dissolved Fe[2+]. This dissolved fraction accumulated progressively across space and time, exceeding China's groundwater quality threshold (0.3 mg/L) at 90% of monitoring points by experiment termination despite near-complete toluene removal. The study confirms that iron-rich aquifers provide significant natural attenuation capacity for petroleum hydrocarbons but concurrently pose substantial secondary contamination risks through highly mobile Fe[2+] generation. Therefore, it is recommended to include solidphase ferrous iron [Fe(II)] as an indicator in natural attenuation assessments and to take into account biogeochemical by-products such as Fe[2+] in risk assessment efforts.},
}
@article {pmid41199942,
year = {2025},
author = {Zeng, W and Yang, L and Cui, L and Liang, C and Zhu, D and Fang, Y and Zhang, Y and Liu, H},
title = {Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699705},
pmid = {41199942},
issn = {1664-302X},
abstract = {INTRODUCTION: Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.<br><br>METHODS: This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species-Haemaphysalis flava, Haemaphysalis longicornis, and Rhipicephalus sanguineus sensu lato-were collected and analyzed through metagenomic sequencing.<br><br>RESULTS: The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.<br><br>DISCUSSION: These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.},
}
@article {pmid41199613,
year = {2025},
author = {Kagemasa, S and Kuroda, K and Nakai, R and Sato, M and Li, YY and Kubota, K},
title = {Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70231},
doi = {10.1111/1758-2229.70231},
pmid = {41199613},
issn = {1758-2229},
support = {JP18H01564//Japan Society for the Promotion of Science/ ; JP21H01460//Japan Society for the Promotion of Science/ ; JP23H02545//Japan Society for the Promotion of Science/ ; JP23K27236//Japan Society for the Promotion of Science/ ; JP23K19153//Japan Society for the Promotion of Science/ ; JP24H00328//Japan Society for the Promotion of Science/ ; JP21J11654//Japan Society for the Promotion of Science/ ; //Tohou University - AIST matching fund/ ; //MEXT WISE Program for Sustainability in Dynamic Earth (SyDE), Japan/ ; },
mesh = {*Sewage/microbiology ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Wastewater/microbiology ; },
abstract = {Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46-1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.},
}
@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.<br><br>RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3&#xa0;min for taxonomic analysis and 10&#xa0;min for strain-level analysis against the human microbial gene catalogue when processing 10&#xa0;M paired reads - operating within a modest 5&#xa0;GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.<br><br>CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}
@article {pmid41198952,
year = {2025},
author = {Makarova, KS and Shmakov, SA and Wolf, YI and Mutz, P and Altae-Tran, H and Beisel, CL and Brouns, SJJ and Charpentier, E and Cheng, D and Doudna, J and Haft, DH and Horvath, P and Moineau, S and Mojica, FJM and Pausch, P and Pinilla-Redondo, R and Shah, SA and Siksnys, V and Terns, MP and Tordoff, J and Venclovas, &#x10c; and White, MF and Yakunin, AF and Zhang, F and Garrett, RA and Backofen, R and van der Oost, J and Barrangou, R and Koonin, EV},
title = {An updated evolutionary classification of CRISPR-Cas systems including rare variants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41198952},
issn = {2058-5276},
support = {Intramural funds//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.},
}
@article {pmid41198823,
year = {2025},
author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, &#xd3;},
title = {The association of the rumen virome with methane emissions in dairy cattle.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1534},
pmid = {41198823},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; },
abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.},
}
@article {pmid41197746,
year = {2025},
author = {Yu, PF and Jiang, DL and Wang, D and Ma, XG and Jun-Li, and Han, LY and Wang, A and Fu, YB and Jin, X},
title = {Manganese cycle-mediated synchronous bacteria-algae/anammox coupled denitrification system under low-temperature conditions: Performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133593},
doi = {10.1016/j.biortech.2025.133593},
pmid = {41197746},
issn = {1873-2976},
abstract = {The treatment of high-nitrogen complex wastewater in an efficient, economical, and environmentally friendly manner has attracted growing attention in recent years. However, slow reaction rates remain a significant obstacle to its broad application. This study investigated the addition of Mn@BC to enhance the low-temperature resistance of an anaerobic ammonia oxidation (anammox) process coupled with denitrification. The results demonstrated that under 17℃ conditions, the average nitrogen removal efficiency increased to 82% with the addition of Mn@BC, representing a 9% improvement compared to the addition of BC alone. Moreover, Mn@BC promoted the secretion of extracellular polymeric substances and diversified the microbial community structure.The incorporation of microalgae created a synergistic microalgal-bacterial system that maintained a phosphorus removal rate of 50% and reduced the reliance on external organic carbon, as confirmed by TOC analysis.The underlying intra- and extracellular metabolic pathways, formed by functional genes including mtrC, nirS/K, and c-Cyts, were elucidated using metagenomic sequencing. Therefore, the development of a high-efficiency nitrogen and phosphorus removal process capable of synchronizing microalgal-bacterial interactions, overcoming low-temperature inhibition, enhancing microbial synergy, and reducing carbon source dependency holds practical application value for treating high-nitrogen and low-temperature wastewater, while also providing theoretical support for constructing microalgal-bacterial synergistic systems to achieve efficient autotrophic nitrogen removal.},
}
@article {pmid41197744,
year = {2025},
author = {Li, Y and Wang, G and Yang, Y and Liu, L and Dang, X and Li, YY and Chen, R},
title = {Operational thresholds and microbial mechanisms in high-solid anaerobic membrane bioreactors treating swine wastewater: from process performance to metabolic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133596},
doi = {10.1016/j.biortech.2025.133596},
pmid = {41197744},
issn = {1873-2976},
abstract = {This study investigated swine wastewater treatment using a high-solid anaerobic membrane bioreactor (HSAnMBR), focusing on microbial adaptive mechanisms and process stability under stepwise-increased organic loading rates (OLRs: 5-26 g COD/L/d). The HSAnMBR achieved high efficiency at OLRs ≤ 17 g COD/L/d, with COD removal > 96 % and optimal methane yield (0.28 L CH4/g CODremoved). However, OLR elevation to 26 g COD/L/d induced volatile fatty acid (VFA) accumulation (5.57 g/L), causing acute methanogenic inhibition that reduced methane yield efficiency by 39 %. System functionality was rapidly restored within 10 days after OLR reduction to 21 g COD/L/d. Microbial analysis revealed divergent diversity dynamics: bacterial alpha diversity peaked at 14 g COD/L/d before declining, while archaeal diversity increased continuously, enhancing functional redundancy. Sludge acclimation enriched key functional taxa (such as Clostridium_sensu_stricto and hydrogenotrophic methanogens), forming a resilient "metabolic complementarity-functional substitution" network that maintained process stability under VFA stress. Metagenomic evidence confirmed metabolic pathway restructuring, including upregulation of hydrogenotrophic methanogenesis genes (e.g., coenzyme F420 biosynthesis) and a decline in acetoclastic dominance. This work deciphers the microbial mechanisms enabling high-load operation of HSAnMBRs, establishing the foundation for energy-efficient swine wastewater valorization.},
}
@article {pmid41197631,
year = {2025},
author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL},
title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.007},
pmid = {41197631},
issn = {1932-7420},
abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.},
}
@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}
@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}
@article {pmid41197513,
year = {2025},
author = {Luo, J and Hou, C and Wang, Z and Gui, N and Wang, YX and Jiang, X and Mu, Y and Shen, J},
title = {Simultaneous removal of nitrate and ammonia at the sulfur/pyrite-microbe interface: A novel insight of pyrite in wastewater polishing treatment for nitrogen metabolism.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140316},
doi = {10.1016/j.jhazmat.2025.140316},
pmid = {41197513},
issn = {1873-3336},
abstract = {The development of advanced nitrogen removal technologies for municipal wastewater effluents is critical to meeting increasingly stringent discharge standards. We present a sulfur/pyrite-microbe interfacial system that optimizes nitrogen-transformation pathways to achieve simultaneous removal of NO3[-]-N and NH4[+]-N with reduced sulfate production. This overcomes the drawbacks of conventional sulfur autotrophy (poor NH4[+] removal and excessive sulfate production) and stand-alone iron systems (low denitration rate and easy passivation), delivering synchronous ammonia and nitrate elimination in a single step. A comprehensive analysis of the microstructure and composition of the bio-abiotic interface was performed to elucidate the regulatory role of pyrite in electron transfer and substance transformation. The formation of secondary minerals, structural alterations in extracellular proteins, and enhanced activity of redox-active proteins collectively activated both intracellular and extracellular electron transfer channels. Pyrite-induced quorum sensing promoted iron transport and stimulated microbial metabolic functions. Driven by Fe(II)/Fe(III) redox cycling, nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) reduced sulfate production and suppressed sulfur disproportionation. Metagenomic analysis further confirmed that Feammox, rather than conventional Anammox, served as the dominant pathway for NH4[+]-N conversion. Pilot-scale validation demonstrated robust nitrogen removal (TN > 90 %) and low sulfate production with a treatment cost 40 % lower than conventional carbon-driven systems. This study offers a sustainable, low-carbon alternative for advanced nitrogen polishing and provides mechanistic insights into bio-abiotic interface engineering for wastewater treatment.},
}
@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}
@article {pmid41197330,
year = {2025},
author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE},
title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.},
journal = {Nutrition research (New York, N.Y.)},
volume = {144},
number = {},
pages = {1-15},
doi = {10.1016/j.nutres.2025.10.004},
pmid = {41197330},
issn = {1879-0739},
abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.},
}
@article {pmid41196658,
year = {2025},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196712},
pmid = {41196658},
issn = {1558-8238},
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.},
}
@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/spectrum.00944-25},
pmid = {41196057},
issn = {2165-0497},
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}
@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173225},
doi = {10.1128/spectrum.01732-25},
pmid = {41196055},
issn = {2165-0497},
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}
@article {pmid41196050,
year = {2025},
author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N},
title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095425},
doi = {10.1128/msystems.00954-25},
pmid = {41196050},
issn = {2379-5077},
abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.},
}
@article {pmid41195400,
year = {2025},
author = {Zhili, G and Jie, L and Peihao, Y},
title = {Macro- and metabolome-based characterization between gut microbiota and metabolites in patients with colorectal adenomas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1628315},
pmid = {41195400},
issn = {1664-302X},
abstract = {OBJECTIVE: The gut microbiota has been recognized as a significant regulator in the development and progression of colorectal adenoma (CRA). However, few studies have investigated the presence and association of resident microbial species and metabolites in patients with CRA. Our aim was to analyze differences in gut microbiome composition and metabolites, as well as to evaluate their diagnostic potential for CRA.<br><br>METHODS: We conducted metagenomic and metabolomic analyses on fecal samples from 90 subjects, including 60 patients with CRA (CRA group) and 30 healthy subjects who served as normal controls (NC group). By integrating fecal metagenomic and metabolomic data, we identified gut microbiota-associated metabolites that showed significant abundance changes in CRA patients. Furthermore, we explored whether these metabolites and microbial species could distinguish CRA patients from healthy individuals.<br><br>RESULTS: 16S rRNA gene sequencing and untargeted metabolomics analysis revealed microbial changes that distinguished CRA patients from controls. Microbial population analysis showed that the CRA group formed distinct clusters from the controls, with significant &#x3b2;-diversity (PCA and PCoA analyses, p < 0.05). At the phylum level, the dominant taxa in terms of relative abundance included Firmicutes, Ascomycota, Mycobacteria, Actinobacteria, and Clostridia. Differential analysis of the gut flora based on species abundance revealed significant differences in taxonomic composition between healthy individuals and CRA patients. KEGG functional enrichment analysis indicated that the differential flora were primarily involved in metabolic pathways, including metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, amino acid biosynthesis, and cofactor biosynthesis. In this study, three microbial species-Fusobacterium mortiferum, Alistipes, and Bacteroides fragilis-were validated as discriminators between healthy individuals and CRA patients, with Alistipes showing higher classification efficacy. Metabolomic analysis revealed differences in tryptophan metabolism, protein degradation products, amides, and phenolic acid metabolites. KEGG enrichment results indicated that metabolic pathways were the most significantly enriched. Differential metabolites were mainly associated with the biosynthesis of plant secondary metabolites. Procrustes and Venn analyses were performed on functional entries of the two omics datasets, highlighting enriched pathways including Metabolic pathways, Glycerophospholipid metabolism, Sphingolipid metabolism, and Alpha-linolenic acid metabolism. A review of the literature confirmed that the differential flora and metabolites are associated with adenoma growth.<br><br>CONCLUSION: In this study, metagenomic and metabolomic analyses were conducted in subjects with CRA. The findings based on fecal metagenomic and metabolomic assays suggest that intestinal microecology is altered in CRA patients, leading to changes in gut cellular structure.},
}
@article {pmid41195399,
year = {2025},
author = {, },
title = {Correction: Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721706},
doi = {10.3389/fmicb.2025.1721706},
pmid = {41195399},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1652229.].},
}
@article {pmid41195309,
year = {2025},
author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F},
title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.},
journal = {Pediatric diabetes},
volume = {2025},
number = {},
pages = {3013063},
pmid = {41195309},
issn = {1399-5448},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; },
abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.<br><br>METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included &#x3b1;/&#x3b2;-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.<br><br>RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2]&#x2009;=&#x2009;0.0562, p=0.003 and R [2]&#x2009;=&#x2009;0.0343, p=0.003). HLA-C [&#x2217;] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2]&#x2009;=&#x2009;0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2]&#x2009;=&#x2009;0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [&#x2217;] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19&#x2009;&#xb1;&#x2009;0.14 vs. 0.26&#x2009;&#xb1;&#x2009;0.19&#x2009;&#xb5;g/mL, p=0.029).<br><br>CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [&#x2217;] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.},
}
@article {pmid41194765,
year = {2025},
author = {Li, J and Zhao, S and Guo, F and Zhang, W and Chen, M and den Haan, R and Xin, F and Jiang, Y and Jiang, M},
title = {Strategies to Improve the Efficiency of Enzymatic Carbon Dioxide Conversion In Vitro.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00760},
pmid = {41194765},
issn = {2161-5063},
abstract = {With the rapid industrial development, massive fossil fuel use has caused excessive carbon dioxide (CO2) emissions, triggering global warming and environmental issues. Thus, CO2 recovery and reuse have become a research focus, among which artificially designed in vitro biocatalytic pathways for converting CO2 into high-value chemicals show promise, with advantages like shorter routes, higher efficiency and lower energy consumption compared to natural pathways. However, challenges remain due to natural enzymes' issues in specificity, affinity, efficiency, stability and oxygen sensitivity. To tackle these problems, extensive research efforts have been undertaken. These include elucidating the mechanisms and catalytic efficiencies of carbon-fixing enzymes from diverse sources, as well as developing and refining novel in vitro carbon fixation pathways. Moreover, significant progress has been made in computer-aided investigations of enzyme structure, function, and engineering optimization, alongside advancements in enzyme immobilization strategies, cofactor regeneration systems, and the development of artificial cofactors. By summarizing the latest research progress in recent years, we can identify the current bottlenecks and challenges in in vitro enzymatic CO2 conversion, propose effective methods to enhance the efficiency of CO2 conversion, and thus promote the development of research in related fields.},
}
@article {pmid41194716,
year = {2025},
author = {Liu, YH and Sheng, SY and Hu, HB and Wang, Y and Zhang, LW and Feng, YF and Feng, YY},
title = {Effects of drought on the thermal adaptation of soil microbial respiration: A review.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {10},
pages = {2965-2977},
doi = {10.13287/j.1001-9332.202510.032},
pmid = {41194716},
issn = {1001-9332},
mesh = {*Droughts ; *Soil Microbiology ; Climate Change ; Soil/chemistry ; *Adaptation, Physiological/physiology ; Ecosystem ; Carbon Cycle ; },
abstract = {Drought induced by global climate change affects the thermal adaptation of soil microbial respiration, which has complex consequences on the carbon (C) cycle. Drought can either enhance C emissions and create a positive feedback loop, or promote C sequestration and generate a negative feedback effect. We reviewed the effects of drought on microbial thermal adaptation, analyzed the underlying mechanisms, and summarized current research findings and related debates. Drought significantly influences microbial thermal adaptation through altering soil aggregate structure, organic carbon molecular composition, and microbial community structure. Due to variations in climatic zones, ecosystem types, and soil conditions, the impacts of drought on microbial thermal adaptation exhibit regional variety and complexity. Future research should focus on experimental designs that simulate natural environments, utilizing diverse organic substrates (e.g., cellulose, oxalic acid and xylan) to generate more accurate data and explore the synergistic effects of drought with other environmental factors (e.g., elevated CO2 concentrations, increased ultraviolet radiation, and nitrogen deposition) to reveal their combined impacts on microbial thermal adaptation. Advanced techniques like metagenomics and DNA-stable isotope probing should be warranted to further reveal the microbial mechanisms involved in the regulation of drought on microbial thermal adaptation.},
}
@article {pmid41194562,
year = {2025},
author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A},
title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70199},
doi = {10.1111/1462-2920.70199},
pmid = {41194562},
issn = {1462-2920},
support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Archaea/genetics/metabolism/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.},
}
@article {pmid41194295,
year = {2025},
author = {Breukers, E and Kim, H and Banihashem, F and Andersson, K and Leijon, M and Westin, R and Sjölund, M and Zohari, S},
title = {The first detection of swine orthopneumovirus in a pig farm in Sweden: a case report.},
journal = {Porcine health management},
volume = {11},
number = {1},
pages = {56},
pmid = {41194295},
issn = {2055-5660},
abstract = {BACKGROUND: Respiratory diseases are globally a major challenge in today's pig production. Despite the efforts to manage the disease, the number of pigs affected is still increasing, indicating gaps in the current knowledge. In 2016, a novel pneumovirus, swine orthopneumovirus, was detected in the USA. Since then, the virus has been detected in a few European countries and in South Korea. However, the wider distribution of the virus is still greatly unknown, as well as its clinical relevance.<br><br>CASE PRESENTATION: This report describes the first detection of swine orthopneumovirus in a Swedish pig herd. The virus was detected as the result of an investigation conducted between September 2023 to June 2024, where all clinical samples (n&#x2009;=&#x2009;682) sent to the Swedish Veterinary Agency for diagnostic purposes from 112 Swedish pig farms exhibiting clinical signs of respiratory disease were screened for the presence of swine orthopneumovirus. The virus was detected in one piglet producing farm that had a respiratory disease outbreak in autumn 2023, which presented with cough and nasal discharge. In November 2023, 11 nasal swabs were collected, of which 9 were PCR-positive for swine orthopneumovirus. In addition, each sample was also PCR-positive for Mesomycoplasma hyorhinis and Pasteurella multocida, and 2 samples were PCR-positive for Actinobacillus pleuropneumoniae, indicating a polymicrobial respiratory infection.<br><br>CONCLUSIONS: This report emphasises the importance of ongoing efforts to identify emerging pathogens and determine their clinical significance. Therefore, further research is needed to assess the distribution and potential clinical relevance of swine orthopneumovirus.},
}
@article {pmid41194257,
year = {2025},
author = {Parsons, C and Fournier, GP},
title = {Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.},
journal = {Biology direct},
volume = {20},
number = {1},
pages = {107},
pmid = {41194257},
issn = {1745-6150},
support = {EAR-1615426//National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Bacteria/genetics/enzymology ; Phylogeny ; *Matrix Metalloproteinases/genetics ; *Evolution, Molecular ; Archaea/genetics/enzymology ; *Biological Evolution ; Metagenome ; },
abstract = {BACKGROUND: The early evolution of animals is characterized by the emergence of complex tissues, organs, and integument, made possible in part by the diversification of groups of structural proteins. The abundance of this new kind of organic material in the environment would have provided novel nutrient opportunities for microbes, as part of the beginnings of animal-microbial coevolution. Indeed, a diverse ensemble of extant microbial groups appear to possess the enzymatic ability to cleave collagen, the most abundant animal-specific protein, through the use of matrix metalloproteinases (MMPs). In animals, MMPs serve to reshape the extracellular matrix in the course of development, but their prevalence in the microbial world has been largely overlooked.<br><br>RESULTS: MMPs have extensive diversity in Bacteria, Eumetazoa, and Streptophyta. We show that in marine metagenomes, MMP abundance is highly correlated with chitinase abundance, implying that even microbial MMPs are associated with animal-derived substrates. Reconstructing the phylogeny of MMP proteins reveals a history of rapid diversification, as well as multiple interkingdom and interdomain horizontal gene transfers. Included among these is a transfer to the ancestral lineage of the archaeal family Methanosarcinaceae, constraining this group to postdate the evolution of collagen, and therefore animal diversification.<br><br>CONCLUSIONS: MMPs have an unusual genetic history, marked by multiple instances of gene transfer between bacteria and multicellular eukaryotes, a smoking gun for some of the earliest coevolution between prokaryotes and metazoans. By calculating an end-Permian divergence of Methanosarcina, we demonstrate that the phylogenies of substrate-specific enzymes can provide valuable older-bound age calibrations for improving molecular clock age estimates across the Tree of Life.},
}
@article {pmid41194238,
year = {2025},
author = {Ellis, VA and Theodosopoulos, A and Sharma, I and Bardil, A and Stjernman, M and Hellgren, O},
title = {Simultaneous population genomics of hosts and their parasites with selective whole genome amplification.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {448},
pmid = {41194238},
issn = {1756-3305},
support = {NIH/NIGMS P20 GM103446, S10 OD028725/GF/NIH HHS/United States ; DEL00854, NE1943, NE2443//USDA Hatch/ ; VR 2021-03663//Swedish Research Council/ ; },
mesh = {Animals ; *Haemosporida/genetics ; *Host-Parasite Interactions/genetics ; *Protozoan Infections, Animal/parasitology ; *Bird Diseases/parasitology ; *Genome, Protozoan ; DNA, Protozoan/genetics ; Genomics ; *Passeriformes/parasitology/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: Generating parasite genomes is challenging when little of the DNA in infected host tissue is from the parasite. We used selective whole genome amplification (SWGA) to generate genomic data from wildlife samples of the avian haemosporidian Haemoproteus majoris (lineage PARUS1) and its host, the blue tit (Cyanistes caeruleus).<br><br>METHODS: We used SWGA to amplify the parasite DNA in nine avian blood samples collected between 1996 and 2021, and subsequently performed short-read sequencing and bioinformatically separated the host and parasite reads in each sample.<br><br>RESULTS: SWGA increased the percentage of parasite reads significantly. Sequencing to a depth of about 56 million reads (forward and reverse) per sample resulted on average (&#xb1; standard error [SE]) in 11.3X&#x2009;&#xb1;&#x2009;1.85 for the host genome and 1.17X&#x2009;&#xb1;&#x2009;0.446 mean depth of coverage for the host and parasite, respectively, after SWGA. Furthermore, about 74% of the host genome (genome size approx. 1.2&#xa0;Gb) and 33% of the parasite genome (approx. 23.9&#xa0;Mb) had at least 1X coverage on average; two samples had 1X coverage of approximately 60% of the parasite genome. Parasite sequencing success was positively correlated with parasitemia. When comparing the parasite sequences in the four best samples, we identified 9895 sites (minimum 5X coverage) that varied among the infections. When filtering the full dataset to at least six samples per variant, we identified 14,512,339 and 7068 sites that varied among samples in the host and parasite populations, respectively, revealing variation among samples and years.<br><br>CONCLUSIONS: SWGA facilitates dual host-parasite population genomics in this system and will greatly expand our understanding of host-parasite interactions over space and time.},
}
@article {pmid41194219,
year = {2025},
author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH},
title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {136},
pmid = {41194219},
issn = {2524-6372},
support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; },
abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.<br><br>RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and &#x3b1;-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.<br><br>CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.},
}
@article {pmid41194006,
year = {2025},
author = {Ivanova, A and Buzova, V},
title = {A novel enzymatic approach for a targeted fungal growth inhibition.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {719},
pmid = {41194006},
issn = {1471-2180},
support = {03-ZP23-087//SkyLab AG/ ; 03-ZP23-087//SkyLab AG/ ; },
abstract = {BACKGROUND: Dandruff represents a complex, multifactorial disorder characterized by impaired barrier function, altered lipid composition, and microbial imbalance. The principal pathogenic mechanism, however, involves excessive colonization by Malassezia species, notably M. furfur, M. restricta and M. globosa, on the scalp. Standard antifungal options often lead to undesirable effects, including itching and irritation, and may negatively impact the scalp microbiome. This study evaluates combination of chitinase and chitosanase, targeting fungal cell wall chitin and chitosan, as a promising targeted approach for scalp Malassezia spp.<br><br>METHODS: The in vitro antifungal activities of chitinase (100 U/g) and chitosanase (200 U/g) were evaluated against Malassezia furfur, Malassezia restricta, and Malassezia globosa at concentrations ranging from 0.125% to 5% w/w. Their efficacy was compared to that of conventional antifungal agents, including climbazole, piroctone olamine, selenium sulfide, zinc pyrithione, and propanediol caprylate. Cytotoxicity was assessed using fibroblast cell lines via MTT assay and fluorescence microscopy. A clinical study (n&#x2009;=&#x2009;18) evaluated the impact of a solution containing 0.25% chitinase and 0.25% chitosanase on scalp M. furfur and M. restricta DNA and RNA levels using quantitative PCR (qPCR). A metagenomic analysis was conducted to assess the impact of enzymatic treatment on bacterial composition and diversity.<br><br>RESULTS: Individually, 0.25% chitinase and 0.25% chitosanase inhibited Malassezia spp. growth by 23.85% and 26.15%, respectively (p&#x2009;<&#x2009;0.05). When combined at 0.25%, they achieved 98.38% inhibition (p&#x2009;<&#x2009;0.05), with complete suppression observed at 0.5%. In a clinical study, a 3-hour scalp treatment with a solution containing 0.25% chitinase and 0.25% chitosanase followed by quantitative PCR of post-treatment samples demonstrated significant reductions in DNA and RNA levels of M. furfur and M. restricta. DNA content decreased 2.4- and 1.9-fold, and RNA levels declined 2.4- and 4.6-fold, respectively. Cytotoxicity was detected only at concentrations&#x2009;&#x2265;&#x2009;7.6%, well above the effective antifungal doses. The metagenomic analysis demonstrated that a three-hour scalp treatment with chitinase - chitosanase solution increased alpha diversity (Chao1 index) and doubled the number of identifiable operational taxonomic units (OTUs).<br><br>CONCLUSIONS: The chitinase-chitosanase combination offers a promising targeted approach for scalp Malassezia spp. control without broad antimicrobial effects.},
}
@article {pmid41193697,
year = {2025},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {41193697},
issn = {1759-5053},
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}
@article {pmid41193636,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {Author Correction: A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-025-02212-3},
pmid = {41193636},
issn = {2058-5276},
}
@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}
@article {pmid41192565,
year = {2025},
author = {Tóth, GE and Petersen, M and Chevenet, F and Sikora, M and Tomazatos, A and Bialonski, A and Baum, H and Horváth, B and Siriyasatien, P and Heitmann, A and Jansen, S and Offergeld, R and Lachmann, R and Schmidt, M and Schmidt-Chanasit, J and Cadar, D},
title = {Blood donors as sentinels for genomic surveillance of West Nile virus in Germany using a sensitive amplicon-based sequencing approach.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106647},
doi = {10.1016/j.jinf.2025.106647},
pmid = {41192565},
issn = {1532-2742},
abstract = {BACKGROUND: West Nile virus (WNV) has emerged as a public health concern in Germany since its first detection in 2018, with evidence of expanding geographic spread. Genomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. However, genome recovery from low-viremia samples such as those obtained through blood donor screening remains technically challenging.<br><br>AIM: To develop and validate a sensitive amplicon-based sequencing protocol optimized for WNV lineage 2 and apply it to low-titer samples to support genomic surveillance in Germany.<br><br>METHODS: A novel primer scheme was designed for WNV lineage 2 and applied to 43 nucleic acid testing (NAT)-positive blood donor samples collected between 2020 and 2024. Amplicon-based sequencing performance was benchmarked against metagenomic next-generation sequencing (mNGS). Recovered genomes were subjected to phylogenomic analysis to assess viral diversity and transmission dynamics.<br><br>RESULTS: The amplicon protocol enabled genome recovery (>70% coverage) from samples with viral loads as low as ~10&#xb9; RNA copies/&#xb5;L, outperforming metagenomic NGS (mNGS). Of the 43 samples, 30 yielded complete or near-complete genomes. Six distinct WNV subclades (2A-2F), including German strains, were identified, indicating multiple introductions into Germany from Central Europe. Subclade 2F emerged as the dominant and widely distributed group. Berlin, Brandenburg, Saxony, and Saxony-Anhalt were identified as persistent transmission hubs.<br><br>CONCLUSION: This study highlights blood donors as valuable sentinels for WNV genomic surveillance. The validated amplicon-based sequencing approach enables sensitive, scalable genome recovery from low-viremia samples, and when integrated with routine blood donor screening, provides a robust framework for early detection, transmission dynamics, and public health preparedness.},
}
@article {pmid41192489,
year = {2025},
author = {Meng, F and Wang, L and Xu, J and Li, X and Hao, J},
title = {Enhanced electron transfer mediated by surface functional groups of targetedly modified sludge-based biochar for sustainable microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133600},
doi = {10.1016/j.biortech.2025.133600},
pmid = {41192489},
issn = {1873-2976},
abstract = {While unmodified sludge-based biochar (SBBC) exhibits limited electron transfer capacity in chain elongation (CE), its surface functional groups are recognized as critical factor influencing direct interspecies electron transfer (DIET). This study employed three modification methods, i.e., H2O2, HNO3, and anthraquinone sulfonate (AQS), to explore the effects of modified SBBC on CE process. Results indicated that the AQS-modified SBBC (SBBC-AQS) exhibited optimal electron transfer properties and electrochemical activity. Thus, SBBC-AQS greatly promoted DIET-mediated CE, leading to 62% higher caproate production compared to no biochar. Further recycling experiments confirmed the reusability of SBBC-AQS, along with the biofilm formation. Lastly, metagenomic analysis revealed that modified SBBC improved the abundance of CE bacteria such as Clostridium kluyveri, and introduced electron-transferring bacteria such as Petrimonas, so as to reinforce ethanol oxidation and medium-chain fatty acids production. This study offers novel insights into the sustainable material and microbes synergistic regulation to achieve an efficient CE system.},
}
@article {pmid41192488,
year = {2025},
author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y},
title = {Microbial necromass analogues reshape composting humification pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133583},
doi = {10.1016/j.biortech.2025.133583},
pmid = {41192488},
issn = {1873-2976},
abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.},
}
@article {pmid41192424,
year = {2025},
author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z},
title = {Assessment of enzyme diversity in the fermented food microbiome.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101430},
doi = {10.1016/j.cels.2025.101430},
pmid = {41192424},
issn = {2405-4720},
abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid41192191,
year = {2025},
author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB},
title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {57},
number = {},
pages = {101666},
doi = {10.1016/j.cbd.2025.101666},
pmid = {41192191},
issn = {1878-0407},
abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.},
}
@article {pmid41192179,
year = {2025},
author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC},
title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140319},
doi = {10.1016/j.jhazmat.2025.140319},
pmid = {41192179},
issn = {1873-3336},
abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.},
}
@article {pmid41192168,
year = {2025},
author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA},
title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {92},
number = {},
pages = {127787},
doi = {10.1016/j.jtemb.2025.127787},
pmid = {41192168},
issn = {1878-3252},
abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).<br><br>MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.<br><br>RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.<br><br>CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.},
}
@article {pmid41192067,
year = {2025},
author = {Świderek, K and Arafet, K and de Sousa Batista, V and Grajales-Hernández, D and López-Gallego, F and Moliner, V},
title = {Insights into the Catalytic Activity of a Metagenome-Derived Urethanase.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c13147},
pmid = {41192067},
issn = {1520-5126},
abstract = {The discovery of urethanases shows an opportunity to access the biotechnological recycling of polyurethane-based plastics (PURs), widely used in the manufacture of everyday materials. However, the mechanistic understanding of these enzymes remains under debate. In this work, we report a QM/MM-based mechanistic study of the metagenome-derived urethanase UMG-SP2 catalyzing the degradation of a urethane-like model compound, 4-nitrophenyl benzylcarbamate (pNC). A high-quality structural model generated with AlphaFold2, prior to the availability of the crystal structure, accurately captured the Ser-Ser-Lys catalytic triad characteristic of amidase signature enzymes. Highly accurate constant-pH nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) simulations provided the full titration curve of active site Lys, explaining the need for alkaline media for the enzyme to be active. The generation of the free energy landscape, obtained by means of free energy perturbation methods with the M06-2X DFT functional describing the QM region of the full system, reveals an esterase-like three-step mechanism of UMG-SP2, i.e., acylation, hydrolysis, and decarboxylation, with all steps being kinetically feasible. Our computational results show very good agreement with experimental kinetic data, with a calculated free energy barrier of 21.2 kcal·mol[-1] for the rate-determining step compared to 22.9 kcal·mol[-1] derived from the experimentally measured turnover frequency (TOF). The present results also open the door for the final decarboxylation occurring in the solution after the release of the product of the hydrolysis step or within the active site. These findings provide an atomistic insight into the urethanase function and establish a robust framework for the future design of biocatalysts targeting polyurethane degradation.},
}
@article {pmid41192043,
year = {2025},
author = {Kumar, A and Xu, C and Dakal, TC},
title = {Microbiome based precision medicine through integrated multiomics and machine learning.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128384},
doi = {10.1016/j.micres.2025.128384},
pmid = {41192043},
issn = {1618-0623},
abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.},
}
@article {pmid41192026,
year = {2025},
author = {Chen, Y and Kong, X and Mao, X and Fan, X and Yuan, J},
title = {Unlocking methanogenesis at 45°C: Synergistic roles of Zero-Valent iron and magnetite in Restoring cellulose anaerobic digestion.},
journal = {Waste management (New York, N.Y.)},
volume = {210},
number = {},
pages = {115225},
doi = {10.1016/j.wasman.2025.115225},
pmid = {41192026},
issn = {1879-2456},
abstract = {Anaerobic digestion (AD) operated at transitional temperature is a promising technology for treating de-oiled food waste (FW). However, under such conditions, the metabolic activity of methanogens will be significantly negatively affected compared to conventional mesophilic or thermophilic conditions, which limits its practical application. In this study, the AD of cellulose at 45 °C were investigated, and the synergistic effects of zero-valent iron (ZVI) and magnetite (Fe3O4) on enhancing methanogenesis were explored. The results indicated that the combination of ZVI and Fe3O4 played a crucial role in promoting cellulose methanogenesis during AD at 45 °C. Specifically, the methane yield reached 300.1 mL/g VS, representing a 58 % increase compared to the control group. Further analysis revealed that ZVI + Fe3O4 enhanced the levels of coenzyme F420 and acetate kinase. Firmicutes and Methanosarcina were the dominant microbial groups involved in normal methanogenesis at 45 °C, and a positive correlation between these two groups was observed. Metagenomic sequencing further demonstrated that the combination of ZVI and Fe3O4 synergistically increased the abundance of genes associated with both acetate cleavage and CO2 reduction methanogenic pathways. The dominant pathways achieved a dynamic equilibrium, functioning according to the available substrates at different stages within the reactor. Life Cycle Assessment (LCA) results indicated that coupling ZVI and Fe3O4 could effectively reduce carbon emissions and fossil resource depletion. The study provided theoretical evidence for the application of AD in treating cellulose-based substrates at transitional temperatures.},
}
@article {pmid41191113,
year = {2025},
author = {Cheng, J and Yang, F and Zhang, L and Zhao, J and Zhang, X and Qiao, H and Yan, Z and Luo, Y and Dai, Y},
title = {Genomic Analysis, Metabolite Characterization, and Wheat Seedling Growth Promotion of Variovorax Endophyticus sp. nov., A Novel Endophyte from Wheat Root Tissue.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {2},
pmid = {41191113},
issn = {1432-0991},
support = {41877042//National Natural Science Foundation of China/ ; 2023YB007//Hebei Normal University of Science and Technology/ ; 2022JDTD0027//Science and Technology Department of Sichuan Province/ ; },
mesh = {*Triticum/microbiology/growth &amp; development ; *Plant Roots/microbiology/growth &amp; development ; *Endophytes/genetics/isolation &amp; purification/classification/metabolism ; Phylogeny ; *Comamonadaceae/genetics/isolation &amp; purification/classification/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; *Seedlings/growth &amp; development/microbiology ; Base Composition ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Genome, Bacterial ; Bacterial Typing Techniques ; Genomics ; },
abstract = {A bacterial strain CY25R-8[T] (= CGMCC 1.16908[T] = KACC 21250[T]) was isolated from the root tissues of wheat. It is aerobic, motile (with a single flagellum), Gram-negative, rod-shaped and yellow, and capable of growing at 10-40 ℃, pH 3.0-10.0 and NaCl 0.0-5.0%; its major fatty acids were C16:0, C17:0 cyclo, summed feature 8 and 3; its genomic DNA G + C content was 69.5%. Its respiratory quinone was ubiquinone-8 and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol diphospatidylglycerol and unidentified aminophospholipid. Strain CY25R-8[T] exhibited the highest 16S rRNA gene sequence similarity (99.0%-99.6%) with the type strains of several Variovorax species. However, the dDDH and ANI values between strain CY25R-8[T] with these type strains were 28.6%-29.5% and 84.65%-86.0%, respectively. These values indicated that strain CY25R-8[T] represents a novel species of the genus Variovorax. The name Variovorax endophyticus sp. nov. is proposed. Furthermore, genomic comparisons with uncharacterized isolates and uncultured strains (metagenome-assembled genomes) revealed no close relatives of CY25R-8[T], suggesting this species is novel and potentially aquatic. Through LC-MS, NMR, and MS data, 25 metabolites were identified in strain CY25R-8[T], with cyclo (L-Phe-L-Ser), cyclo (L-Phe-D-4-OH-Pro), H-DPro-β[3]-Glu-NH2 1-ααβ and pGlu-His-Pro-OH being the major compounds. Notably, strain CY25R-8[T] is the first reported natural producer of H-DPro-β[3]-Glu-NH2 1-ααβ. As an endophyte of wheat, strain CY25R-8[T] also demonstrated the ability to enhance wheat seedling growth by promoting main root elongation in vivo. These findings suggest that V. endophyticus CY25R-8[T] has potential applications in biotechnology and agriculture.},
}
@article {pmid41190884,
year = {2025},
author = {van Scheijen, S and Neerincx, AH and Weersink, EJM and Altenburg, J and Majoor, C and van Muijlwijk-Koezen, JE and Maitland-van der Zee, AH and Abdel-Aziz, MI and , },
title = {Metagenomics approach to predict antibiotic resistance genes in sputum samples of adult people with cystic fibrosis: a pilot study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0229924},
doi = {10.1128/spectrum.02299-24},
pmid = {41190884},
issn = {2165-0497},
abstract = {UNLABELLED: Lung infections in people with cystic fibrosis (CF) cause lung damage, which is the leading factor in the morbidity and mortality of CF. Prescription of antibiotics to treat these infections is essential to maintain a higher quality of life and increase life expectancy. Determination of antibiotic susceptibility (ABS) is done by culture-dependent, phenotypic methods. These procedures take several days, while timely intervention is key. The analysis of antibiotic resistance genes by use of shotgun metagenomics might offer a time-sensitive alternative. Twenty people with CF with a homozygous Phe508del mutation provided 68 sputum samples during different visits over a period of roughly a year. After shotgun sequencing, the samples were analyzed using the deep learning tool deepARG. These results were compared with the results from routine ABS testing. The performance was determined by area under the curve-receiver operating characteristics (AUCROC) and sensitivity. Significant results were obtained for the following antibiotic classes: aminoglycoside (AUCROC = 0.81 [95% CI: 0.67-0.95, sensitivity = 73%]), cephalosporin (AUCROC = 0.70 [95% CI: 0.54-0.86, sensitivity = 95%]), and fluoroquinolone (AUCROC = 0.73 [95% CI: 0.56-0.89, sensitivity = 88%]). For other antibiotic classes, results were not significant. Using antibiotic class-specific cut-offs for positive reads of ARGs, a metagenomics approach potentially offers a culture-independent and more time-efficient manner to predict ABS for commonly prescribed antibiotic classes for sputum samples of adult people with CF. The use of metagenomics and artificial intelligence in clinical care will add to more personalized care for people with CF as well as better antibiotic stewardship.<br><br>IMPORTANCE: Damage induced by lung infections in people with cystic fibrosis (CF) is the leading factor to the mortality and morbidity of CF. To treat bacterial infections, people with CF are prescribed antibiotics. Routine antibiotic susceptibility (ABS) testing relies on culture-dependent, phenotypic techniques. These take several days up to more than a week, while timely intervention is key. To bridge this time gap, physicians in CF care use patient history of ABS data to start antibiotics, with risk of resistance to it. This pilot study explores a time saving alternative: the possibility to predict antibiotic resistance genes using shotgun metagenomics and artificial intelligence. By quicker prediction of ABS, people with CF can receive more adequate care, which results in the possible prevention of chronic infections and contributes to antibiotic stewardship.},
}
@article {pmid41190675,
year = {2025},
author = {McHugh, O and Ayilaran, E and Jung, Y},
title = {Maple sap microbial communities and tubing sanitation: dominance of Pseudomonas species.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0069325},
doi = {10.1128/mra.00693-25},
pmid = {41190675},
issn = {2576-098X},
abstract = {Shotgun metagenomic data from maple (Acer saccharum) sap collected via 3/16-inch tubing (new, unsanitized, or sanitized with 400 ppm calcium hypochlorite) during weeks 1 and 5 revealed 317 species. Applying a 5% relative abundance cutoff, 20 dominant species were identified. Pseudomonas_E proteolytica and/or Pseudomonas_E lurida were abundant across conditions.},
}
@article {pmid41190646,
year = {2025},
author = {Brown, KM and Beall, BFN and Bullerjahn, GS and Finlay, JC and Glavina Del Rio, T and Small, GE and Sterner, RW and McKay, RM},
title = {Depth-resolved paired metagenomes and metatranscriptomes from the Lake Erie 'dead zone'.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0101325},
doi = {10.1128/mra.01013-25},
pmid = {41190646},
issn = {2576-098X},
abstract = {Metagenomes and metatranscriptomes were generated from the surface mixed layer and hypolimnion at a NOAA-Great Lakes Environmental Research Laboratory Real-Time Coastal Observation Network (ReCON) site in Lake Erie's central basin during the onset of hypolimnetic hypoxia. Here, we describe the sequencing of the samples, metagenome assembly, and binning of microbial taxa.},
}
@article {pmid41190270,
year = {2025},
author = {Li, W and Li, X and Cheng, J and Liu, J and Liu, J and Wang, Y and Yuan, W and Ren, E},
title = {Lung microbiota of raccoon dogs (Nyctereutes procyonoides) using high-throughput sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677761},
pmid = {41190270},
issn = {1664-302X},
abstract = {Pneumonia frequently causes mass mortality in raccoon dogs, resulting in significant economic loss. Additionally, raccoon dogs carry various zoonotic pathogens. This study systematically assessed pulmonary pathogens in raccoon dogs and their potential public health implications utilizing 2bRAD microbiome sequencing (2bRAD-M) and viral metagenomics. We analyzed 30 lung tissue samples for microbial composition. Sequencing revealed Pseudomonadota, Ascomycota, and Actinobacteria as dominant phyla and Acinetobacter, Escherichia, and Klebsiella as predominant genera. The most abundant species were Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae. In total, 158 species across 84 genera were identified, including 49 potentially zoonotic species. Viral metagenomics revealed Peduoviridae, Rountreeviridae, and Parvoviridae as dominant families, with Valbvirus ValB1MD2, Andhravirus andhra, and Amdoparvovirus carnivoran3 comprising over 80% of the viral composition. These findings highlight the pathogenic complexity of raccoon dog pneumonia and its zoonotic risks, providing crucial insights for disease control and public health management.},
}
@article {pmid41190207,
year = {2025},
author = {You, Y and Liu, X and Wang, L and Khalid, M and Wang, X and Jiang, L and Wang, F and Pang, Z and Peng, Y and Zhao, X},
title = {Integrated metagenomic and soil chemical analyses revealed shifts of microbial nutrient cycling with poplar plantation age.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1513281},
pmid = {41190207},
issn = {1664-462X},
abstract = {INTRODUCTION: Poplar (Populus spp.) is widely recognized as an ideal model system for studying plant-microbial interactions due to its rapid growth, genetic tractability, and ecological importance in afforestation programs. Leveraging these advantages, we investigated how poplar cultivation reshapes soil microbial communities and their nutrient cycling functions. Although plant roots are known to profoundly influence microbial community structure and functionality, comprehensive studies systematically linking poplar-induced microbiome shifts to nutrient cycling remain limited.<br><br>METHODS: Here, we employed an integrative approach combining metagenomic sequencing with soil nutrient analyses to assess poplar-induced changes in microbial community and metabolic activities at the root-soil interface.<br><br>RESULTS: Our analyses revealed three major findings: (1) poplar cultivation significantly altered the composition of microbial communities-including bacteria, fungi, and archaea-and reduced the complexity of microbial interaction networks, as revealed by co-occurrence analysis; (2) poplar cultivation enhanced microbial genetic potential related to degradation pathways for starch, lignin, and aromatic compounds, as well as carbon (C) fixation, while suppressing cellulose/hemicellulose decomposition; and (3) soil nutrient cycling processes involving nitrogen (N), phosphorus (P), and sulfur (S) were reprogrammed through changes in both gene abundance (e.g., nifH, pqqC, aprA) and nutrient availability (e.g., NO3-, P). Moreover, specific microbial taxa showed strong correlations with these functional shifts, i.e., Bacteroidota correlated with P metabolism in roots/soil, Actinobacteria and Firmicutes with organic C turnover, and Gemmatimonadetes and Nitrospirae with nitrate cycling dynamics.<br><br>DISCUSSION: By integrating poplar's roles as both a model species and a driver of ecological change, this study elucidates how afforestation shapes soil ecosystems through complex plant-microbe-environment interactions. These findings provide critical insights for sustainable land management strategies.},
}
@article {pmid41190090,
year = {2025},
author = {Watkinson, JI},
title = {Habitat Disturbance Promotes Shifts in the Abundance of Major Fungal Phyla in the Roots of a Native Orchid, Tipularia discolor.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {6},
pages = {e70096},
pmid = {41190090},
issn = {2575-6265},
abstract = {Orchids are a widely distributed group of flowering plants with important roles in ecosystems around the globe. However, many species are in decline due, in part, to human-driven changes in their habitat. It is well established that orchids are reliant on specific groups of mycorrhizal fungi for growth and reproduction and that these fungi can vary across the range in which an orchid species resides. Recent studies have shown that the orchid fungal mycobiome (mycobiome) includes a diverse array of non-mycorrhizal endophytic fungi that may also contribute to growth and resilience and that can vary across a particular orchid's range. The communities of mycorrhizal and non-mycorrhizal species that make up the orchid mycobiome may be altered by habitat disturbance, which could affect the ability of these plant species to thrive in different environments. Here a metagenomic approach is used to provide a snapshot of the root mycobiome of Tipularia discolor in habitats defined as disturbed or undisturbed. While amplicon sequence variant (ASV) richness and evenness were similar, the structure of the mycobiome differed between the two sites. Orchids growing in disturbed locations were associated with a greater abundance of Basidiomycota and Glomeromycota, while orchids in undisturbed habitats were associated with Ascomycota and Mucoromycota. The overall abundance of mycorrhizal families was similar across the two habitats. The data indicate that habitat disturbance induces a change in the composition of the fungal mycobiome of T. discolor , suggesting that the community of root fungi could be key to the ability of orchids to successfully adapt to different environments.},
}
@article {pmid41189926,
year = {2025},
author = {Chen, X and Qin, H and Song, Y and Lian, Y and Long, Q},
title = {Metagenomics next-generation sequencing for diagnosis of invasive fungal diseases in patients with hematological diseases.},
journal = {IJID regions},
volume = {17},
number = {},
pages = {100780},
pmid = {41189926},
issn = {2772-7076},
abstract = {OBJECTIVES: To investigate the clinical characteristics and risk factors of invasive fungal disease (IFD) in patients with hematological disorders.<br><br>METHODS: From January 2023 to January 2025, 67 patients with blood diseases hospitalized at the Hematology Department who were suspected of infection with IFD underwent metagenomic next-generation sequencing (mNGS) and fungal pathogen detection. Their clinical characteristics and laboratory examinations were retrospectively analyzed.<br><br>RESULTS: A cohort of 67 patients was enrolled in the study, among which 32 cases were diagnosed with IFD through mNGS and etiological culture, while no fungal pathogens were detected in the remaining 35 cases. The diagnostic yield of mNGS for fungal infection detection (47.76%) demonstrated superior sensitivity compared to conventional pathogenic microbial culture (14.93%), &#x3b2;-D-glucan assay (11.94%), and galactomannan assay (2.99%). Within the IFD cohort, Candida species constituted the most prevalent etiology (46.88%, n = 15), followed by Aspergillus (18.75%, n = 6), Penumocystis (12.5%, n = 4), and Rhizomucor (12.5%, n = 4), with other fungal species accounting for the remaining cases (9.37%, n = 3). Multivariate logistic regression analysis revealed six independent risk factors associated with IFD in patients with hematological disorders: cluster of differentiation 4+ T cell count <400 cells/&#xb5;L (odds ratio [OR] = 9.45, P = 8.9&#xd7;10[-5]), elevated C-reactive protein (OR = 3.18, P = 0.027), elevated interleukin (IL)-6 (OR = 5.75, P = 0.001), elevated IL-10 (OR = 3.31, P = 0.033), hypoproteinemia (OR = 42.17, P = 0.013), and neutropenia lasting for more than 10 days (OR = 4.11, P = 0.015).<br><br>CONCLUSIONS: mNGS has high sensitivity in detecting IFD in patients with hematological diseases. Cluster of differentiation 4+ cell count below 400/uL, increased level of C-reactive protein, IL-6, and IL-10, hypoproteinemia, and neutropenia lasting for more than 10 days are independent risk factors for IFD in patients with hematological diseases.},
}
@article {pmid41189709,
year = {2025},
author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J},
title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619059},
pmid = {41189709},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation &amp; purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.<br><br>METHODS: We recruited 91 participants, including 31 treatment-na&#xef;ve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.<br><br>RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in &#x3b1;-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.<br><br>DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.},
}
@article {pmid41189593,
year = {2025},
author = {Huang, Y and Wei, X and Huang, X and Peng, C and Lin, B and Ren, X and He, G and Zhang, X and Jiang, C and Huang, L and Gu, S},
title = {Pneumocystis jirovecii associated with Lung Virome in patients with severe pneumonia.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113710},
pmid = {41189593},
issn = {2589-0042},
abstract = {Pneumocystis jirovecii (P. jirovecii) threatens immunocompromised patients, yet its role in the lung microbiome remains unclear. We performed metagenomic sequencing on bronchoalveolar lavage fluid from two retrospective cohorts: a multicenter study of 1,737 patients with pneumonia and a validation cohort of 72 intubated ICU patients. Participants were categorized into P. jirovecii infection, colonization, or negative groups based on qPCR and clinical characteristics. Our analysis revealed minimal bacterial differences but significant viral and fungal variations. Notably, negative patients with P. jirovecii exhibited the lowest viral diversity. Even after adjusting for potential confounders, including immunosuppression and disease severity, P. jirovecii status remained most strongly associated with virome alterations. Furthermore, in cytomegalovirus-positive individuals, P. jirovecii positivity was significantly associated with higher 28-day mortality. These findings suggest that P. jirovecii colonization represents a distinct intermediate state in the lung microbial ecosystem between infection and negative, shedding light on its potential role in pneumonia pathogenesis and outcomes.},
}
@article {pmid41189414,
year = {2025},
author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y},
title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70201},
doi = {10.1111/1462-2920.70201},
pmid = {41189414},
issn = {1462-2920},
support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.},
}
@article {pmid41189006,
year = {2025},
author = {Popall, RM and Roland, A and Davidson, S and Combet-Blanc, Y and Price, RE and Quéméneur, M and Postec, A and Erauso, G},
title = {Cultivating microbial communities from the serpentinite-hosted Prony Bay hydrothermal field on different carbon sources in hydrogen-fed bioreactors.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {135},
pmid = {41189006},
issn = {2524-6372},
support = {19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: The primary source of carbon is one of the most fundamental questions regarding the development of microbial communities in serpentinite-hosted systems. The hydration of ultramafic rock to serpentinites releases large amounts of hydrogen and creates hyperalkaline conditions that deplete the environment of dissolved inorganic carbon. Metagenomic studies suggest that serpentinite-hosted microbial communities depend on the local redissolution of bicarbonate and on small organic molecules produced by abiotic reactions associated with serpentinization.<br><br>METHODS: To verify these bioinformatic predictions, microbial consortia collected from the Prony Bay hydrothermal field were enriched under anoxic conditions in hydrogen-fed bioreactors using bicarbonate, formate, acetate, or glycine as the sole carbon source.<br><br>CONCLUSIONS: With the exception of glycine, the chosen carbon substrates allowed the growth of microbial consortia characterized by significant enrichment of individual taxa. Surprisingly, these taxa were dominated by microbial genera characterized as aerobic rather than anaerobic as expected. Our results indicate the presence of both autotrophic and heterotrophic taxa that may function as foundation species in serpentinite-hosted shallow subsurface ecosystems. We propose that an intricate feedback loop between these autotrophic and heterotrophic foundation species facilitates ecosystem establishment. Bicarbonate-fixing Meiothermus and Hydrogenophaga, as well as formate-fixing Meiothermus, Thioalkalimicrobium, and possibly a novel genotype of Roseibaca might produce organic compounds for heterotrophs at the first trophic level. In addition, the base of the trophic network may include heterotrophic Roseibaca, Acetoanaerobium, and Meiothermus species producing CO2 from acetate for a more diverse community of autotrophs. The cultivated archaeal community is expected to recycle CH4 and CO2 between Methanomicrobiales and Methanosarcinales with putative Woesearchaeales symbionts.},
}
@article {pmid41188784,
year = {2025},
author = {Luo, H and Wu, P and Yang, H and Zhang, B and Zheng, M and Kuang, W and Li, W and Li, X and Zhang, X and Huang, J and Fan, Q and He, S},
title = {Clinical analysis of Pneumocystis jirovecii pneumonia in children with malignant disease.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {906},
pmid = {41188784},
issn = {1471-2431},
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/complications ; Male ; Female ; Retrospective Studies ; Child ; Child, Preschool ; *Pneumocystis carinii/isolation &amp; purification ; Adolescent ; *Neoplasms/drug therapy/complications ; Glucocorticoids/therapeutic use/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Antifungal Agents/therapeutic use ; Immunocompromised Host ; Tomography, X-Ray Computed ; },
abstract = {OBJECTIVE: To characterize Pneumocystis jirovecii pneumonia (PJP) in pediatric malignancy patients receiving chemotherapy or glucocorticoids, and provide guidance for timely diagnosis and effective treatment.<br><br>METHODS: A retrospective analysis of clinical features, laboratory findings, radiological characteristics, treatment approaches, and outcomes in pediatric malignancy patients who developed PJP.<br><br>RESULTS: Ten patients (1:1 male-to-female ratio; median age 6.50 years, range 2.83-14.58 years) were followed for a median of 14 months (range 6-53 months). Eight developed PJP during chemotherapy and two post-completion. Nine received glucocorticoids in their chemotherapy regimen. PJP prophylaxis was either absent (n&#x2009;=&#x2009;4) or discontinued&#x2009;>&#x2009;1 month prior (n&#x2009;=&#x2009;5). Clinical presentations included fever, dyspnea, and wheezing, often without significant cough. Laboratory findings showed elevated (1,3)-&#x3b2;-D-glucan(BDG)in 7 cases. Chest CT typically revealed bilateral diffuse patchy infiltrates, ground-glass opacities, and nodular shadows. All cases had a positive metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS) result for P. jirovecii from sputum or bronchoalveolar lavage fluid (BALF) samples.Treatment included Trimethoprim-sulfamethoxazole(TMP/SMZ) with/without caspofungin and adjunctive corticosteroids. Eight patients required PICU admission (median stay 7.5 days, range 0-45 days) for respiratory support. Nine patients survived PJP, with one PJP-related death and one death from underlying disease.<br><br>CONCLUSION: High clinical suspicion for PJP is warranted in pediatric malignancy patients presenting with fever, dyspnea, elevated BDG, and characteristic imaging findings, particularly in those with inadequate prophylaxis. Early pathogen detection and treatment initiation are crucial. While TMP/SMZ remains first-line therapy, combination with caspofungin may improve outcomes. Short-term adjunctive corticosteroids may benefit moderate to severe cases.},
}
@article {pmid41184794,
year = {2025},
author = {Chen, J and Chen, C and Xie, Y and Xu, G and Lin, M and Gong, X and Zhang, X and Chen, X and Chen, J and Zhang, L and He, G},
title = {Clinical value of quantitative PCR in diagnosis of suspected mycobacterial pulmonary infections.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1476},
pmid = {41184794},
issn = {1471-2334},
abstract = {BACKGROUND: Due to the difficulty in clinically distinguishing pulmonary infections caused by Mycobacterium tuberculosis (MTB) and Non-tuberculous mycobacteria (NTM), the study utilizes quantitative PCR (qPCR) technology to simultaneously detect MTB, Mycobacterium abscessus complex (MABC), Mycobacterium avium complex (MAC), and Mycobacterium kansasii(M. kansasii),to explore its clinical value in diagnosing of patients suspected mycobacterial pulmonary infections.<br><br>METHODS: A retrospective analysis was conducted on a cohort of 102 patients suspected of mycobacterial pulmonary infections. Samples of sputum and bronchoalveolar lavage fluid were extracted for testing with acid-fast staining (AFS), qPCR, and metagenomic next-generation sequencing (mNGS). Assess the diagnostic performance of AFS, qPCR, and mNGS for four types of mycobacteria based on comprehensive pulmonary tuberculosis (PTB) CRS composite criteria, non-tuberculous mycobacteria (NTM) diagnostic and treatment guidelines, as well as clinical observations.<br><br>RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, and AUC of qPCR for mycobacteria (MTB, MABC, MAC) were 90.00% (76.33&#x2013;97.20), 100.00% (94.22&#x2013;100.00), 100.00% (99.90&#x2013;100.00), 93.93% (85.95&#x2013;97.51), and 0.950 (0.888&#x2013;0.983), respectively. For mNGS, the corresponding estimates were 87.50% (73.19&#x2013;95.81), 96.77% (88.82&#x2013;99.60), 94.59%(81.66&#x2013;98.56),92.30% (84.07&#x2013;96.46), and 0.921(0.851&#x2013;0.965), respectively. The research showed that the sensitivity and specificity of qPCR and mNGS method for detecting mycobacteria are higher than AFS; and there was no statistical difference in the diagnostic performance for mycobacteria between qPCR and mNGS, but qPCR was superior to mNGS in specific values.<br><br>CONCLUSION: Compared with AFS, qPCR has higher sensitivity and specificity but statistical significance needs to be assessed with larger sample sizes for mycobacteria identification. In this regard, qPCR and mNGS demonstrate exhibit similar performance. However, qPCR is less expensive and more convenient for pathogen detection, which make it a promising lower-cost alternative diagnostic method for patients suspected of mycobacterial pulmonary infections in resource-limited settings.},
}
@article {pmid41188680,
year = {2025},
author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA},
title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {547},
pmid = {41188680},
issn = {1573-2983},
support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; },
abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.},
}
@article {pmid41188618,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1295},
pmid = {41188618},
issn = {1573-2959},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; },
mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; },
abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.},
}
@article {pmid41188566,
year = {2025},
author = {Kondratov, IG and Ogarkov, OB and Sinkov, VV and Suzdalnitsky, AE and Koshcheyev, ME and Orlova, EA and Belkova, NL and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI},
title = {Prediction of Metabolic Profile and Virulence Factors of Facultative-Anaerobic Bacteria from Tuberculous Necrosis Foci Based on Whole-Genome Sequencing Data.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {41188566},
issn = {1573-8221},
abstract = {Metagenomics of bacterial communities in tuberculosis caseous necrotic mass indicates the predominance of facultative anaerobes. Nine strains isolated from the tuberculosis necrosis were identified to species and whole-genome sequencing was performed: Staphylococcus hominis (3 strains), S. epidermidis (3 strains), Corynebacterium ureicelerivorans (2 strains), and C. kefirresidentii (1 strain). Prediction of metabolic pathways and virulence factors showed that Corynebacterium and Staphylococcus possess gene sets that are absent in Mycobacterium tuberculosis: lipases and proteases for the degradation of caseous necrosis, glutamate and polysaccharide capsules, ureases capable of increasing pH of the caseum; and Fe(III) uptake systems. The isolated species can form a bacterial consortium with M. tuberculosis at the early (Corynebacterium) and later (Staphylococcus) stages of necrotization of the tuberculosis focus in the lungs.},
}
@article {pmid41188334,
year = {2025},
author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T},
title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38587},
pmid = {41188334},
issn = {2045-2322},
mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; },
abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.},
}
@article {pmid41188324,
year = {2025},
author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI},
title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38611},
pmid = {41188324},
issn = {2045-2322},
support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; },
abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.},
}
@article {pmid41188219,
year = {2025},
author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P},
title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9738},
pmid = {41188219},
issn = {2041-1723},
mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.},
}
@article {pmid41187758,
year = {2025},
author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ},
title = {A global survey of taxa-metabolic associations across mouse microbiome communities.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.010},
pmid = {41187758},
issn = {1934-6069},
abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.},
}
@article {pmid41187361,
year = {2025},
author = {Zhang, T and Xia, Q and Wang, Y and Sun, Y and Pan, D and Cao, J and Zhou, C},
title = {The molecular mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development of dry-cured ham: the insights of metagenomics and metabolomics.},
journal = {International journal of food microbiology},
volume = {445},
number = {},
pages = {111511},
doi = {10.1016/j.ijfoodmicro.2025.111511},
pmid = {41187361},
issn = {1879-3460},
abstract = {To explore the mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development in Jinhua ham, the influences of R. mucilaginosa on fungal community structure, functional enzyme gene expression, key enzyme activities, γ-glutamyl peptides accumulation and taste attributes were investigated during the dry-ripening. In comparison with Pichia kudriavzevii XS-5 (PK), Rhodotorula mucilaginosa XZY63-3 (RX) and no inoculation (CK), the inoculation with Rhodotorula mucilaginosa EIODSF019 (RE) showed the highest overall acceptance and richness. Metagenomics revealed that RE inoculation inhibited Aspergillus abundance, and the profile of Rhodotorula reached 45.94 % at genus level. The treatment of RE increased the gene abundance of amino acid metabolism pathways; the expression levels of γ-glutamyl transpeptidase gene in RE were increased by 83.27 % compared with CK, and the activities of γ-glutamyl transpeptidase increased from 214 U/g proteins of CK to 567 U/g proteins of RE. LC-MS/MS analysis revealed the total contents of γ-glutamyl peptides increased from 136.40 μg/g of CK to 518.18 μg/g of RE. Partial least squares regression and correlation analysis indicated that γ-Glu-Cys and γ-Glu-Gln were mainly responsible for the improvement of overall acceptance and richness of Jinhua ham with RE inoculation.},
}
@article {pmid41187181,
year = {2025},
author = {Xu, P and Huang, Z},
title = {Omadacycline treatment of severe Chlamydia psittaci pneumonia with septic shock diagnosed via metagenomic next-generation sequencing.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {10},
pages = {1570-1576},
doi = {10.3855/jidc.21299},
pmid = {41187181},
issn = {1972-2680},
mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation &amp; purification/drug effects ; High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; *Psittacosis/drug therapy/diagnosis/microbiology ; *Shock, Septic/drug therapy/diagnosis/microbiology ; *Tetracyclines/therapeutic use ; Metagenomics ; Male ; Treatment Outcome ; Doxycycline/therapeutic use ; },
abstract = {INTRODUCTION: Parrot fever, caused by Chlamydia psittaci, is a zoonotic disease typically treated with tetracyclines. Omadacycline, a novel aminomethyl tetracycline, has limited reports on its efficacy in severe Chlamydia psittaci pneumonia in the literature.<br><br>CASE PRESENTATION: We present a case of a patient with severe Chlamydia psittaci pneumonia showing symptoms of chills, high fever, shock, hepatic and renal insufficiency, and acute respiratory failure with copious yellow watery sputum. Chlamydia psittaci was confirmed by metagenomic next-generation sequencing (mNGS). Despite initial treatment with moxifloxacin and doxycycline, the patient did not improve and was subsequently discharged after receiving omadacycline.<br><br>CONCLUSIONS: Our findings highlight the potential of mNGS for rapid diagnosis of Chlamydia psittaci pneumonia and suggest omadacycline as a potential therapeutic option for severe cases that do not respond to conventional treatment.},
}
@article {pmid41187070,
year = {2025},
author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S},
title = {An Ocean of Opsins.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf189},
pmid = {41187070},
issn = {1759-6653},
support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; },
mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; },
abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.},
}
@article {pmid41186403,
year = {2025},
author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M},
title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154725},
doi = {10.1128/aem.01547-25},
pmid = {41186403},
issn = {1098-5336},
abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.<br><br>IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.},
}
@article {pmid41186329,
year = {2025},
author = {Liu, Y and Liu, X and Hu, Y and Gao, F and Yu, W and Cheng, F},
title = {Evaluating untargeted metabolomics pipelines for sports nutrition research: a review.},
journal = {Analytical methods : advancing methods and applications},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5ay01484k},
pmid = {41186329},
issn = {1759-9679},
abstract = {Untargeted metabolomics has emerged as a transformative approach in sports nutrition research, offering an unbiased means to characterize the complex biochemical responses to exercise, training, and dietary interventions. Unlike targeted assays restricted to predefined metabolites, untargeted strategies capture broad metabolic perturbations across lipid, carbohydrate, amino acid, and nucleotide pathways, enabling the discovery of novel biomarkers and unanticipated physiological mechanisms. This review critically evaluates the design and application of untargeted metabolomic pipelines in the context of exercise and nutrition science, from pre-analytical sample handling and analytical platforms such as NMR, LC-MS, and GC-MS, to data processing using tools like XCMS, MZmine, and MS-DIAL, and subsequent statistical and bioinformatic interpretation. Key applications include delineating acute metabolic shocks induced by endurance exercise, identifying athlete-specific metabolic phenotypes shaped by chronic training, and assessing the impact of nutritional interventions such as fruit intake, amino acid supplementation, or polyphenol-rich foods on exercise recovery and oxidative stress. The integration of metabolomics with other omics, particularly microbiome metagenomics and lipidomics, highlights the potential for systems-level insights into host-microbe-diet interactions. Nonetheless, significant challenges remain, including the reproducibility of findings, difficulties in metabolite identification, and the translational gap between large datasets and actionable nutritional strategies. By synthesizing current strengths, limitations, and controversies, this review emphasizes that the future of sports metabolomics lies in methodological standardization, multi-omics integration, and validation of candidate biomarkers in independent cohorts. Collectively, these efforts position untargeted metabolomics as a cornerstone for advancing precision nutrition and personalized performance monitoring in athletes.},
}
@article {pmid41186225,
year = {2025},
author = {Chuang, H-Y and Chen, W-Y and Chen, S-H and Shao, Y-H and Wu, J-H},
title = {Metagenome-assembled genome sequence of Candidatus Loosdrechtia sp. KJ reconstructed from an alkaline anammox reactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0102425},
doi = {10.1128/mra.01024-25},
pmid = {41186225},
issn = {2576-098X},
abstract = {Candidatus Loosdrechtia sp. KJ is an anaerobic ammonium-oxidizing bacterium enriched from a bioreactor operated under alkaline conditions (pH 9.2 ± 0.4). We report its 3.39 Mb draft genome, containing 3,065 predicted coding sequences, 47 tRNA genes, and a single rrn operon.},
}
@article {pmid41186205,
year = {2025},
author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W},
title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {94},
number = {5},
pages = {e70178},
doi = {10.1111/aji.70178},
pmid = {41186205},
issn = {1600-0897},
support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.<br><br>OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.<br><br>RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.<br><br>CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.},
}
@article {pmid41186087,
year = {2025},
author = {Bortoletto, E and Rosani, U},
title = {Domoic Acid Risk and the Potential of Meta-Omics for Environmental Surveillance.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70593},
doi = {10.1111/gcb.70593},
pmid = {41186087},
issn = {1365-2486},
support = {101186013//HORIZON EUROPE European Innovation Council/ ; },
}
@article {pmid41185941,
year = {2025},
author = {Al-Husseini, A and Komijani, M and Sabah, R},
title = {Impact of Dust Storms on Airborne Bacteria, Heavy Metals, and Inflammatory Markers in Asthmatic Patients.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70109},
doi = {10.1002/mbo3.70109},
pmid = {41185941},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Asthma/blood/microbiology ; *Metals, Heavy/analysis ; *Bacteria/classification/isolation &amp; purification/genetics ; Iraq ; *Dust/analysis ; Female ; Male ; Biomarkers/blood ; Adult ; *Air Microbiology ; Cytokines/blood ; Metagenomics ; Middle Aged ; Young Adult ; Adolescent ; Child ; },
abstract = {Asthma, a chronic bronchial disorder prevalent in children/adolescents, is exacerbated under environmental conditions like dust storms. The current study investigated heavy metal levels, airborne bacteria, and serum IL-4/IL-8 in asthmatics during before/after dust storms in Iraq's Al-Anbar, Baghdad, and Kirkuk provinces. Airborne heavy metals were quantified by ICP-MS, serum cytokines by ELISA, and bacterial communities via metagenomics. Statistical analysis was performed using GraphPad Prism (p < 0.05 significant). ICP-MS revealed considerably elevated post-storm concentrations of As, Ag, B, Ba, Co, Hg, Mg, Mn, Ni, Sn, S, Ti, and V. Asthmatic subjects presented with considerably elevated IL-4 and IL-8 post-storm (p < 0.05) compared to controls (p > 0.05). Metagenomics revealed storm-induced bacterial alterations: Al-Anbar contained elevated Burkholderiaceae, Methylophilaceae, and Rhodobacteraceae; Kirkuk contained elevated Ilumatobacteraceae, Microbacteriaceae, Burkholderiaceae, and Rhodobacteraceae. Baghdad's most prevalent species included Rhodocyclaceae (50%), Burkholderiaceae (17%), and Arcobacteraceae (4.5%). Al-Anbar was significantly richer in microbes (Chao1) and more diverse (Shannon) than other regions following the dust storm (p < 0.0001). These findings indicate that dust storms raise heavy metals, alter airborne bacteria, and increase inflammatory cytokines in asthma sufferers, and these emphasize their role in exacerbating asthma in Iraq.},
}
@article {pmid41185633,
year = {2025},
author = {Villarreal, CX and Chan, DD},
title = {Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption.},
journal = {Cellular and molecular bioengineering},
volume = {18},
number = {5},
pages = {369-385},
pmid = {41185633},
issn = {1865-5025},
abstract = {PURPOSE: The gut microbiome interacts with many systems throughout the human body. Microbiome disruption reduces bone tissue mechanics but paradoxically slows osteoarthritis progression. The microbiome also mediates inflammatory and immune responses, including serum cytokines. Towards our long-term goal of studying how the gut microbiome interacts with synovial joint health and disease, we examined how antibiotics-induced changes to microbial taxa abundance associated to serum cytokine levels.<br><br>METHODS: Mice (n&#x2009;=&#x2009;5&#x2009;+&#x2009;) were provided ad libitum access to water containing antibiotics (1 g/L neomycin, 1 g/L ampicillin, or 1 g/L ampicillin with 0.5 g/L neomycin) or control water from 5- to 16-weeks old, corresponding in skeletal development to&#x2009;~&#x2009;10 to&#x2009;~&#x2009;25 years in humans. At humane euthanasia, we collected cecum contents for 16S metagenomics and blood for serum cytokine quantification for comparison to control and among antibiotic groups. We used dimensional reduction techniques, multiomic integration, and correlation to discriminate antibiotic groups and identify specific relationships between high-abundance taxa and serum cytokines.<br><br>RESULTS: Antibiotic treatment significantly lowered diversity, altered phylum relative abundance, and resulted in significant association with specific taxa. Dimensional reduction techniques and multiomic integration revealed distinct antibiotic-associated clusters based on genera relative abundance and cytokine serum concentration. Cytokines IL-6, MIP-1B, and IL-10 significantly contributed to antibiotic discrimination, significantly different among antibiotic treatments, and had significant correlations with specific taxa.<br><br>CONCLUSIONS: Antibiotic treatment resulted in heterogenous response in gut microbiome and serum cytokines, allowing significant microbe-cytokine links to emerge. The relationships identified here will enable further investigation of the gut microbiome's role in modifying joint health and disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-025-00861-2.},
}
@article {pmid41185359,
year = {2025},
author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y},
title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117622},
doi = {10.1016/j.foodres.2025.117622},
pmid = {41185359},
issn = {1873-7145},
mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; },
abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.},
}
@article {pmid41185305,
year = {2025},
author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T},
title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117551},
doi = {10.1016/j.foodres.2025.117551},
pmid = {41185305},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; },
abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}
@article {pmid41185132,
year = {2025},
author = {Lonsing, A and Martens, GA and Resteu, A and Kizina, J and Wilkie, I and Bahr, A and Harder, J},
title = {Anaerobic Limonene Metabolism in a Methanogenic Enrichment Involves a Glycine Radical Enzyme.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70192},
doi = {10.1111/1462-2920.70192},
pmid = {41185132},
issn = {1462-2920},
support = {//Max Planck Society/ ; },
mesh = {*Limonene/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/enzymology/classification ; *Archaea/genetics/metabolism/enzymology/classification ; *Terpenes/metabolism ; Metagenome ; *Glycine/metabolism ; *Cyclohexenes/metabolism ; Phylogeny ; Metagenomics ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Limonene is a natural monoterpene omnipresent in human environments. It enters wastewater and is also metabolised in methanogenic digesters. A stable limonene-degrading methanogenic enrichment culture was investigated by metagenomic, metatranscriptomic and metaproteomic data sets to characterise the microbial community and identify the limonene degradation pathway. Thirty-two metagenome-assembled genomes revealed a complex community of bacteria and methanogenic archaea dominated by Candidatus Velamenicoccus archaeovorus as the top predator, contributing two-thirds of the reads in the metagenome. The presence of several fermenting bacteria (Anaerolineaceae, Aminidesulfovibrio, Smithellaceae, Lentimicrobium) indicated the recycling of necromass in a microbial loop. Only one hydrocarbon-activating enzyme system was expressed, a member of the alkyl- and arylsuccinate synthase family which is a glycine radical enzyme that adds fumarate to hydrocarbons. The limonenylsuccinate synthase gene encodes a modified substrate binding pocket with two smaller amino acids, suggesting an adaptation for the larger structure of limonene. The limonenylsuccinate synthase operon and a ring cleavage operon, as well as genes for the final syntrophic fermentation to acetate, hydrogen and formate were encoded in a Syntrophobacteraceae genome. Almost all genes for this degradation pathway were highly transcribed and expressed, demonstrating a catalytic role for glycine radical enzymes in methanogenic systems degrading limonene.},
}
@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation &amp; purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.<br><br>METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.<br><br>RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types&#xa0;and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r&#x2009;=&#x2009;0.76), siblings (r&#x2009;=&#x2009;0.61) and infants (r&#x2009;=&#x2009;0.54), while co-occurrence analysis found a higher likelihood (Pr&#x2009;>&#x2009;0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.<br><br>CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}
@article {pmid41183495,
year = {2025},
author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC},
title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish Sauce.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf128},
pmid = {41183495},
issn = {1472-765X},
abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/L) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.},
}
@article {pmid41183487,
year = {2025},
author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y},
title = {Lactobacillus gasseri TF08-1 ameliorate high-fat diet induced Nonalcoholic fatty liver disease and regulates gut microbiota in mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf271},
pmid = {41183487},
issn = {1365-2672},
abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.<br><br>METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing Lactobacillus gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-&#x3b1; level decreased by 42.91%. Meanwhile the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered pro-inflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.<br><br>CONCLUSIONS: L. gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.},
}
@article {pmid41183417,
year = {2025},
author = {Liu, S and Xiang, Y and Liu, P and Deng, J and He, J and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z},
title = {Application of metagenomic next-generation sequencing in the precise and rapid diagnosis of spinal infections.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117165},
doi = {10.1016/j.diagmicrobio.2025.117165},
pmid = {41183417},
issn = {1879-0070},
abstract = {OBJECTIVE: To evaluate the comparative diagnostic efficacy of metagenomic next-generation sequencing (mNGS) versus conventional microbiological culture in spinal infections.<br><br>METHODS: A retrospective analysis was conducted in a cohort of 80 patients with suspected spinal infections who underwent concurrent testing via metagenomic next-generation sequencing (mNGS), microbial culture, and histopathological examination. Diagnostic performance of mNGS and microbial culture was compared using a composite clinical reference standard (definitive diagnosis integrating histopathology, clinical history, and laboratory findings) as the diagnostic gold standard.<br><br>RESULTS: Pathogens were detected in 64 cases (80 %) by mNGS, compared to 34 cases (42.5 %) via conventional microbial culture, demonstrating a statistically significant difference in detection rates (P < 0.001). Using clinical diagnosis (histopathology combined with medical history and laboratory findings) as the gold standard, mNGS exhibited superior sensitivity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) in tissue specimens. Conversely, microbial culture showed higher specificity. In pus specimens, mNGS maintained advantages in sensitivity, accuracy, and PPV, while culture demonstrated higher specificity and NPV.<br><br>CONCLUSION: Compared to conventional microbial culture, mNGS demonstrates superior diagnostic performance in spinal infections, with significantly higher pathogen detection rates and enhanced sensitivity, accuracy PPV and NPV. mNGS exhibits significant advantages over culture in identifying both common pathogens and fastidious organisms, while also demonstrating robust fungal detection capabilities. Additionally, in tissue specimens, mNGS demonstrates relatively pronounced advantages compared to conventional microbial culture. For purulent specimen testing, comprehensive sensitivity and specificity in diagnosis can be achieved through a combined strategy of mNGS and microbial culture.},
}
@article {pmid41183305,
year = {2025},
author = {Yang, R and Ma, J and Abebe, H and Tu, Y},
title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08498},
pmid = {41183305},
issn = {1520-5118},
abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.},
}
@article {pmid41183096,
year = {2025},
author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ},
title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013667},
doi = {10.1371/journal.ppat.1013667},
pmid = {41183096},
issn = {1553-7374},
abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.},
}
@article {pmid41182689,
year = {2025},
author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ},
title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {21},
pages = {e71207},
doi = {10.1096/fj.202502006RR},
pmid = {41182689},
issn = {1530-6860},
mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; },
abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.},
}
@article {pmid41182549,
year = {2025},
author = {Dandare, SU and Dabai, IA and Kumaresan, D and Allen, CCR},
title = {A Novel Salicylaldehyde Dehydrogenase from Alpine Soil Metagenome Reveals a Unique Catalytic Mechanism.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41182549},
issn = {1559-0291},
support = {NGCA-2014-78//Commonwealth Scholarship Commission/ ; },
abstract = {Metagenomic approaches have revolutionised the discovery of novel enzymes with ecological and biotechnological significance from different environments. Here, we report the comprehensive characterisation of a novel salicylaldehyde dehydrogenase (SALDAP) obtained from an alpine soil metagenome. Phylogenetic analysis revealed that SALDAP is the first experimentally characterised Alphaproteobacterial SALD, forming a distinct evolutionary clade among known bacterial enzymes. The recombinant enzyme exhibited strict specificity for NAD[+] and exceptional catalytic efficiency toward aromatic aldehydes, with benzaldehyde as the preferred substrate. Kinetic analyses showed catalytic efficiencies exceeding 10[6] M[-1] s[-1] for aromatics, whereas aliphatics were oxidised with much lower efficiency, consistent with ecological specialisation for aromatic catabolism in alpine soils enriched in lignin-derived compounds. SALDAP was most active under mildly alkaline conditions (optimum pH 8.0) and tolerated a range of chemical environments, though high concentrations of certain metals and solvents were inhibitory. Differential scanning fluorimetry demonstrated that the enzyme was stabilised by ligand binding, with maximal thermal stability observed when both substrate and cofactor were present. Structural alignment with Pseudomonas NahF and docking analyses revealed that SALDAP employs a distinctive catalytic configuration involving ASN-137, ARG-145, GLU-238, and CYS-272, highlighting a non-canonical role for ASN-137 in substrate binding and stabilisation. Based on these findings, we propose a mechanistic model for SALDAP that expands the catalytic diversity of the aldehyde dehydrogenase superfamily. This study establishes a new paradigm for aromatic aldehyde oxidation, underscores the ecological significance of SALDAP in alpine soil microbiomes, and provides a foundation for engineering novel biocatalysts for bioremediation and synthetic biology applications.},
}
@article {pmid41182235,
year = {2025},
author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E},
title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf247},
pmid = {41182235},
issn = {1751-7370},
abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.},
}
@article {pmid41181472,
year = {2025},
author = {Iftikhar, F and Iftikhar, A and Khalid, M and Talha, M and Waafira, A},
title = {Gut microbial signatures in autoimmune hepatitis: unlocking diagnostic and therapeutic potential.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {10},
pages = {6868-6869},
pmid = {41181472},
issn = {2049-0801},
abstract = {Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease with unclear etiology but likely results from a complex interplay of genetic susceptibility and environmental triggers. Emerging evidence highlights the role of gut microbiota in AIH pathogenesis, with specific genera such as Veillonella, Lactobacillus, and Oscillospira demonstrating diagnostic value. Dysbiosis-associated biomarkers like lipopolysaccharide and aspartate aminotransferase further support a microbial role in disease onset and progression. Despite these promising developments, rare AIH variants remain poorly characterized due to methodological and population-level limitations. Moving forward, large-scale, longitudinal studies integrating metagenomics, metabolomics, and host genomic data are needed to establish subtype-specific microbial markers and assess the efficacy of targeted interventions such as probiotics and bacteriophage therapy.},
}
@article {pmid41181328,
year = {2025},
author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS},
title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660939},
pmid = {41181328},
issn = {2235-2988},
mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation &amp; purification ; Haemophilus influenzae/isolation &amp; purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Infant ; },
abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.<br><br>METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.<br><br>RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.<br><br>DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.},
}
@article {pmid41181319,
year = {2025},
author = {Wang, Z and Song, L and Li, D and Jin, Y},
title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1693796},
pmid = {41181319},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; },
abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.},
}
@article {pmid41181040,
year = {2025},
author = {Jeyaraman, M and Balasubramanian, E and Jeyaraman, N and Nallakumarasamy, A and Muthu, S},
title = {Metagenomic analysis of gut microbiome and spondyloarthropathy: A systematic review.},
journal = {World journal of orthopedics},
volume = {16},
number = {10},
pages = {108374},
pmid = {41181040},
issn = {2218-5836},
abstract = {BACKGROUND: Spondyloarthritis (SpA), a prevalent chronic inflammatory disorder, predominantly impacts the axial skeleton, including the spine and sacroiliac joints. Emerging evidence implicates gut dysbiosis in the pathogenesis of SpA.<br><br>AIM: To evaluate the association between gut microbiome alterations and SpA through metagenomic sequencing analyses.<br><br>METHODS: A systematic review was conducted by querying English-language databases, including PubMed, EMBASE, and Google Scholar, spanning 2000 to 2023. From an initial pool of 150 studies, four articles meeting stringent inclusion and exclusion criteria were selected for analysis.<br><br>RESULTS: The reviewed studies identified an enrichment of opportunistic pathogenic bacterial species, such as Clostridium spp., Prevotella spp., and Bacteroides spp., alongside viral families including Gratiaviridae and Quimbyviridae, in individuals with ankylosing spondylitis compared to healthy controls. Dysregulated metabolic pathways were highlighted as potential mediators of chronic inflammation and arthritic manifestations. Notably, treatment with tumor necrosis factor inhibitors demonstrated efficacy in mitigating SpA symptoms and restoring gut microbial balance.<br><br>CONCLUSION: The findings underscore a significant presence of pathogenic gut microbiota in SpA patients, suggesting a pivotal role in disease progression. Future investigations should focus on species-specific microbial targets to develop innovative therapies for preventing and managing SpA and associated gut dysbiosis.},
}
@article {pmid41180884,
year = {2025},
author = {Sharma, P and Kapoor, N and Langer, S},
title = {Comparative Analysis of Gut Bacterial Communities in Fish and Shellfish of Great Himalayan River System.},
journal = {Indian journal of microbiology},
volume = {65},
number = {3},
pages = {1734-1747},
pmid = {41180884},
issn = {0046-8991},
abstract = {The gut microbiota comprises a unique micro-ecosystem and plays important role in various metabolic functions of the host. Cirrhinus mrigala and Maydelliathelphusa masoniana are two important species of fish and shellfish found in Chenab and Ravi rivers of Himalayan river system. This is the first report on the core gut microbiota of M. masoniana and C. mrigala using Illumina Miseq Sequencing. Gut bacterial diversity of crabs and fishes are studied from the rivers as well as farms. The core microbiome of crab gut samples consists of genera: Bacteroides, Dysgonomonas, Lactobacillus, Leptotrichia, Acinetobacter, Prevotella, Prevotella 1, Pseudomonas, Fusobacterium and Streptococcus. The core microbiome of fish gut samples consists of genera: Acinetobacter, Lactobacillus, Methanosaeta, Prevotella and Pseudomonas. The result shows higher relative abundance of Bacteroides and Lactobacillus in river Ravi than Chenab. Gut bacterial diversity of fishes and crabs of river Chenab is comparatively lower than the river Ravi. Three genera (Bacteroides, Oceanobacillus and Lactococcus) show significant variation (p value < 0.05) in fishes and crabs. Our study generated sequencing data on the gut microbiota of M. masoniana and C. mrigala can establish a base for the development of therapeutic approaches in dealing with the health conditions of diseased fishes and crabs. Gut microbial characterization will not only help in growth and development of the host but also helps in minimizing the disease susceptibility.},
}
@article {pmid41180871,
year = {2025},
author = {Kumari, A and Rao, KVB},
title = {Exploring the Bacterial Diversity of Rajgir Hot Spring in India and its Antibacterial Potential.},
journal = {Indian journal of microbiology},
volume = {65},
number = {3},
pages = {1490-1497},
pmid = {41180871},
issn = {0046-8991},
abstract = {UNLABELLED: Hot springs naturally produce geothermally heated water and are renowned for their diverse microbial communities. Metagenomics studies unveil this microbial diversity. In this study, the bacterial community, along with thermophilic actinobacteria from the Rajgir hot spring, located in Bihar, India, was analyzed using 16S rRNA gene metagenomics sequencing. The sediment temperature was recorded at 45 °C. Investigation of the hot spring ecology revealed the presence of 16 bacterial phyla, with actinobacteria being abundant. Streptomyces, Sphingomonas, Gemmatimonas, Paracoccus, Aeromicrobium, and Actinomyces were among the most common genera found in the sediment samples. These six genera exhibited the highest abundance, with Streptomyces being the most prevalent at 19%, followed by other genera at 13%, 11%, 11%, 10%, and 9%, respectively. Actinobacteria isolated from the hot spring samples were further examined for their antibacterial activities against pathogenic bacteria. Isolates from the Rajgir hot spring demonstrated potential antibacterial activity based on their inhibition zones on agar plates. The results of the antimicrobial screening revealed that AIBRSS1 exhibited the most significant inhibition zone, measuring 26 mm, against Listeria monocytogenes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01482-z.},
}
@article {pmid41180687,
year = {2025},
author = {Muhammad Abdur Rehman, A and Rizwan, MH and Khalid, M and Talha, M and Waafira, A},
title = {Revolutionizing endocarditis diagnosis: AI meets metagenomics for rare Bartonella detection.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {11},
pages = {7772-7773},
pmid = {41180687},
issn = {2049-0801},
abstract = {Bartonella endocarditis is notoriously challenging to diagnose due to its insidious onset, nonspecific symptoms, and the limitations of conventional culture-based techniques. Artificial intelligence (AI)-driven metagenomic next-generation sequencing (mNGS) represents a transformative diagnostic approach by integrating machine learning algorithms with culture-independent sequencing data to improve accuracy and sensitivity. This technique overcomes barriers such as culture bottlenecks and post-surgical sample limitations, achieving high diagnostic specificity while enabling the detection of rare or novel pathogens. Despite challenges including limited reference databases, contamination risks, and cost-related barriers in low-resource settings, AI-enhanced metagenomics offers a promising path toward faster and more precise diagnosis of Bartonella endocarditis. Its integration into clinical workflows, supported by continuous algorithm development, cost optimization, and standardized protocols, has the potential to improve patient outcomes in rare infectious diseases.},
}
@article {pmid41180610,
year = {2025},
author = {Deng, Q and Yang, Y and Gao, S and Lu, M and Zhao, Y and Wang, Z},
title = {Integrated Molecular Diagnostics Unmask Legionella Pneumophila and Fungal Coinfection in an Immunocompromised Host: A Case Study of Precision Antimicrobial Stewardship.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5549-5556},
pmid = {41180610},
issn = {1178-6973},
abstract = {BACKGROUND: Legionella pneumophila poses significant diagnostic challenges in immunocompromised hosts due to its fastidious growth requirements and nonspecific clinical presentation. Conventional culture methods have limited sensitivity (30-80%), while molecular diagnostics require multi-platform validation to ensure reliability.<br><br>CASE DESCRIPTION: A 57-year-old woman with rheumatic heart disease, chronic renal failure, and immunosuppression presented with acute respiratory failure. Initial investigations revealed leukocytosis (19.03&#xd7;10[9]/L), hyponatremia (127 mmol/L), elevated procalcitonin (42.55 ng/mL), and bilateral pulmonary infiltrates. Bronchoalveolar lavage fluid (BALF) analysis employed three molecular methods: isothermal amplification for screening (positive for L. pneumophila on ICU admission), digital PCR (dPCR, 4,455 copies/mL after 10-fold dilution) reconfirmed L. pneumophila infection, and metagenomic next-generation sequencing (mNGS; 384,661 Legionella reads alongside 3,474 Candida glabrata reads). Subsequent fungal &#x3b2;-D-glucan testing (674.8 pg/mL) and culture validated Candida glabrata coinfection. Antimicrobial therapy from targeted moxifloxacin/azithromycin to co-infection therapy with carbapenem escalated from Imipenem-cilastatin to sulbactam/cefoperazone for suspected gram-negative coinfection and fluconazole escalated to amphotericin B for resistant candidiasis guided by CRP/PCT trends.<br><br>CONCLUSION: Integrated molecular diagnostics enable rapid pathogen identification in critically ill immunocompromised hosts. Multi-platform verification (isothermal amplification/dPCR/mNGS) overcomes technical limitations of single methods, while serial biomarker monitoring optimizes antimicrobial stewardship for mixed infections.},
}
@article {pmid41180402,
year = {2025},
author = {Chen, C and Xu, D and Jiang, B and Lu, X and Yu, C and Wang, Y and Wang, H and Li, J and Zhu, J},
title = {Precipitation-driven restructuring of rhizosphere microbiota enhances alpine plant adaptation.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1641511},
pmid = {41180402},
issn = {1664-462X},
abstract = {INTRODUCTION: Climate-driven precipitation changes are increasingly threatening alpine ecosystems, yet the adaptive responses of soil microbiomes to rainfall variability remain poorly characterized. This knowledge gaphinders our ability to predict ecosystem resilience under future climate scenarios.<br><br>METHODS: We combined metagenomic sequencing with detailed physicochemical analyses to examine how natural precipitation events reshape the microbial communities in both rhizosphere and bulk soils associated with Poa alpigena in the alpine sandy ecosystems of Qinghai Lake.<br><br>RESULTS: Rainfall significantly reduced bacterial alpha diversity, particularly in bulk soils, and triggered a compositional shift from drought-resistant taxa (e.g., Geobacter, Pseudomonas) to moisture-adapted genera (e.g., Azospirillum, Methylobacterium). Actinobacteria remained consistently dominant (31.56-34.62%), while Proteobacteria abundance decreased markedly in the rhizosphere post-rainfall. Metabolic reconstruction revealed a transition from pre-rainfall carbohydrate catabolism to post-rainfall anaerobic energy production and carbon fixation pathways. The rhizosphere microbiome uniquely displayed drought-induced biofilm formation and rainfall-enhanced branched-chain amino acid metabolism. Soil moisture and total carbon were identified as primary drivers of microbial restructuring in bulk soils, whereas root exudates conferred stability to rhizosphere communities against hydrological fluctuations.<br><br>DISCUSSION: These results elucidate microbiome-mediated adaptive strategies to precipitation changes in alpine sandy ecosystems, highlighting the critical buffering role of plant-microbe interactions. The study provides a mechanistic basis for predicting and restoring climatevulnerable wetlands under increasingly variable hydrological regimes.},
}
@article {pmid41180097,
year = {2025},
author = {Jin, S and Meng, S and Huang, Q and Xie, H and Zheng, J and Wang, R},
title = {Joint application of multiplex drop-off digital PCR, droplet digital PCR, and metagenomic next-generation sequencing for the diagnosis of suspected infectious diseases: A retrospective cohort study.},
journal = {Journal of intensive medicine},
volume = {5},
number = {4},
pages = {407-418},
pmid = {41180097},
issn = {2667-100X},
abstract = {BACKGROUND: Critically ill patients in ICUs are highly vulnerable to infectious diseases. Early and accurate identification of pathogens is vital for initiating appropriate antimicrobial therapy. To evaluate the diagnostic effectiveness in patients with suspected infectious diseases; three different molecular technologies and conventional microbiological tests were used.<br><br>METHODS: A total of 97 individuals suspected of having infectious diseases were retrospectively enrolled from July 2023 to January 2024 at Shanghai General Hospital. Samples were collected for metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction (ddPCR), multiplex drop-off digital polymerase chain reaction (MDO-dPCR), and conventional microbiological tests (CMTs) for suspected pathogen detection. The diagnostic efficacies of the three molecular technologies and CMTs were compared, and the effects of their joint application on clinical outcomes were evaluated. Intergroup comparisons were performed using the Kruskal-Wallis test, with a P-value <0.05 considered statistically significant.<br><br>RESULTS: Joint detection exhibited a high negative predictive value. The sensitivity of MDO-dPCR, ddPCR, and mNGS was 52.6%, 48.5%, and 96.6%, respectively; and the corresponding specificity was 72.5%, 73.3%, and 50.0%. A positive correlation was observed between pathogen copies detected using MDO-dPCR and procalcitonin (Pearson's &#x3c1;=0.21, P=0.039), acute physiology and chronic health evaluation II (Pearson's &#x3c1;=0.24, P =0.018), and sequential organ failure assessment (Pearson's &#x3c1;=0.25, P=0.012). Therapeutic regimens were adjusted in 51.5% of the patients (50/97) based on the results of the combination tests.<br><br>CONCLUSIONS: In the present study, we highlighted the significance of molecular technologies for the early diagnosis of patients with suspected infections. These technologies can serve as a complement to CMTs and should be implemented promptly to guide clinicians in providing timely and effective anti-infective treatments. Future studies should aim to confirm these findings in large-scale clinical trials to refine diagnostic protocols, while also incorporating cost-utility analyses.},
}
@article {pmid41179961,
year = {2025},
author = {Schnabel, E and Xavier, CAD and Whitfield, AE and Dubrow, Z and Pham, G and Cieniewicz, E},
title = {Exploring the Virome of Blackberry and Wild Rubus spp. in South Carolina.},
journal = {Phytobiomes journal},
volume = {9},
number = {1},
pages = {80-94},
pmid = {41179961},
issn = {2471-2906},
abstract = {Numerous viruses infect blackberry, and they are associated with virus disease complexes with complicated etiologies. Blackberry virus diseases limit the lifespan of blackberry production in the Southeastern United States. Although some previous research has been conducted to understand which viruses are prevalent in South Carolina, a comprehensive study on the virome of blackberry has not been done in this region. Additionally, the role of wild Rubus as a virus inoculum source is likely underappreciated and represents a potential opportunity for disease management. We took a comprehensive approach to characterize viral genome sequences from known and novel viruses using metatranscriptomic sequencing of blackberry and wild Rubus spp. leaf samples collected in 2021 from eight sites across South Carolina. We detected 17 known and 6 novel plant viruses and describe relevant genome sequence information. Although the etiologies of these novel viruses are yet to be elucidated, they should be considered part of the blackberry/wild Rubus virome and further studied. We describe instances of potential connectivity of virus populations between cultivated blackberry and wild Rubus for several viruses at several sites. In addition to plant viruses, we describe numerous viruses likely associated with foliar fungi, referred to as Rubus leaf-associated viruses. This study revealed a diverse landscape of both known and novel viruses in blackberry and wild Rubus in South Carolina and has stimulated topics for future research, such as temporal analyses of virus spread at the landscape scale and investigating potential vectors and the biological relevance of novel viruses.},
}
@article {pmid41179353,
year = {2025},
author = {Carboni, S and Poirier, AC and Peralta-Aguilar, AP and Watsa, M and Erkenswick, G and Melin, AD},
title = {The Scent Gland Microbiomes of Wild Tamarins Provide New Insight Into Microbial Contributions to Olfactory Communication.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72335},
pmid = {41179353},
issn = {2045-7758},
abstract = {The microbiome of mammalian scent glands is thought to contribute to the production of odorant compounds involved in sensory communication. Yet, the extent to which glandular microbiomes contain bacteria relevant to odor production and vary by host species, scent marking behavior, or gland morphology remains poorly understood, particularly in wild animals. We sampled microbes collected from skin swabs of suprapubic and sternal scent glands in wild Peruvian saddleback tamarins (Leontocebus weddelli; n = 19) and emperor tamarins (Tamarinus imperator; n = 20) to better understand glandular microbial communities. We aimed to: (1) profile glandular microbiomes of both species, focusing on odor-related taxa and metabolic pathways, and (2) determine whether suprapubic glands, more often in contact with the external environment, had higher diversity and distinct composition of odor-related taxa and pathways compared to sternal glands. We generated metagenomic reads using short-read DNA shotgun sequencing from glandular swabs. We identified 18 odor-associated microbial taxa in both tamarin species, mainly Staphylococcus and Corynebacterium, and 26 pathways, including pyruvate fermentation and amino acid metabolism. Suprapubic glands had lower Shannon alpha diversity relative to sternal glands, especially in L. weddelli. The glands of L. weddelli also differed in taxonomic composition, with odor-related taxa more abundant in suprapubic glands. Our results provide evidence for the involvement of scent gland microbiomes in host communication biology. Glandular specializations differed not only between closely related tamarin species but also between gland types within the same individuals, suggesting a nuanced pattern of host-microbe coevolution that may shape interactions important for olfactory communication.},
}
@article {pmid41179309,
year = {2025},
author = {Yan, L and He, B and Deng, Q and Qiu, Y and Lin, L and Shi, B and Wang, J and Chen, F},
title = {Is systemic inflammation a missing link between oral microbiome and oral squamous cell carcinoma? Results from multi-omics integration analyses.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2574326},
pmid = {41179309},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate whether systemic inflammation mediates the relationship between oral microbiome alterations and oral squamous cell carcinoma (OSCC) through multi-omics integration analyses.<br><br>METHODS: Metagenomic sequencing of unstimulated saliva samples from 65 OSCC patients and 65 matched controls was performed. Plasma levels of 34 inflammatory cytokines were profiled using Luminex assay. Six machine learning models identified potential diagnostic microbial markers. Mediation analysis assessed whether inflammation serves as a mechanistic link between oral microbiota and OSCC.<br><br>RESULTS: OSCC patients exhibited reduced species richness and significant beta diversity alterations. Among 155 differential species identified, 25 were enriched in OSCC, including Capnocytophaga sputigena, Gemella haemolysans, Staphylococcus aureus, and several Streptococcus species, with higher abundance in poor oral hygiene conditions. The Boruta-CatBoost model achieved exceptional diagnostic performance (bootstrap AUC&#x2009;=&#x2009;0.991; 5-fold cross-validation AUC&#x2009;=&#x2009;0.947). Functional profiling revealed 22 metabolic pathways over-represented in OSCC, notably lipopolysaccharide biosynthesis. Nine circulating cytokines (IL-22, IL-6, IL-2, CCL5, GM-CSF, IL-1&#x3b2;, TNF-&#x3b1;, IL-18, IFN-&#x3b1;) were significantly elevated in OSCC patients. Mediation analysis revealed that IL-22 partially mediated the effect of Staphylococcus aureus on OSCC risk, while CCL5 mediated associations of Gemella haemolysans and Streptococcus species with OSCC (mediation proportions: 29.9-50.1%).<br><br>CONCLUSION: Our multi-omics integration suggests that systemic inflammation, particularly through IL-22 and CCL5 upregulation, serves as a mechanistic link between specific oral bacteria and OSCC risk, which could provide new strategies for OSCC prevention and early intervention.},
}
@article {pmid41178975,
year = {2025},
author = {Li, B and Xu, W and Wang, W and Mao, M and Huang, X and Zhang, E},
title = {Discrepancies in gut microbial communities and serum metabolites of Hu sheep with different backfat thickness.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667088},
pmid = {41178975},
issn = {1664-302X},
abstract = {Although market demand for lean meat continues to rise, the regulatory mechanisms governing backfat thickness (BFT) metabolism remain poorly understood. This study employed a multi-omics approach to investigate BFT-associated differences in Hu sheep with distinct fat deposition phenotypes. From 160 genetically similar Hu sheep, we selected 12 individuals with non-significant weight differences (P > 0.05) but extreme divergence in BFT [6 high-BFT (HBF) and 6 low-BFT (LBF) individuals]. Using integrated metagenomics and metabolomics, we systematically compared ileal microbial community structure and serum metabolic profiles between the two groups. HBF sheep showed significantly increased adiposity and altered ileal microbiota composition, characterized by elevated abundances of Carnobacterium, Parabacteroides distasonis, Lactiplantibacillus, and Bifidobacterium. Serum metabolomics identified key differential glycerophospholipids-1-(9Z-octadecenoyl)-2-(11Z-eicosenoyl)-glycero-3-phosphate, PE-NMe(15:0/20:3(5Z,8Z,11Z)), PE-NMe2(18:1(9Z)/20:0), and PE-NMe2(18:1(9Z)/22:1(13Z))-all enriched in glycerophospholipid metabolism pathways. Integrated correlation analysis revealed strong associations between P. distasonis abundance and these phospholipids. These results demonstrate BFT-related adaptive remodeling of the serum metabolome and gut microbiota, identifying P. distasonis as a potential modulator of the host-microbe metabolic axis in ovine adiposity regulation.},
}
@article {pmid41178973,
year = {2025},
author = {Teixeira, MJ and Barbosa, DJ and Dinis-Oliveira, RJ and Freitas, AR},
title = {Redefining postmortem interval estimation: the need for evidence-based research to bridge science and justice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1646907},
pmid = {41178973},
issn = {1664-302X},
abstract = {Classical methods for postmortem interval (PMI) estimation have been applied for nearly a century. Contrary to the notion of being simple or easily accessible, these approaches require highly specialized training, including a medical degree, postgraduate specialization in forensic pathology, and extensive practical experience. Classical PMI estimation relies on observable physical and chemical changes in the human cadaver, such as rigor mortis, livor mortis, algor mortis, and transformative processes during decomposition. These methods are fundamental in medicolegal practice but remain largely influenced by environmental and individual variability. Recent advances in forensic research, particularly in microbiology and biochemistry, have introduced innovative approaches that complement traditional methods, offering greater accuracy and reliability, though resource-intensive. Emerging approaches leverage the predictable postmortem succession of microbial communities (thanatomicrobiome) and biochemical alterations in cadaver fluids and tissues. Techniques such as metagenomics, metatranscriptomics, and metabolomics enable detailed analysis of these changes, while computational models and machine learning further refine PMI estimates. Despite advancements, challenges persist, including variability due to environmental factors and limited access to human decomposition data. Integrating multi-omics approaches and artificial intelligence offers a path forward, addressing these limitations and enhancing the accuracy of PMI estimation. This review provides a comprehensive overview of PMI estimation, critically examining classical approaches and highlighting cutting-edge methodologies rooted in thanatomicrobiology and thanatochemistry. We emphasize the transformative potential of multi-omics integration and artificial intelligence in improving PMI accuracy. Importantly, we propose a paradigm shift: redefining PMI estimation through evidence-based, interdisciplinary research that bridges scientific rigor and judicial application. Transdisciplinary collaboration and standardized methodologies will be essential to translate emerging knowledge into robust forensic tools that serve both science and justice.},
}
@article {pmid41178971,
year = {2025},
author = {Du, H and Hao, X and Lin, B and Zhu, Y and Yang, Y and Tang, M and Wu, W and Wang, D and Lin, B and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the role of intestinal microbiota in mitigating acute radiation-induced intestinal injury through high-energy X-ray FLASH radiotherapy via metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1601244},
pmid = {41178971},
issn = {1664-302X},
abstract = {OBJECTIVES: This study preliminarily examines the potential correlation between the gut microbiome and the protective effects of FLASH radiotherapy (FLASH-RT) on intestinal tissue using metagenomic analysis.<br><br>METHODS: Compact single high-energy X-ray source (CHEXs) FLASH-RT was employed for FLASH irradiation, while EBT3 radiochromic film and a fast current transformer were used to measure the absolute dose and the pulsed beam characteristics. Sham radiotherapy (control), FLASH-RT (333&#x202f;Gy/s), and Conventional dose rate radiotherapy (CONV-RT, 0.07&#x202f;Gy/s) were performed on whole abdomen of normal C57BL/6J female mice (10&#x202f;Gy, 12&#x202f;Gy, 14&#x202f;Gy). At 72&#x202f;h post-irradiation, intestinal contents from normal C57BL/6J female mice were collected for metagenomic analysis. The survival status, body weight, and damage to normal tissues were observed.<br><br>RESULTS: At 28&#x202f;days post-whole abdomen irradiation with doses of 12&#x202f;Gy, the survival rate of the FLASH group was higher than that of the CONV group (p&#x202f;<&#x202f;0.05). Histological analysis of intestinal tissues by H&amp;E staining revealed significantly less acute intestinal damage and inflammation in the FLASH group compared to the CONV group. Further macrobiome analysis using LEfSe indicated that the abundance of beneficial bacteria, including Weissella, Lactobacillus ruminis and Lactobacillus taiwanensis was significantly higher in the FLASH group than in the CONV group. Moreover, compared to the CONV group, the FLASH group exhibited significant upregulation of several signaling pathways, including the glycosaminoglycan degradation, PI3K/Akt and arabinogalactan biosynthesis Mycobacterium signaling pathway.<br><br>CONCLUSION: Compared to CONV-RT, high-energy X-ray FLASH irradiation exerts radioprotective effects on normal intestinal tissue. Alterations in the gut microbiota and associated signaling pathways may be linked to the protective effects of FLASH.},
}
@article {pmid41178960,
year = {2025},
author = {Abildinova, GZ and Benberin, VV and Vochshenkova, TA and Mussin, NM and Afshar, A and Tamadon, A},
title = {Distinct gut microbial species, but not phylum-to-genus composition, associate with insulin resistance: a unique perspective from the Kazakh population.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683885},
pmid = {41178960},
issn = {1664-302X},
abstract = {OBJECTIVES: Links between gut microbiota and insulin resistance (IR) vary across populations. We profiled the fecal microbiota of Kazakh adults to test whether community composition associates with IR at broad (phylum → genus) and species levels.<br><br>METHODS: In a cross-sectional case control study (N&#x202f;=&#x202f;200; IR&#x202f;=&#x202f;183, controls&#x202f;=&#x202f;17), TyG indexed IR status. 16S rRNA sequencing (two primer pools; nine hypervariable regions) characterized taxa. After CSS normalization, we compared presence/absence across groups (&#x3c7;[2]) and modeled species with univariate and multivariable logistic regressions, using absence of each species as the predictor.<br><br>RESULTS: High-level composition did not differ between IR and controls (phylum, class, family, genus; all p&#x202f;>&#x202f;0.05). In contrast, several species differed. In univariate models, absence of Actinomyces odontolyticus (OR&#x202f;=&#x202f;25.55, p&#x202f;=&#x202f;0.010), Bifidobacterium kashiwanohense (OR&#x202f;=&#x202f;12.69, p&#x202f;=&#x202f;0.015), Lactobacillus sp. (OR&#x202f;=&#x202f;5.71, p&#x202f;=&#x202f;0.020), and Streptococcus lactarius (OR&#x202f;=&#x202f;6.27, p&#x202f;=&#x202f;0.044) associated with higher IR odds, suggesting protection when present; whereas absence of Alistipes onderdonkii (OR&#x202f;=&#x202f;0.30, p&#x202f;=&#x202f;0.044) and Prevotella copri (OR&#x202f;=&#x202f;0.19, p&#x202f;=&#x202f;0.003) associated with lower IR odds, suggesting risk when present. In multivariable models, these signals persisted: absence of P. copri (OR&#x202f;=&#x202f;0.146, p&#x202f;=&#x202f;0.003) and Roseburia inulinivorans (OR&#x202f;=&#x202f;0.143, p&#x202f;=&#x202f;0.011) predicted lower IR odds (risk alignment), while absence of Lactobacillus sp. (OR&#x202f;=&#x202f;8.29, p&#x202f;=&#x202f;0.016) and Coprococcus catus (OR&#x202f;=&#x202f;7.04, p&#x202f;=&#x202f;0.004) predicted higher IR odds (protective alignment).<br><br>CONCLUSION: In this Kazakh cohort, no broad compositional signal emerged, but species-specific associations were strong and bidirectional. Findings highlight population-specificity and identify candidate species associated with IR that may serve as hypothesis-generating targets for future validation. Any attempt to modulate these taxa for insulin resistance is unproven and requires function-resolved, diet-measured longitudinal studies and randomized trials before clinical application. The IR:control imbalance (183:17) increases uncertainty for low-prevalence taxa; species-level findings are hypothesis-generating and require validation in a more balanced design. Because 16S rRNA profiling does not measure gene functions or metabolites, these species-IR associations are hypothesis-generating and warrant validation using shotgun metagenomics and metabolomics.},
}
@article {pmid41177622,
year = {2026},
author = {Sun, C and Zhao, W and Yue, W and Cheng, H and Long, A and Yin, J and Sun, F and Wang, Y},
title = {Degradation of polymeric carbohydrates coupled with cellular motility driving microbial niche separation in the Pearl River Estuary surface sediment.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {414-423},
doi = {10.1016/j.jes.2025.04.032},
pmid = {41177622},
issn = {1001-0742},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Estuaries ; Rivers/microbiology ; Carbohydrates ; Metagenome ; *Carbohydrate Metabolism ; },
abstract = {Estuaries are key areas for organic carbon cycling, where polymeric carbohydrates are abundant and chemically diverse. The recycling of these polymers by microbes depends on a variety of carbohydrate-active enzymes (CAZymes). However, it remains unclear whether other gene traits, particularly those related to cell motility toward polymeric carbohydrates, are intertwined with carbohydrate depolymerization and niche specialization in estuarine sediment soils. In this study, estuarine sediments were incubated with four prevalent polymeric carbohydrates (laminarin, fucan, cellulose, and chitin) under anaerobic conditions. Based on metagenomic analysis, we identified potential responses to the degradation and utilization of polymeric carbohydrate substrates from the perspectives of CAZymes and sugar transporters. The analysis of metagenomic gene data also revealed a positive correlation between chemotaxis and the abundance of CAZymes genes. Furthermore, metagenomes-assembled genomes (MAGs) that exhibited higher abundance in polysaccharide-treated samples compared to controls also featured elevated copies of genes involved in polysaccharide utilization loci (PULs), chemotaxis, as well as those associated with flagellar or gliding movement. SprB and CTDs associated with gliding proteins genes are essential for type IX secretion system-mediated secretion of CAZymes and gliding motility in Bacteroidota. The enhanced potential for mobility, coupled with the ability to degrade polymeric carbohydrates, may enable these bacteria to exploit nutrients beyond carbon sources, thereby potentially broadening their ecological niches.},
}
@article {pmid41177619,
year = {2026},
author = {Yang, R and Wei, Y and Jiang, J and Kong, X and Wu, S and Tang, Q and Liu, Y and Luo, L and Ali, EAE and Chen, H},
title = {Adaptation of microbial gene polymorphisms of the partial nitritation-anammox process for maintaining denitrification performance and robustness under salinity stress.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {39-50},
doi = {10.1016/j.jes.2025.04.028},
pmid = {41177619},
issn = {1001-0742},
mesh = {*Denitrification ; *Salt Stress ; Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; Wastewater ; Salinity ; Ammonium Compounds/metabolism ; Nitrification ; Bacteria/genetics ; },
abstract = {To explore the adaptive mechanisms of the partial nitritation-anammox (PNA) process under high salinity stress during kitchen wastewater treatment, focusing on their physiological and molecular responses through metagenomic analysis. An airlift inner-circulation partition bioreactor (AIPBR) was developed, featuring an inner cylinder and a flow guide tube to create distinct oxygen gradients, facilitating the study of microbial adaptation under varying salt conditions. The AIPBR was operated with synthetic wastewater containing ammonium concentrations of 1800 ± 100 mg/L and salinity gradients ranging from 1 to 10 g/L, followed by a fixed salinity period at 6 g/L, with ammonium concentrations approximately 850 mg/L. High-throughput metagenomic analysis revealed shifts in functional genes and metabolic pathways in response to salinity stress. Anammox bacteria adapted by enriching genes involved in the synthesis of osmoprotective compounds and activating energy-producing pathways like the tricarboxylic acid cycle (TCA). These adaptations, along with modifications in membrane composition, were essential for sustaining system stability under elevated salinity. Under prolonged high salinity stress, anaerobic ammonium oxidizing (AnAOB) exhibited improved salt tolerance, maintaining a total nitrogen removal efficiency above 85 % and stabilizing after an adaptation phase. The metagenomic data revealed a marked enrichment of genes associated with ion transport, stress response mechanisms, and DNA repair pathways. Changes in microbial community composition favored salt-tolerant species, supporting system stability. These findings highlight the applicability of the developed bioreactor for scaling up the PNA process to handle high-salinity wastewater, providing a promising avenue for sustainable nitrogen removal in challenging environments.},
}
@article {pmid41177609,
year = {2026},
author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W},
title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {300-307},
doi = {10.1016/j.jes.2025.04.024},
pmid = {41177609},
issn = {1001-0742},
mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; },
abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.},
}
@article {pmid41177409,
year = {2025},
author = {Lin, S and Pan, M and Ma, Y and Chen, Z and Lyu, T and Dong, R and Ruan, R and Liu, S},
title = {Microalgae-mediated shaping of bacterial communities enhances antibiotic removal and antibiotic resistance control.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133577},
doi = {10.1016/j.biortech.2025.133577},
pmid = {41177409},
issn = {1873-2976},
abstract = {The microalgae-bacteria symbiosis sludge (MBSS) system offers a promising strategy for efficient wastewater treatment and nutrients upcycling. However, maintaining stable and effective performance facing antibiotic stress remains a significant challenge. This study explored the regulation strategy of microbial succession towards sulfadiazine (SDZ)-containing wastewater remediation while controlling antibiotic resistance genes (ARGs) spread in MBSS system. The MBSS achieved efficient SDZ removal of up to 99.8%, with an optimal microalgae-to-activated sludge inoculation ratio of 1:3. However, the highest nutrient upcycling efficiencies (33.7% for nitrogen and 98.6% for phosphorus) were observed at an inoculation ratio of 1:1. Metagenomics analysis revealed that genera Chlorella and Micractinium of Chlorophyta were strongly positively correlated with SDZ removal. Moreover, microalgae inoculation significantly modulated the microbial community structure, promoting the dominance of genera Rhodanobacter and Dokdonella in MBSS. This microbial succession could potentially facilitate bacterial co-degradation of SDZ and contribute to a substantially reduced level of ARGs (with the relative abundance of sul1 and sul2 decreasing to 22.9% post-treatment). Overall, the strategy of regulating microalgae inoculation in the MBSS significantly enhanced antibiotic removal and nutrient recovery while controlling the proliferation and spread of ARGs by directing microbial community succession.},
}
@article {pmid41177051,
year = {2025},
author = {Guo, Y and Lin, X and Song, B and Zhao, C and Riaz, M and Ishfaq, M},
title = {Biochar remodeled rhizosphere microbial community structure and function to alleviate sugar beet under fomesafen phytotoxicity.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127821},
doi = {10.1016/j.jenvman.2025.127821},
pmid = {41177051},
issn = {1095-8630},
abstract = {Residual fomesafen in soybean field soil can adversely affect subsequent sugar beet crops. Biochar has been shown to alleviate this damage, the regulatory mechanisms by which it influences the rhizosphere microbial community and its functions in the presence of fomesafen residues remain unclear. This study employed plant physiological assessments, amplicon sequencing, and metagenomic analysis to investigate root physiology, the rhizosphere soil microbial community, and their functional responses to fomesafen toxicity with biochar addition. By comparing sterilized soil with normal soil, that all measured indices in the sterilized soil were reduced, confirming that biochar mitigates fomesafen phytotoxicity through soil microorganisms. Biochar increased root biomass by 37.50 % under fomesafen residue stress, reduced malondialdehyde content in sugar beet roots, enhanced antioxidant enzyme activity, and improved soil multifunctionality by 13.95 %. Furthermore, biochar significantly restored the richness and diversity of rhizosphere fungi and bacteria under fomesafen residue stress. The relative abundance of Dehalococcoidia, a potential herbicide-degrading bacterium, increased significantly under fomesafen stress (90.32 %) and peaked under biochar mitigation treatment (94.02 %), suggesting its potential as a biomarker for fomesafen residues. Biochar alleviated fomesafen's impact on the microbial network, restoring it to a molecular ecological network similar to the control. Metagenomic analysis revealed that biochar increased the Calvin-Benson-Bassham cycle (29.87 %), the nitrogen fixation pathway (21.42 %), and the phosphate transport pathway (10.60 %). By enhancing soil multifunctionality and reshaping rhizosphere microbial communities, biochar improves the stress resistance of sugar beet roots and mitigates damage caused by fomesafen. This finding is significant for maintaining the microecological balance of the rhizosphere.},
}
@article {pmid41177050,
year = {2025},
author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y},
title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127839},
doi = {10.1016/j.jenvman.2025.127839},
pmid = {41177050},
issn = {1095-8630},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.},
}
@article {pmid41177031,
year = {2025},
author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Bernstein, A and Cupples, AM},
title = {Identification of the dominant methanotrophs in trichloroethene degrading enrichment cultures from multiple sources.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140268},
doi = {10.1016/j.jhazmat.2025.140268},
pmid = {41177031},
issn = {1873-3336},
abstract = {The current study examined the potential of bioremediation to clean up trichloroethene (TCE) contaminated sites using co-metabolic TCE biodegradation in methanotrophic enrichment cultures. Methanotrophic cultures were developed from both uncontaminated soils (agricultural soils) and impacted sediment from two sites. Following the enrichment of methanotrophs, the cultures were tested for their ability to degrade TCE. Whole genome sequencing data indicated the dominance of the genus Methylocystis and, to a lesser extent, the genera Methylobacter and Methylomicrobium. Fourteen Methylocystis, Methylobacter and Methylomicrobium metagenome assembled genomes (MAGs) were obtained. Twelve particulate methane monooxygenase operons (pmoCAB) were also obtained. The collected operons contained sequences similar to those classifying within the genera Methylocystis, Methylobacter and Methylomicrobium phylotypes. Three operons (mmoXYBZDC) were obtained for soluble methane monooxygenase, with mmoX classifying most closely to other Methylocystis mmoX genes. The newly obtained sequences were compared to commonly used primers for the biomarkers pmoA (A189f and mb661r) and mmoX (536 f and 898r). In summary, TCE degrading methanotrophic cultures were easily developed from both uncontaminated soils and impacted sediments and whole genome sequencing data indicated the importance of the genus Methylocystis across many of the methanotrophic enrichments.},
}
@article {pmid41177025,
year = {2025},
author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S},
title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140254},
doi = {10.1016/j.jhazmat.2025.140254},
pmid = {41177025},
issn = {1873-3336},
abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.},
}
@article {pmid41176044,
year = {2025},
author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and da Costa, MDF and Bueno, MG},
title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107894},
doi = {10.1016/j.actatropica.2025.107894},
pmid = {41176044},
issn = {1873-6254},
abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20%, 40%, and 60%) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.},
}
@article {pmid41175772,
year = {2025},
author = {Eshghdoostkhatami, Z and Li, Z and Faghihinezhad, M and Cupples, AM},
title = {Characterization of propanotrophic enrichments from agricultural soils capable of 1,4-dioxane biodegradation to sub-μg/L levels.},
journal = {The Science of the total environment},
volume = {1005},
number = {},
pages = {180824},
doi = {10.1016/j.scitotenv.2025.180824},
pmid = {41175772},
issn = {1879-1026},
abstract = {Major challenges to 1,4-dioxane bioremediation concern chemical characteristics that result in migration and persistence, often resulting in large and dilute plumes. In this study, the objectives were to 1) develop propanotrophic enrichment cultures from agricultural soils and determine if they could degrade high and low concentrations of 1,4-dioxane, 2) investigate the feasibility of bioaugmentation for 1,4-dioxane biodegradation in laboratory microcosms and 3) identify dominant propanotrophs and propane monooxygenase genes in the propanotrophic enrichments. Agricultural soils were selected as inocula as they commonly contain microorganisms capable of the biodegradation of a wide range of agricultural chemicals. Propanotrophic enrichment cultures were established from three soils by repeatedly amending propane. Following this, the biodegradation trends for high (3 mg/L) and low (∼200 μg/L) concentrations of 1,4-dioxane were investigated. The experiments also involved bioaugmentation to impacted site sediment microcosms. Prior to their use in bioaugmentation, DNA was extracted from the propanotrophic cultures for shotgun sequencing and analyses with KBase. The easy development of propanotrophic enrichments from agricultural soils suggests a natural abundance of propanotrophs in the soils. Rapid (often <2 weeks) 1,4-dioxane biodegradation was observed in the enrichment cultures at high or low 1,4-dioxane concentrations. 1,4-Dioxane was degraded close to or below the limit of detection (0.46 μg/L) following bioaugmentation. Eighteen propanotrophic metagenome assembled genomes, classifying as Methylibium, Mycobacterium, Rhodococcus opacus, Rhodococcus wratislaviensis and Mesorhizobium, contained full propane monooxygenase operons. Sequences for twenty-two propane monooxygenase operons were retrieved. Sequences for one subunit (prmA) were compared to the closest matches in GenBank. Overall, the developed cultures have potential for use in bioaugmentation to address in situ 1,4-dioxane contamination.},
}
@article {pmid41147335,
year = {2025},
author = {Gurnani, B and Kaur, K},
title = {Advancing diagnostics in Pythium insidiosum keratitis: the emerging role of point-of-care imaging and biosensor-based detection devices.},
journal = {Expert review of medical devices},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17434440.2025.2582616},
pmid = {41147335},
issn = {1745-2422},
abstract = {INTRODUCTION: Pythium insidiosum keratitis (PIK) is a rapidly progressive, aggressive corneal infection that closely mimics fungal keratitis but fails to respond to conventional antifungal therapy. Misdiagnosis and delayed intervention frequently result in poor outcomes, including high rates of therapeutic keratoplasty and irreversible vision loss. Timely and accurate identification is therefore vital, yet conventional microbiological methods are slow, and histopathology is invasive and often inconclusive. Recent advances in imaging, molecular diagnostics, and biosensor technology are revolutionizing diagnostic possibilities.<br><br>AREAS COVERED: Modern tools such as anterior segment optical coherence tomography (AS-OCT) and in vivo confocal microscopy(IVCM) permit rapid, noninvasive visualization of characteristic stromal patterns. Molecular platforms, including PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and multiplex panels, provide precise results within hours. Innovative lateral flow immunoassays (LFIA), aptamer-based electrochemical biosensors, and artificial intelligence (AI)-assisted image interpretation expand point-of-care capabilities, while metagenomic sequencing aids in culture-negative cases.<br><br>EXPERT OPINION: The integration of imaging, molecular, and biosensor modalities marks a paradigm shift in PIK diagnostics. PortableAS-OCT, handheld IVCM, and rapid multiplex panels promise to reduce diagnostic delay, minimize unnecessary antifungal use, lower keratoplasty rates, and improve visual prognosis. Collaborative validation and affordable access remain essential for global impact.},
}
@article {pmid41175763,
year = {2025},
author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X},
title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140321},
doi = {10.1016/j.jhazmat.2025.140321},
pmid = {41175763},
issn = {1873-3336},
abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.},
}
@article {pmid41175752,
year = {2025},
author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H},
title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140318},
doi = {10.1016/j.jhazmat.2025.140318},
pmid = {41175752},
issn = {1873-3336},
abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.},
}
@article {pmid41175696,
year = {2025},
author = {Li, N and Zhang, Y and Qu, Z and Xu, J and Ming, A and Sun, H and Huang, L},
title = {Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128381},
doi = {10.1016/j.micres.2025.128381},
pmid = {41175696},
issn = {1618-0623},
abstract = {The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)-which plays a key role in soil phosphorus cycle-was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.},
}
@article {pmid41175632,
year = {2025},
author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D},
title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107665},
doi = {10.1016/j.marenvres.2025.107665},
pmid = {41175632},
issn = {1879-0291},
abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.},
}
@article {pmid41175494,
year = {2025},
author = {Ramirez Pavon, JA and Aparecido da Silva Neves, N and de Oliveira Martins, A and Pinho, JB and Juscineide de Souza, V and Patroca da Silva, S and Ribeiro Cruz, AC and Barbosa de Almeida Medeiros, D and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Viral diversity in vertebrates from Alto Pantanal, Mato Grosso, 2019.},
journal = {Virology},
volume = {614},
number = {},
pages = {110729},
doi = {10.1016/j.virol.2025.110729},
pmid = {41175494},
issn = {1096-0341},
abstract = {The Alto Pantanal is a key yet unexplored Brazilian wetland for studying vertebrate viral profiles. This study presents viral taxonomic profiles from vertebrate sera sampled in May, June and October of 2019 in Porto São Luiz and Pirizal, Alto Pantanal. A total of 13 frogs, 19 bats, 23 caimans, 36 equids, 20 domestic hens, 140 birds and 16 humans were sampled. After nucleic acid extraction, individual samples were pooled by species and subjected to a metagenomic approach. Viral reads accounted for less than 0.2 % in each pool, except in domestic hens (35.8 %), yielding an overall viral abundance variation among pools of 48.83 %. In total, twenty-nine viral genomic sequences were retrieved from five pools. In equids, two coding-complete genomes were identified belonging to species Copiparvovirus ungulate8 and Mutorquevirus equid2. In domestic hens, four coding-complete genomes of species Alpharetrovirus avileu were detected, along with partial genomes of three gyroviroviruses of species Gyrovirus homsa1, Gyrovirus galga1 and a putative novel unclassified gyrovirus. In humans, 15 genomes of known human anelloviruses were identified, as well as partial sequences of Orthoflavivirus ilheusense and Erythroparvovirus primate species. In caimans, a partial genome belonging to genus Betadintovirus was detected. In frogs, one partial sequence of a putative novel pegivirus, and a coding-complete sequence of an unclassified retrovirus (Rhinella marina endogenous retrovirus) were found. These findings provide valuable insights into viral circulation within the diverse Pantanal biome, and support viral genomic surveillance efforts in the region.},
}
@article {pmid41175489,
year = {2025},
author = {Fan, Z and Wu, H and Feng, Y and Sun, L and Yuan, L and Muhammad, T},
title = {Biochar mitigates biodegradable microplastic-induced greenhouse gas emissions in lake sediments: Unraveling microbial mechanisms and particle-size effects.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127799},
doi = {10.1016/j.jenvman.2025.127799},
pmid = {41175489},
issn = {1095-8630},
abstract = {Accumulation of biodegradable microplastics (MPs) in freshwater sediments exacerbates greenhouse gas (GHG) emissions, though effective mitigation strategies are still poorly understood. This study investigated the potential of biochar (BC) for carbon sequestration and its role in suppressing MP-induced GHG emissions. Herein, we elucidated the effects of biodegradable MPs Poly (butylene-adipate-co-terephthalate) (PBAT) and different-sized (bulk- and nano-) BC on carbon dioxide (CO2) and methane (CH4) emissions. Results revealed that PBAT significantly reduced sediment pH and oxidation-reduction potential while increasing carbon content, leading to a 50.5 % rise in CO2 and 487.9 % in CH4 emissions. Nano-BC alone reduced CO2 emissions by 46.8 %, whereas no inhibitory effect was observed under MPs pollution. Critically, bulk- and nano-BC strongly inhibited cumulative CH4 emissions in MP-polluted sediment by 14.7 % and 50.6 %, respectively. BC countered PBAT-induced increases in sedimentary amino acids and humic substances by limiting key bacterial phyla involved in organic matter decomposition. Furthermore, BC reduced the abundance of MP-enriched microbes such as p_Firmicutes, f_Methanoregulaceae, and f_Methanotrichaceae, suppressed microbial metabolic functions and carbohydrate-active enzymes, and promoted CH4 oxidation and carbon fixation via genes including cutL, coxL, and coxA. Simultaneously, BC diminished methanogenic gene expression (mcrB, mcrA2). This work demonstrates the pronounced stimulatory effect of biodegradable MPs on sediment carbon mineralization and establishes the multi-level mechanism through which BC (particularly nano-BC) mitigates climate change effectively.},
}
@article {pmid41175312,
year = {2025},
author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S},
title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41175312},
issn = {2509-2723},
support = {22A17//Florida Department of Health/ ; },
abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.},
}
@article {pmid41175161,
year = {2025},
author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV},
title = {Gellan gum-based media recover more diverse microbial communities from soil material.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {338},
pmid = {41175161},
issn = {1432-072X},
support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation &amp; purification/classification/genetics/growth &amp; development ; *Microbiota ; },
abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.},
}
@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, M&#xc0; and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
doi = {10.1111/liv.70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}
@article {pmid41174628,
year = {2025},
author = {Wei, M and Ai, X and Gu, D and Zhang, S and Xu, K and Li, S and Mao, S and Li, M},
title = {Ultra-broad hybrid capture-based targeted next-generation sequencing for sensitive plasma pathogen cfDNA detection in bloodstream infections.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1203},
pmid = {41174628},
issn = {1479-5876},
support = {2025YFC3409100//National Key Research and Development Program/ ; 24SF1903500//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 23YF1431300//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Female ; Male ; Middle Aged ; Aged ; *Sepsis/microbiology/blood ; Adult ; Retrospective Studies ; },
abstract = {BACKGROUND: The limited genomic targeting range of current targeted next-generation sequencing (tNGS) workflows results in limited detection of pathogen-derived cell-free DNA (cfDNA), making it challenging to apply this approach to bloodstream infections (BSIs). Here, we developed an ultra-broad hybrid capture-based tNGS method to detect plasma pathogen-derived cfDNA and evaluate its suitability for the diagnosis of BSI.<br><br>METHODS: This study introduced an ultra-broad hybrid capture-based tNGS method featuring an ultra-broad pathogen panel (1872 pathogens) and high-density probe coverage. To adequately evaluate its performance, we conducted retrospective tests in 208 suspected BSI patients (139 immunocompromised), comparing tNGS results with mNGS, conventional microbiological testing (CMT), and comprehensive clinical diagnoses.<br><br>RESULTS: In pathogen detection, the concordance between ultra-broad hybrid capture-based tNGS and mNGS results was 93.75%. The diagnostic accuracy of tNGS in BSI was comparable to mNGS (76.44% vs. 75.00%) and significantly higher than CMT (45.67%, p&#x2009;<&#x2009;0.0001). In immunocompromised populations, the diagnostic accuracy of tNGS was similar to mNGS (77.70% vs. 76.98%). tNGS detected 92.09% (163/177) of pathogens identified by mNGS. Two of the missed pathogens were not included in the 1872 pathogens panel, and both were from the immunocompromised group.<br><br>CONCLUSIONS: Ultra-broad hybrid capture-based tNGS exhibits sensitivity and accuracy comparable to mNGS, effectively covering a relatively wide range of pathogens, and may serve as an economic screening tool for BSI in the future.},
}
@article {pmid41174528,
year = {2025},
author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S},
title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {703},
pmid = {41174528},
issn = {1471-2180},
}
@article {pmid41174518,
year = {2025},
author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B},
title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {704},
pmid = {41174518},
issn = {1471-2180},
mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; },
abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.<br><br>RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.<br><br>CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.},
}
@article {pmid41174459,
year = {2025},
author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C},
title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117386},
doi = {10.1016/j.foodres.2025.117386},
pmid = {41174459},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.},
}
@article {pmid41174397,
year = {2025},
author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C},
title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117319},
doi = {10.1016/j.foodres.2025.117319},
pmid = {41174397},
issn = {1873-7145},
mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; },
abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.},
}
@article {pmid41174177,
year = {2025},
author = {Simmonds, P and Butković, A and Grove, J and Mayne, R and Mifsud, JCO and Beer, M and Bukh, J and Drexler, JF and Kapoor, A and Lohmann, V and Smith, DB and Stapleton, JT and Vasilakis, N and Kuhn, JH},
title = {Taxonomic expansion and reorganization of Flaviviridae.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {3026-3037},
pmid = {41174177},
issn = {2058-5276},
support = {MC_UU_00034/1//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 107653/Z/15/Z//Wellcome Trust (Wellcome)/ ; NIHR203338)//DH | National Institute for Health Research (NIHR)/ ; },
mesh = {Phylogeny ; *Flaviviridae/classification/genetics/enzymology ; RNA-Dependent RNA Polymerase/genetics ; Evolution, Molecular ; Genome, Viral ; Host Specificity ; Viral Proteins/genetics ; RNA Helicases/genetics ; },
abstract = {Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family.},
}
@article {pmid41174125,
year = {2025},
author = {Dobrzyński, J and Jakubowska, Z},
title = {Pseudomonas protegens as a biocontrol agent against phytopathogenic fungi - mini review.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {11},
pages = {428},
pmid = {41174125},
issn = {1573-0972},
mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Pseudomonas/metabolism/physiology/genetics ; *Biological Control Agents/metabolism ; *Fungi/pathogenicity ; Antifungal Agents/metabolism/pharmacology ; Phloroglucinol/analogs &amp; derivatives/metabolism ; Secondary Metabolism ; Chitinases/metabolism ; Phenols ; Pyrroles ; },
abstract = {Pseudomonas protegens, a member of the P. fluorescens complex, is an important biocontrol agent with high potential in sustainable agriculture. It produces diverse secondary metabolites, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), orfamides, and protegenins, as well as hydrolytic enzymes such as chitinases, which contribute to antifungal activity, fungal cell wall degradation, and induction of systemic resistance (ISR) in plants. Despite these insights, gaps remain in understanding the regulation of metabolite biosynthesis, variability of ISR across crops, and the field efficacy of P. protegens. Future research should employ omics approaches (metagenomics, transcriptomics) to optimize biocontrol strategies, explore natural inducers of metabolite production, and evaluate colonization efficiency under field conditions. This review synthesizes current knowledge on P. protegens, highlighting its importance, mechanisms of action, existing knowledge gaps, and directions for future research.},
}
@article {pmid41173910,
year = {2025},
author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW},
title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9658},
pmid = {41173910},
issn = {2041-1723},
support = {R01NS055349//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; T32GM148382//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation &amp; purification/genetics ; Metagenome ; Enterobacteriaceae/isolation &amp; purification/genetics ; Patient Discharge ; },
abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.},
}
@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}
@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}
@article {pmid41173365,
year = {2025},
author = {Liu, H and Qu, Y and Yue, Y and Cui, X and Wang, X and Wang, C and Geng, Z and Zhang, L and Sun, M and Huo, M},
title = {Low-dose chlorite drives stable nitrite accumulation for partial denitrification.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123234},
doi = {10.1016/j.envres.2025.123234},
pmid = {41173365},
issn = {1096-0953},
abstract = {Achieving stable and efficient nitrite accumulation in partial denitrification (PD) requires precise control techniques, which poses a challenge to its practical application. This study introduces a new strategy using chlorite (ClO2[-]) as a regulatory factor to halt denitrification at the nitrite stage, ensuring stable and efficient PD. The effectiveness of this approach was assessed in a continuously operated PD biofilter. At different ClO2[-] concentrations, the nitrite accumulation rate (NTR) reached its peak at 97.6% at 1.00 mg/L ClO2[-], with effluent nitrate-nitrogen (NO3[-]-N) as low as 0.61 mg/L. The chlorite-regulated PD filter exhibited a rapid start-up period, reaching optimal performance within 7 days and maintaining stable operation for over 30 days. Moreover, this PD biofilter sustained a nitrite accumulation rate above 67.5% across a wide range of carbon/nitrogen ratios (C/N) (2-4) and remained efficient at an extremely short hydraulic retention time of 30 min. Additionally, ClO2[-] easily degrade into non-toxic chloride ion (Cl[-]) and oxygen (O2) in the environment, thereby preventing secondary pollution. Metagenomic analysis identified Thauera (16.4%), Simplicispira (14.7%), and Flavobacterium (14.0%) as key contributors to nitrite accumulation. Furthermore, according to the real-time quantitative polymerase chain reaction (qPCR) results, chlorite exposure upregulated the nitrate reductase gene (nar) and downregulated the nitrite reductase gene (nir). Finally, the final effluent Total Inorganic Nitrogen (TIN) concentration of 10.26 mg/L was achieved through the Partial denitrification/Anammox (PD/A) coupling process. This study provides new insights into nitrite accumulation in PD/A and presents valuable guidance for optimizing the PD/A process in engineering applications.},
}
@article {pmid41173342,
year = {2025},
author = {Vanbiervliet, Y and Aerts, R and Maessen, L and Wauters, J and Maertens, J and Lagrou, K},
title = {Laboratory innovations to diagnose invasive mould infections - what is relevant, what is not?.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.10.017},
pmid = {41173342},
issn = {1469-0691},
abstract = {BACKGROUND: Invasive mould infections (IMI) carry high morbidity and mortality. Conventional diagnostics - histopathology, culture and microscopy - rely on invasive sampling and lack sensitivity, particularly during early phases of infection. Rare and mixed mould infections are frequently diagnosed too late or missed.<br><br>OBJECTIVES: To provide a narrative review of recent innovations in diagnosing IMIs, highlighting advances, identifying areas where progress remains limited, and assessing gaps in current diagnostic algorithms to guide future directions.<br><br>SOURCES: We performed a literature search regarding diagnostic methods for IMIs without date restrictions, including experimental and clinical studies, systematic reviews and meta-analyses.<br><br>CONTENT: Rapid lateral-flow assays and single-sample chemiluminescent immunoassays for detecting Aspergillus antigens in blood and BALF now complement enzyme immunoassays (EIA). Novel targets, such as urinary glycans and siderophores in various biological matrices, show potential to diagnose IMI. Targeted PCRs for Aspergillus and Mucorales enable earlier detection than conventional methods and rapid detection of resistance in case of A. fumigatus, though isolated Aspergillus PCR positivity is challenging to interpret. Metagenomic next-generation sequencing (mNGS) expands pathogen detection but is limited by costs and technical and interpretative challenges. A shift towards assays based on the host immune response (functional immune assays and biochemical markers) shows promise but remains investigational.<br><br>IMPLICATIONS: Due to different commercially available test formats, Aspergillus antigen detection assays can now be implemented in many hospitals. Implementation of Mucorales PCR tests improves the diagnosis of mucormycosis also in the setting of coinfections. Multimodal pathogen-based strategies that integrate antigen assays, targeted PCRs, and, in select cases, mNGS enable earlier, more accurate, and comprehensive diagnosis of IMIs ultimately improving clinical outcomes; but the need for rapid, accurate, non-invasive diagnostic tests for IMIs remains. Host-response based assays are not yet clinic-ready. Prospective multicentre studies are needed to standardize diagnostic thresholds, validate novel diagnostic markers and to evaluate impact on patient outcomes and cost-effectiveness.},
}
@article {pmid41173130,
year = {2025},
author = {Gonzalez, G and Carr, MJ and Byrne, H and Colgan, A and Hare, D and Sawa, H and De Gascun, CF and Matthijnssens, J and Yandle, Z},
title = {Complex evolutionary dynamics including reassortment drive genome diversity in human rotavirus species a circulating in Ireland.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105848},
doi = {10.1016/j.meegid.2025.105848},
pmid = {41173130},
issn = {1567-7257},
abstract = {Rotavirus A (RVA), belonging to the species Rotavirus alphagastroenteritidis, is among the most frequently diagnosed viral causes of gastroenteritis. The inclusion of RVA vaccines in the primary childhood immunisation schedules of multiple countries has led to significant reductions in yearly-reported cases. Nevertheless, such interventions may exert selective pressures that could result in the emergence of novel vaccine escape variants. RVA classification has traditionally focused on two of eleven gene segments encoding the capsid proteins, VP4 and VP7, which limits evolutionary assessments of genomic diversity and reassortments involving the other segments. A viral metagenomics approach (NetoVIR) was employed to investigate the genomic diversity of RVA in Ireland. The analysis focused on clinical samples (n = 140) collected from patients between 2015 and 2021. Besides the Wa-like or DS-1-like genotype constellations, 4/140 genomes (3 %) were identified as reassortant, with an NSP2 genotype 1 in a DS-1-like constellation. Also, we confirmed the circulation of OP354-like P[8] strains in six G9P[8] samples. Notably, these strains show dissimilarity in the antigenic epitopes of the VP4 protein compared to the Rotarix vaccine. Furthermore, we detected strains with an equine-like G3 (EQL-G3) VP7 gene within a DS-1-like constellation (n = 5/140, 4 %) and the unusual combination of G1P[8] with a DS-1-like constellation in 6/22 (27 %) of the G1P[8] samsples. Our study supports using a viral metagenomic approach for RVA genetic characterisation to determine pathogen diversity and reassortments. The public health implications of the identified reassortant RVA strains, requires investigations for any potential impacts on vaccine efficacies.},
}
@article {pmid41172871,
year = {2025},
author = {Lalucat, J and Busquets, A and Mulet, M and Riesco, R and García-Valdés, E and Gomila, M},
title = {Genome insights into Hydrogenophaga taeniospiralis and its R-body genetic determinants.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {6},
pages = {126664},
doi = {10.1016/j.syapm.2025.126664},
pmid = {41172871},
issn = {1618-0984},
abstract = {The genome of Hydrogenophaga taeniospiralis 2K1[T], the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H2 in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, Malikia and Serpentinimonas, are highlighted and the delineation of the genus Hydrogenophaga is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of Hydrogenophaga strains. H. taeniospiralis 2K1[T] is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other Hydrogenophaga genomes and strains from other genera.},
}
@article {pmid41172852,
year = {2025},
author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140283},
doi = {10.1016/j.jhazmat.2025.140283},
pmid = {41172852},
issn = {1873-3336},
abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.},
}
@article {pmid41172529,
year = {2025},
author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ},
title = {Biological dynamics of no-tillage soils in the western region of Paraná.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e298630},
doi = {10.1590/1519-6984.298630},
pmid = {41172529},
issn = {1678-4375},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; },
abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.},
}
@article {pmid41172139,
year = {2025},
author = {Yang, S and Zhang, J and Ou, Y and Liu, W and Tian, X and Hou, LJ and Dong, HP},
title = {Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf242},
pmid = {41172139},
issn = {1751-7370},
abstract = {Aerobic methanotrophs encode a hydroxylamine oxidoreductase, which facilitates the oxidation of ammonia to nitrite or nitric oxide, potentially leading to nitrous oxide production. Aerobic methane oxidation has been documented in shallow marine waters or the water column of the open ocean. However, little is known about the distribution pattern of marine aerobic methanotrophs containing hydroxylamine oxidoreductase and their contribution to marine nitrous oxide emissions. Here, by analyzing global marine metagenomes, we show that hydroxylamine oxidoreductase-containing aerobic methanotrophs were widely distributed across diverse marine habitats, with higher abundances in methane seep systems and estuary regions than in other environments. Among these, aerobic methanotrophs belonging to Gammaproteobacteria were the most widely distributed and abundant functional group. We also identified a second order within Gammaproteobacteria (Ga0077536) potentially capable of aerobic methanotrophy, and a complete repertoire of denitrification genes in a gammaproteobacterial methanotroph, expanding the phylogenetic and functional diversity of marine aerobic methanotrophs. By using enrichments of estuarine methanotrophs in combination with 15N stable isotope tracing and metatranscriptomic analysis, we indicate that marine aerobic methanotrophs take part in ammonia oxidation and nitrous oxide production. The ammonia oxidation can persist for approximately 6 days, and the nitrous oxide produced is at least partially derived from the hydroxylamine oxidation. Given the prevalence of denitrification genes in aerobic methanotrophs, methane oxidation may also be coupled to NOx- reduction under anoxic marine conditions, potentially contributing to nitrous oxide production. The intrinsic nature of aerobic methanotrophs could partially offset the mitigation of global warming achieved through the methane consumption.},
}
@article {pmid41171744,
year = {2025},
author = {Jia, X and Peng, J and Lv, J and Li, Y and Luo, Z and Xiang, J and Hou, Y and Zheng, Q and Han, B},
title = {Metagenomic analysis reveals the abundance changes of bacterial communities and antibiotic resistance genes in the influent and effluent of hospital wastewater.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335723},
pmid = {41171744},
issn = {1932-6203},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification ; Hospitals ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Sewage/microbiology ; },
abstract = {The presence of substantial quantities of antibiotics and their metabolites in hospital wastewater can lead to the accumulation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Research on the influent and effluent sewage of hospitals is crucial for understanding the effectiveness of wastewater treatment systems in inactivating ARB and ARGs. Key features of microbial communities and ARGs in influent and effluent wastewater - including taxonomic diversity and relative abundance - were assessed via metagenomic sequencing. The treatment process resulted in a reduction of the overall bacterial count in hospital wastewater. However, a notable increase in relative abundance was observed for three phyla, 16 genera, and 21 species post-treatment. Bacteria harboring ARGs were predominantly identified as belonging to Pseudomonadota and Bacillota. A total of 354 ARGs were detected in the influent, while 331 were identified in the effluent samples, with a general decrease in absolute abundance. Nevertheless, the relative abundance of certain ARGs, such as mphG, fosA8, and soxR, was found to increase in the effluent across all samples. Seasonal fluctuations also played a role in the distribution of microbial communities and ARGs. These findings underscore the role of hospital wastewater treatment systems in reducing the discharge of ARB and ARGs into the environment, while also revealing potential shortcomings in the wastewater treatment process that necessitate further improvement for more effective removal of these ARGs.},
}
@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.<br><br>METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.<br><br>CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}
@article {pmid41171444,
year = {2025},
author = {U, A and Chacko, A and Priyadarshini, M and P P, R},
title = {Utilization of Chlorella vulgaris biomass in microbial fuel cell as a feed and the study on its degradation pathway.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {8},
pages = {1104-1117},
pmid = {41171444},
issn = {0273-1223},
support = {//Cochin University of Science and Technology/ ; },
mesh = {*Chlorella vulgaris/metabolism ; *Bioelectric Energy Sources/microbiology ; *Biomass ; Waste Disposal, Fluid/methods ; },
abstract = {Microbial fuel cells (MFCs) represent an advanced and environmentally friendly bioenergy technology with significant potential for simultaneous power generation and wastewater treatment. This study specifically compared the anodic performance of MFCs with Chlorella vulgaris versus those fed with acetate. Dual-chamber MFCs were constructed for simultaneous electricity generation and wastewater treatment. In addition, microbial communities of both the MFCs and the gene function of MFC-Ch were analyzed through metagenomic sequencing. When comparing all the electrochemical parameters produced from MFCs, MFC-Ch is slightly more efficient than MFC-A. Metagenomic analysis showed that Proteobacteria was the predominant phylum in MFC-A, whereas Bacteroidota was predominant in MFC-Ch. COG (Clusters of Orthologous Groups) analysis of the primary metabolic pathways in the anolyte of MFC-Ch revealed a relatively high abundance of genes associated with several metabolic pathways during MFC operation, including amino acid transport and metabolism, carbohydrate transport and metabolism, and coenzyme transport and metabolism. The study on carbohydrate and protein degradation indicated that protein metabolism occurred to a greater extent than carbohydrate metabolism. This aligns with the known ability of some bacteria present in the sludge to promote amino acid metabolism in MFCs, a finding further supported by the positive correlation observed in the COG analysis.},
}
@article {pmid41171134,
year = {2025},
author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L},
title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1115},
pmid = {41171134},
issn = {1362-4962},
support = {2021YFA0717001//National Key R&amp;D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; },
abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.},
}
@article {pmid41171126,
year = {2025},
author = {She, J and Qian, PY and Wu, L},
title = {DOO: integrated multi-omics resources for deep ocean organisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1096},
pmid = {41171126},
issn = {1362-4962},
support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; },
abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.},
}
@article {pmid41171125,
year = {2025},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1118},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; ERC-AdG-669830/ERC_/European Research Council/International ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}
@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}
@article {pmid41170985,
year = {2025},
author = {Gamage, C and Graves, A and Li, G and Thieulent, CJ and Balasuriya, UBR and Morrow, J and Vissani, A and Parreño, V and Matthijnssens, J and Carossino, M},
title = {Coding-complete genome sequences of group B equine rotavirus from central Kentucky, USA, reveal circulation of a single genome constellation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0074425},
doi = {10.1128/mra.00744-25},
pmid = {41170985},
issn = {2576-098X},
abstract = {Equine rotavirus B (ERVB) has caused foal diarrhea in central Kentucky since 2021. Coding-complete genome sequences from 14 strains circulating in 2024 revealed >99% nucleotide identity to the 2021 prototype ERVB strain RVB/Horse-wt/USA/KY1518/2021, with a conserved genomic constellation (G3-P[3]-I3-R3-C3-M3-A4-N3-T3-E3-H3).},
}
@article {pmid41170455,
year = {2025},
author = {Ruan, L and Chen, S and Zhang, J and Peng, G},
title = {Infected left atrial myxoma with Streptococcus gordonii: case report and literature review.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1635642},
pmid = {41170455},
issn = {2234-943X},
abstract = {Cardiac myxoma is a relatively common type of benign heart tumor, but infectious myxoma is rare. The symptoms of non-infected cardiac myxoma and infected cardiac myxoma are similar and mostly nonspecific, which can easily lead to delayed diagnosis, missed diagnosis, and delayed treatment. A 57-year-old male patient presented with nonspecific systemic symptoms such as anorexia, fever, and cough, and was initially considered to have gastrointestinal disease or pulmonary infection. Preoperative bacterial culture was negative, and imaging features were consistent with cardiac myxoma. A small amount of vegetation was found attached to the surface of the tumor. Postoperative blood culture, surgical specimen culture, and postoperative blood metagenomic next-generation sequencing (mNGS) examination all showed positive results for Streptococcus gordonii, confirming the diagnosis of infectious left atrial myxoma. For patients with febrile cardiac myxoma, it is crucial to be vigilant against concurrent infections. Blood cultures should be performed before administering antibiotics. In cases where blood cultures are negative, a combination of mNGS, PCR, and transesophageal echocardiography (TEE) should be utilized for differential diagnosis, with particular attention paid to the characteristics of vegetations on the tumor surface.},
}
@article {pmid41170433,
year = {2025},
author = {Zhang, S and Chu, M and Sun, X},
title = {The arms race in bacteria-phage interaction: deciphering bacteria defense and phage anti-defense mechanisms through metagenomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687307},
pmid = {41170433},
issn = {1664-302X},
abstract = {Bacteriophages are viruses that specifically infect bacteria and co-evolve with their hosts through mutual interactions. They represent one of the most significant drivers of microbial diversity, influencing its evolution, generation, and maintenance. To counter bacteriophage infection, bacteria have developed sophisticated immune systems, including both passive adaptations, such as inhibiting phage adsorption and preventing DNA entry, and active defense systems such as restriction-modification systems and CRISPR-Cas systems. The ongoing arms race between bacteriophages and bacteria has left distinct evolutionary signatures in their genomic sequences. Advances in large-scale genomic and metagenomic sequencing technologies, coupled with bioinformatics approaches, have greatly enhanced our understanding of bacteria-phage interaction mechanisms, driving progress in bacteriophage biology. This review systematically analyses the diverse immune strategies bacteria employ against phage infection, elucidates the coordination and interrelationships among different anti-phage mechanisms, and highlights potential directions for future research.},
}
@article {pmid41170420,
year = {2025},
author = {Guo, Y and Zhang, N and Pei, D},
title = {Gut microbiota heterogeneity in non-alcoholic fatty liver disease: a narrative review of drivers, mechanisms, and clinical relevance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645298},
pmid = {41170420},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent metabolic disorder, is increasingly recognized as a complex condition influenced by gut microbiota dysbiosis. However, the heterogeneity in findings across studies has hindered the clinical translation of microbiota-based interventions. In this narrative review, we synthesize current evidence on gut microbial alterations in patients with NAFLD, with a focus on the sources of variability that contribute to inconsistent results. We included human studies (2000-2024) that compared gut microbiota profiles between NAFLD patients and healthy controls using 16S rRNA or metagenomic sequencing; key drivers of microbial changes include clinical factors (metabolic comorbidities, disease progression), biological variables (diet, genetics), and methodological biases (sequencing platform differences, diagnostic criteria variability). Emerging evidence highlights the role of non-bacterial components (fungi, viruses) in modulating bacterial communities and disrupting host metabolic pathways, exacerbating hepatic inflammation and lipid accumulation. To overcome current limitations, we propose integrating multi-omics approaches (metagenomics, metabolomics, and proteomics) with a longitudinal study design to capture dynamic microbiota-host interactions. Precision microbiota therapies, including strain-specific probiotics, engineered microbial consortia, and fecal microbiota transplantation tailored to individual dysbiosis profiles, are emerging as promising strategies for targeted interventions. Addressing these challenges is essential to identifying reliable microbial biomarkers and developing personalized strategies for NAFLD prevention and treatment. Future research should harmonize methodologies, validate causal mechanisms, and optimize microbiota-based therapies to bridge experimental findings and clinical application.},
}
@article {pmid41170165,
year = {2025},
author = {Shi, Y and Lin, Z and Chen, Z and Ye, C and Yu, J and Xi, J and Geng, Y and Zou, M and Ren, H and Wang, L and Wang, B and Xu, F and Zheng, X and Xiang, G},
title = {High-throughput and Efficient Assay for Central Nervous System Infection with Targeted Nanopore Sequencing Technology.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5461-5471},
pmid = {41170165},
issn = {1178-6973},
abstract = {INTRODUCTION: Central nervous system (CNS) infections represent a significant global public health concern and are characterized by high morbidity and mortality rates. In this study, we developed an integrated diagnostic approach for CNS infections by combining high-throughput nanopore sequencing with multiplex PCR amplification, designated targeted nanopore sequencing (tNPS).<br><br>METHODS: The tNPS assay employed a dual detection strategy incorporating pathogen-specific primers targeting 17 prevalent CNS pathogens (seven bacteria, one fungus and nine DNA viruses), with universal primers for the comprehensive amplification of full-length 16S ribosomal RNA (16S rRNA) and internal transcribed spacer (ITS) regions.<br><br>RESULTS: Analytical validation of tNPS was successfully carried out using the 12 positive reference strains (seven bacteria, one fungus, and four DNA viruses) individually, the ZymoBIOMICS microbial community (eight bacteria and two fungi), the laboratory synthetic community of bacteria and fungi (seven bacteria and one fungus), and the laboratory synthetic community of viruses (five DNA viruses). With accelerated turnaround time within 8&#xa0;h, the tNPS also assayed 11 clinical cerebrospinal fluid (CSF) samples, which further confirmed the feasibility of precise identification of CNS pathogens compared to CSF culture and metagenomic next-generation sequencing.<br><br>DISCUSSION: Our tNPS as a culture-independent diagnostic assay offered enhanced efficiency, high-throughput capability, and an expanded pathogen detection spectrum, facilitating potential implementation in molecular diagnosis of CNS infection.},
}
@article {pmid41169729,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Unveiling Common Bean (Phaseolus vulgaris L) RNA- and DNA-Based Virome in Western Kenya: Insights From Metatranscriptomic and Metagenomic Signatures.},
journal = {Advances in virology},
volume = {2025},
number = {},
pages = {6690945},
pmid = {41169729},
issn = {1687-8639},
abstract = {Common bean (Phaseolus vulgaris L) is Kenya's second most important agricultural product after maize, serving as a vital source of protein for many rural families in Western Kenya. However, viral diseases caused by RNA and DNA viruses greatly impair bean productivity, often leading to yield losses of up to 100%, thus contributing to food insecurity. Global research has isolated 168 viruses of plants that have detrimental effects on common beans; however, no extensive profiling of these viruses has been done in Western Kenya. The scope of this study was to delineate the whole virome that infects common beans through a comprehensive disease diagnostic survey. Sixty-one diseased samples were collected, and nucleic acids were extracted using standard extraction protocols (DNA &amp;RNA Qiagen) and sequenced on the Illumina platform. Metagenomic analysis revealed several DNA-based viruses, such as Badnavirus spp, Caulimovirus maculatractylodei, Pandanus badnavirus, Okra enation leaf curl virus, and Paper mulberry vein-banding virus, while metatranscriptomic analysis uncovered viruses like Tomato leaf curl Cameroon alphasatellite, Physalis Rugose Mosaic Virus, Citrus endogenous paretrovirus, Natevirus nate, and Bracoviriform facetosae. To the best of our knowledge, this study provides a comprehensive inventory of viral entities associated with common beans not documented in Africa. This information is essential for defining plant defense mechanisms, guiding crop protection strategies, lowering agriculture-related risks, strengthening resistance, and advancing resilience.},
}
@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth &amp; development/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.<br><br>RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (>&#x2009;23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2&#xa0;days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15&#xa0;days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.<br><br>CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}
@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}
@article {pmid41168776,
year = {2025},
author = {Heng Wu, and Dong, T and Li, A and Chen, J and Zhang, H and Lv, H and Yang, C and Guo, X and Yang, X and Qiu, L and Miao, C and Yao, Y},
title = {An innovative strategy for overcoming ultra-high ammonia nitrogen inhibition on anaerobic methanogenesis via stepwise domestication.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {223},
pmid = {41168776},
issn = {2049-2618},
mesh = {*Methane/biosynthesis/metabolism ; Anaerobiosis ; *Ammonia/metabolism ; Animals ; Cattle ; Methanosarcina/metabolism/genetics ; *Nitrogen/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/classification/genetics ; Manure/microbiology ; Domestication ; Metagenomics/methods ; },
abstract = {BACKGROUND: The world is facing both an increasingly severe energy crisis and a growing problem of agricultural pollution. The utilization of agricultural waste by anaerobic digestion (AD), has received increasing attention. AD using representative waste cow dung results in total ammonia nitrogen (TAN) accumulation and inhibition of methanogens resulting in reduced CH4 production. However, there is a lack of highly efficient in-situ biological domestication strategies to enhance the TAN tolerance of methanogens in AD systems.<br><br>RESULTS: In this study, an incremental approach to gradually increasing the TAN concentration has been used for overcoming the problem. The results showed that at an ultra-high concentration of 6124.09&#xa0;mg/L TAN, a 48-day domesticated AD system functioned stably and the cumulative CH4 production reached 72.81&#xa0;mL/g volatile solids, whereas the undomesticated AD system failed to produce CH4. After domestication, the lactate dehydrogenase concentration decreased to 96.44&#xa0;ng/L and the adenosine triphosphate concentration increased to 48.77&#xa0;nmol/L, confirming that microbial activity improved. Hydrolytic and acidogenic bacteria were enriched, with Methanosarcina (79.73%) dominating the domesticated AD system, primarily Methanosarcina mazei. Metagenomic analysis showed that with two-component system enrichment, the key inhibited steps from glycerate-1,3P2 to pyruvate (2.498&#x2030;), and from acetyl-CoA and acetyl phosphate to acetic acid (1.141&#x2030; and 0.798&#x2030;), as well as vital methanogenic genes mcrA (0.128&#x2030;), mcrB (0.127&#x2030;), and mcrG (0.065&#x2030;), were both enriched, which favored a stable methanogenic system. More importantly, this ultra-high resistance AD system also showed the potential to increase the CH4 production per unit substrate at the Minhe biogas plant with 24,000&#xa0;m[3] operation scale in Shandong Province, China.<br><br>CONCLUSIONS: Stepwise increase the TAN concentration is a novel method that was demonstrated to be a practical and sustainable way to overcome ultra-high TAN inhibition (6124.09&#xa0;mg/L). During domestication, the two-component system may regulate the microbial collaborative network to ensure microbial activity and high abundance enrichment, thus potentially constructing a methanogenic system dominated by hydrogenotrophic and acetoclastic methanogenesis, holding a promising application prospect. This study helped recognize the potential of methanogens in tolerating ultra-high inhibition and developed an achievable AD technology for robustly treating fecal residue and wastewater in practice.},
}
@article {pmid41168702,
year = {2025},
author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML},
title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {64},
pmid = {41168702},
issn = {1297-9686},
support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.<br><br>RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.<br><br>CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.},
}
@article {pmid41168432,
year = {2025},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, &#xc2; and Castrillo, G and Wagner, MR},
title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41168432},
issn = {2058-5276},
support = {IOS-2016351//National Science Foundation (NSF)/ ; IOS-2016351//National Science Foundation (NSF)/ ; IOS-2016351//National Science Foundation (NSF)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.},
}
@article {pmid41168431,
year = {2025},
author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ},
title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41168431},
issn = {2058-5276},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.},
}
@article {pmid41168291,
year = {2025},
author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM},
title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37987},
pmid = {41168291},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; },
abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.},
}
@article {pmid41167954,
year = {2025},
author = {Chen, T and Jin, D and Ye, H},
title = {[Balamuthia mandrillaris amebic encephalitis in children: a case report].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {37},
number = {4},
pages = {447-450},
doi = {10.16250/j.32.1915.2024285},
pmid = {41167954},
issn = {1005-6661},
support = {2019xkj175//Anhui Medical University Scientific Research Fund/ ; },
mesh = {Humans ; *Balamuthia mandrillaris/isolation &amp; purification/physiology/genetics ; Male ; *Encephalitis/diagnosis/parasitology ; *Amebiasis/diagnosis/parasitology ; Child ; Child, Preschool ; Female ; *Infectious Encephalitis/diagnosis/parasitology ; },
abstract = {Balamuthia mandrillaris amebic encephalitis is a rare but highly fatal parasitic disease in the central nervous system caused by amebae infections. This disease is characterized by complex, diverse and non-specific clinical manifestations and high difficulty in diagnosis, resulting in a high likelihood of missing diagnosis and misdiagnosis. This article presents the diagnosis and treatment of a child with definitive diagnosis B. mandrillaris amebic encephalitis as revealed by metagenomic next-generation sequencing of cerebrospinal fluids, so as to provide insights into clinical diagnosis and treatment of B. mandrillaris amebic encephalitis.},
}
@article {pmid41167953,
year = {2025},
author = {Xue, T and Du, W and Zhao, Y and Xu, J},
title = {[Metagenomic next - generation sequencing technology and its application in diagnosis of Pneumocystis jirovecii infection: a review].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {37},
number = {4},
pages = {434-446},
doi = {10.16250/j.32.1374.2024277},
pmid = {41167953},
issn = {1005-6661},
support = {32200168//National Natural Science Foundation of China/ ; BYJL044//Shanxi Medical University Science and Technology Guidance Project for Higher Education in Shangxi Province/ ; 2020150//Shanxi Provincial Traditional Chinese Medicine Research Project/ ; 2023RC-2-7//Lvliang Municipal Talent Introduction Program/ ; 2020-BS-268//Liaoning Provincial Department of Science and Technology Doctoral Startup Project/ ; XD1905//Shanxi Medical University Doctoral Research Startup Fund/ ; 2020L0223//Shanxi Provincial Higher Education Science and Technology Innovation Project/ ; },
mesh = {Humans ; *Pneumocystis carinii/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; *Metagenomics/methods ; },
abstract = {Pneumocystis jirovecii is an opportunistic fungal pathogen causing fatal Pneumocystis jirovecii pneumonia (PJP) among immunocompromised patients. Conventional pathogen detection Methods have limitations, which hinders early diagnosis and treatment of PJP, resulting in misdiagnosis and underdiagnosis, and high mortality rates. Metagenomic next-generation sequencing (mNGS), which is high in sensitivity and specificity for pathogen detection, enables accurate detection of P. jirovecii and P. jirovecii co-infection with other pathogens, which facilitates timely diagnosis and treatment of PJP. This review summarizes the advances in mNGS technology and its application in diagnosis of PJP, highlighting its critical clinical value in improving diagnostic effectiveness, guiding clinical therapy, and preventing nosocomial transmission of PJP.},
}
@article {pmid41167483,
year = {2025},
author = {Cao, Y and Zhu, Y and He, W and Zou, Z and Chen, J and Yang, M and Yu, Y},
title = {Fe2O3 nanoparticles drive enhanced composting humification by modulating bacteriophage-bacteria interactions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133575},
doi = {10.1016/j.biortech.2025.133575},
pmid = {41167483},
issn = {1873-2976},
abstract = {Although bacteria are responsible for decomposing organic matter and forming humic substances (HS) during composting, the role of bacteriophages in carbon metabolism cannot be ignored. In this study, integrated metagenomics and untargeted metabolomic analysis were used to explore the interaction mechanism between bacteriophages and bacteria on the humification process in composting with added Fe2O3 nanoparticles (NPs). The results showed that Fe2O3 NPs optimized the function of the bacterial community by maintaining a high relative abundance of Bacillota, promoting organic matter degradation, and significantly increasing the HS concentration by 27 % on day 30 of composting. Specifically, the higher Bacillota relative abundance directly enhanced the relative abundance of cellulose phosphorylase (GH94), activated the glycolysis pathway, and led to a significant enrichment of metabolites such as phenols, organic acids, and amino acids on day 14 of composting, thereby strengthening energy metabolism. Furthermore, lysis of the host (Bacillota) by bacteriophages released cellular contents, providing key precursors for HS condensation. Concurrently, lysis by bacteriophages interrupted metabolism of the host, preventing complete mineralization of some carbon, thereby converting easily mineralizable carbon into sequestered HS carbon. Fe2O3 NPs also accelerated lignin depolymerization, enriching aromatic precursors and providing core structural units for humification. This study reveals that Fe2O3 NPs stimulate the synergistic action of the functional bacterium Bacillota and remodeling of the microbial-virus interaction network to drive efficient lignocellulose degradation and humification, thus providing a new strategy for optimizing composting processes based on viral regulation.},
}
@article {pmid41167475,
year = {2025},
author = {Hamelin, B and Hosch, S and Neidhöfer, C and Ruf, MT and Haslbauer, JD and Field, CM and Schläpfer, P and Manzo, M and Neumayr, A and Kuenzli, E and Mancuso, M and Sachs, M and Mensah, N and Bernhard, R and Klaus-Wirthner, B and Concu, M and Nienhold, R and Kuehl, R and Baettig, V and Weisser-Rohacek, M and Gosert, R and Tzankov, A and Tschudin-Sutter, S and Khanna, N and Leuzinger, K and Keller, PM and Mertz, KD},
title = {Unbiased DNA pathogen detection in tissues: Real-world experience with metagenomic sequencing in pathology.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {},
number = {},
pages = {104254},
doi = {10.1016/j.labinv.2025.104254},
pmid = {41167475},
issn = {1530-0307},
abstract = {Pathogen detection in formalin-fixed paraffin-embedded (FFPE) tissue remains challenging. We implemented metagenomic next-generation sequencing (mNGS) in our clinical diagnostic workflow to evaluate its feasibility, diagnostic yield, and pathogen spectrum in routine infectious pathology cases. Between November 2021 and April 2025, we analyzed 623 FFPE tissue samples using a low-depth mNGS workflow on the Thermo Fisher Ion Torrent platform with a CLC Genomics Workbench bioinformatics pipeline. Our assay was designed to detect DNA pathogens. When possible, results were validated by orthogonal methods including species-specific PCRs, 16S/ITS PCR, and immunohistochemistry on tissue sections. Among 623 samples analyzed, at least one potentially pathogenic and plausible microorganism was identified in 229 samples (36.8%), while 334 (53.6%) were negative and 60 (9.6%) were uninterpretable due to quality control failures or suspected contamination. Of the 229 positive samples, 145 (63.3%) involved bacteria, 37 (16.2%) viruses, 28 (12.2%) fungi, and 9 (3.9%) parasites; mixed infections with more than one pathogen were detected in 10 (4.4%) samples. The most frequently identified bacterial family was Mycobacteriaceae (n=27), including Mycobacterium xenopi (n=8), which is not routinely covered by syndromic multiplex PCR panels. Notable viral and fungal detections included a novel human circovirus and Coccidioides posadasii. Despite variable sample quality and DNA input, mNGS yielded reliable results in a wide range of tissue types. Metagenomic NGS is a feasible, valuable addition to routine infectious pathology diagnostics, particularly in complex or inconclusive cases. The assay improved the diagnostic yield compared to conventional PCR, expanded the range of detectable pathogens, and proved robust even in low-quality FFPE samples. These results support broader adoption of mNGS in tissue-based pathogen diagnostics.},
}
@article {pmid41167355,
year = {2025},
author = {Feng, Y and Liu, S and Huang, X and Geng, Y and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Ferroptosis Triggered by Gill Dysbiosis Mediates Immune Failure in Grass Carp Overwintering Syndrome.},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {110965},
doi = {10.1016/j.fsi.2025.110965},
pmid = {41167355},
issn = {1095-9947},
abstract = {Overwintering syndrome (OWS) causes massive mortality in grass carp (Ctenopharyngodon idella) during early spring, yet its pathogenesis beyond the "low-temperature-pathogen" paradigm remains unclear. This study investigates the cascade mechanism through integrated multi-omics analyses on gill tissues of healthy and OWS-affected grass carp. Gill histopathology revealed progressive necrotizing inflammation in OWS-affected grass carp. Transcriptomics identified 962 differentially expressed genes, highlighting upregulation of cytokine signaling, porphyrin metabolism, and ferroptosis alongside downregulation of adrenergic pathways. Ferroptosis was confirmed through the suppression of glutathione peroxidase 4 (GPX4) and the accumulation of iron in necrotic lamellae. Mucous cell depletion and eosinophil disintegration compromised the mucosal barriers of the gills. Metagenomic analysis first revealed a state of microbial dysbiosis, marked by bacterial dominance comprising 92.21% of the community, along with an enrichment of biofilm and exotoxin genes and a reduction in immune modulation, all exacerbating barrier dysfunction. Subsequent integrated correlation analysis linked the specifically enriched bacteria taxa, including Caldilinea sp. CFX5 and Ilumatobacter sp., to the upregulation of metabolic and virulence pathways, while also revealing significant microbiota-gene interactions that modulate gill immune and metabolic functions. Although previously reported pathogens like Flavobacterium and Aeromonas showed increased abundance in OWS-affected fish, their overall abundance remained low. Based on these findings, we propose a "Dysbiosis-Ferroptosis-Collapse" axis, in which microbiota-driven barrier disruption promotes iron overload and the suppression of GPX4, triggering non-resolving inflammation and ion dyshomeostasis. Targeting this cascade provides a novel theoretical framework for intervening in and developing new treatments for OWS.},
}
@article {pmid41167204,
year = {2025},
author = {Donovan, J and Cresswell, FV and Figaji, A and Thwaites, GE},
title = {Integrating metagenomic sequencing into diagnostic pathways for tuberculous meningitis - Authors' reply.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(25)00628-0},
pmid = {41167204},
issn = {1474-4457},
}
@article {pmid41167203,
year = {2025},
author = {Lin, SY and Chen, CJ and Lu, PL},
title = {Integrating metagenomic sequencing into diagnostic pathways for tuberculous meningitis.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(25)00627-9},
pmid = {41167203},
issn = {1474-4457},
}
@article {pmid41167188,
year = {2025},
author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I},
title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.001},
pmid = {41167188},
issn = {1934-6069},
abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.},
}
@article {pmid41166605,
year = {2025},
author = {Huang, XC and Zheng, SJ and Hu, YL and Cao, YE and Liu, YY and Dai, K and Zeng, RJ and Zhang, F},
title = {Comprehensive Insights into the Role of Hydrogen Bonds in the Anaerobic Fermentation of Insoluble Exopolysaccharides in Waste Activated Sludge: Taking Chondroitin Sulfate as an Example.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11116},
pmid = {41166605},
issn = {1520-5851},
abstract = {The hydrogen bond confers the structural recalcitrance of insoluble exopolysaccharides, but its role in the anaerobic fermentation of waste activated sludge (WAS) is seldom reported. As a typical high-molecular-weight exopolysaccharide with poor solubility, chondroitin sulfate (CS) was used to elucidate the role of hydrogen bonds in WAS fermentation. The chondroitin sulfate-degrading consortium (CSDC) was enriched for 180 days, but the methane production was limited (∼18%). The methane production was significantly improved by 88.2%, and extracellular enzyme activity increased by 11.8% after the fast acidic pretreatment of CS. The disruption of the hydrogen bond was confirmed by combining 41.6% reduction of particle size, 46.7% decrease of surface height, blue shifts in the O-H vibrational spectra, and 38.1% decline of interfacial free energy. The molecular dynamics simulation further showed that the hydrogen bond number after the fast acidic pretreatment was reduced from 51.4 ± 2.7 to 44.9 ± 2.1. Co-occurrence network analysis identified Thermovirga as a keystone taxon to facilitate microbial cooperation. The metagenomics and metaproteomics analyses revealed that Proteiniphilum and Mariniphaga served as key producers of extracellular CS-degrading enzymes, primarily CS lyase (EC 4.2.2.5). Above all, these findings demonstrate that the hydrogen bond represents a non-negligible structural constraint on the degradability of insoluble exopolysaccharides.},
}
@article {pmid41166306,
year = {2025},
author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L},
title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116483},
doi = {10.1016/j.celrep.2025.116483},
pmid = {41166306},
issn = {2211-1247},
abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.},
}
@article {pmid41166145,
year = {2025},
author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K},
title = {A multi-omics analysis reveals a gut microbiome-LPC metabolic axis driving postoperative inflammation in cardiopulmonary bypass patients.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002722},
pmid = {41166145},
issn = {1540-0514},
abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.<br><br>METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamics pattern of these microbiota and metabolites, as well as their associations with the postoperative risk. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.<br><br>RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50e-10) and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influence the postoperative risk. The predictive model for ICU stay duration achieved a mean absolute error (MAE) of 1.27 days and an R&#xb2; of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.<br><br>CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating non-infectious inflammatory responses and host imbalance, offering a multi-omics framework for decoding systemic complications beyond classical sepsis paradigms.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates.},
}
@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}
@article {pmid41165328,
year = {2025},
author = {Eshak, MIY and Breithaupt, A and Tews, BA and Luttermann, C and Franzke, K and Scheibe, M and Woelke, S and Beer, M and Rubbenstroth, D and Pfaff, F},
title = {Wǔhàn sharpbelly bornavirus infects and persists in cypriniform cells.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0132225},
doi = {10.1128/jvi.01322-25},
pmid = {41165328},
issn = {1098-5514},
abstract = {Our recent study using in silico data mining identified novel culterviruses (family: Bornaviridae) in fish, including a variant of Wuhan sharpbelly bornavirus (WhSBV) in grass carp kidney and liver cell lines. Here, metagenomic sequencing of different fish cell lines revealed WhSBV in two cell lines from grass carp (Ctenopharyngodon idella; order: Cypriniformes). Using these cell lines, we investigated the ability of WhSBV to infect and establish persistent infection in other cell lines from bony fish (Cypriniformes, Chichliformes, Salmoniformes, Centrarchiformes, and Spariformes), reptiles (Testudines and Squamata), birds (Galliformes), and mammals (Primates and Rodentia). WhSBV showed efficient replication and a time-dependent increase in viral RNA levels in cypriniform cells, whereas replication was limited, confined to single cells, and lacked a clear time-dependent increase in cells from other bony fish and reptiles. No replication was detected in avian and mammalian cells. In situ hybridization and electron microscopy confirmed the presence of viral RNA and particles in infected cypriniform cells. Transcriptomic sequencing revealed minimal innate immune activation during early stages of infection and antiviral response only at later stages, suggesting that WhSBV establishes persistence by evading early immune recognition. In addition, we identified polycistronic viral mRNAs regulated by specific transcriptional start and termination sites and RNA splicing. Viral proteins were detected, confirming previous in silico predictions. These findings provide insights into the potential infectivity, persistence mechanisms, and transcriptional strategies of WhSBV. This study validates previous findings from in silico data mining, further reinforcing its effectiveness as a powerful tool for discovering hidden viruses.IMPORTANCEUnderstanding the diversity and host range of viruses is crucial for assessing their ecological role, associated diseases, and zoonotic potential. However, many newly discovered viruses are characterized using sequence data alone because isolates are often difficult to obtain. Using cell culture models, this study characterizes Wuhan sharpbelly bornavirus (WhSBV), a member of the genus Cultervirus. Here, we demonstrate its ability to establish persistent infection in cypriniform fish cell lines, while exhibiting restricted replication in certain non-cypriniform fish. The identification of polycistronic transcription, splicing events, and immune evasion mechanisms advances our understanding of the molecular biology of WhSBV and culterviruses in general. By validating in silico predictions, this study highlights the power of computational approaches in uncovering viral diversity. As cypriniform fish include economically important species such as carp, understanding the dynamics of WhSBV host range and infection biology may be crucial for future aquaculture health management.},
}
@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
doi = {10.1002/alz.70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Gen&#xe8;ve/ ; //Fondation Segr&#xe9;, Gen&#xe8;ve/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Gen&#xe8;ve/ ; //Fondation Edmond J. Safra, Gen&#xe8;ve/ ; //Fondation Minkoff, Gen&#xe8;ve/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et Ren&#xe9; Keller, Gen&#xe8;ve/ ; //Fondation AETAS, Gen&#xe8;ve/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //H&#xf4;pitaux Universitaires de Gen&#xe8;ve/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.<br><br>METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.<br><br>RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from&#xa0;<&#xa0;2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.<br><br>DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.<br><br>HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}
@article {pmid41164876,
year = {2025},
author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K},
title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.125.322968},
pmid = {41164876},
issn = {1524-4636},
abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.<br><br>METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age&#xb1;SD, 57.75&#xb1;5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3&#xd7;. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.<br><br>RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.<br><br>CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.},
}
@article {pmid41164228,
year = {2025},
author = {Wei, S and Yin, H and Hu, X and Chi, Y and Zhang, L and Zhang, B and Qian, K and Xu, W},
title = {Detection of antimicrobial peptides from fecal samples of FMT donors using deep learning.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1689589},
pmid = {41164228},
issn = {2297-1769},
abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) represent a class of short peptides that are widely distributed in organisms and are regarded as an effective means to tackle bacterial resistance, potentially functioning as substitutes for onventional antibiotics.<br><br>METHODS: We employed metagenomics in combination with deep learning to mine AMPs from the 120 fecal microbiota transplantation (FMT) donor metagenome. Subsequently, a comprehensive analysis of the candidate AMPs was conducted through metaproteomic cross-validation, solubility analysis, cross-validation with other prediction tools, correlation analysis, and molecular dynamics simulations. Finally, four candidate AMPs were selected for chemical synthesis, and experimental validation identified two with broad-spectrum antimicrobial activity. Furthermore, molecular docking was utilized to further analyze the antimicrobial mechanisms of the candidate AMPs.<br><br>RESULTS: Our approach successfully predicted 2,820,488 potential AMPs. After a comprehensive analysis, four candidate AMPs were selected for synthesis, two of which exhibited broad-spectrum antimicrobial activity. Molecular docking provided further insight into the binding mechanisms of these peptides.<br><br>DISCUSSION: This study demonstrates the feasibility of discovering functional AMPs from the human fecal microbiome using computational and experimental approaches, highlights the potential of mining novel AMPs from the fecal microbiome, and provides new insights into the therapeutic mechanisms of FMT.},
}
@article {pmid41164129,
year = {2025},
author = {Zhang, Z and Lin, J and Song, X and Yi, X and Zhou, H and Xu, Z},
title = {Acute intracranial EBV and CMV infections after chemoimmunotherapy for EBV-associated nasopharyngeal carcinoma: a case report and literature review.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1608787},
pmid = {41164129},
issn = {2234-943X},
abstract = {A 36-year-old male patient presented to our hospital complaining of epistaxis for 3 months and persistent headaches with facial numbness for 3 days. After a series of exams, he was diagnosed with nasopharyngeal carcinoma (T4N2M1, stage IVB, AJCC 8th), with a biopsy consistent with non-keratinizing squamous cell carcinoma, and received a combination therapy of gemcitabine, cisplatin, and tislelizumab. Following the first dose, headaches and facial numbness were relieved. On the third day, however, he developed recurrent fever, with a peak body temperature of 39.2 °C, and developed severe paroxysmal stabbing pain in the right frontal region suggestive of trigeminal neuralgia, along with numbness on the right face. We considered multiple possibilities and provided symptomatic treatments, but with poor efficacy. Subsequently, given the emergence of prominent neurological symptoms and fever, we proceeded with a lumbar puncture for cerebrospinal fluid (CSF) analysis. Metagenomic next-generation sequencing (mNGS) of CSF detected the presence of Epstein-Barr virus (EBV) and cytomegalovirus (CMV), and acute intracranial viral infections were considered. After treatment with ganciclovir, the patient's body temperature returned to normal, and headaches and facial numbness were alleviated, and no pathogens were detected in a follow-up examination. We report a case of trigeminal neuralgia emerging post-chemoimmunotherapy, accompanied by CSF positivity for EBV and CMV, where antiviral intervention with ganciclovir resulted in significant symptom alleviation.},
}
@article {pmid41164002,
year = {2025},
author = {Ferreira, R and Coelho, L and Santos, JD and Sobral, D and Isidro, J and Mixão, V and Pinto, M and Nunes, A and Borrego, MJ and Lopo, S and Oleastro, M and Sousa, R and Palminha, P and Veríssimo, C and Gargaté, MJ and Guiomar, R and Cordeiro, R and Macedo, R and Bajanca-Lavado, P and Paixão, P and Duarte, S and Vieira, L and Borges, V and Gomes, JP},
title = {Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656831},
pmid = {41164002},
issn = {1664-302X},
abstract = {Probe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance of two Illumina probe-based panels, the Respiratory and the Urinary Pathogen ID panels (RPIP and UPIP), using 99 clinical samples of 15 different matrices (e.g., cerebrospinal fluid, plasma, serum, urine, swabs, biopsies, etc.) available from Portuguese National Reference Laboratories. This sample set involved 114 "PCR-positive hits" (Ct values range of 9.7-41.3; median of 28.4) for 52 non-redundant human pathogens. For a more detailed bioinformatics assessment, as a complement of the Illumina turnkey solution (Explify), we applied an extended version of our INSaFLU-TELEVIR(+) metagenomics pipeline. Whereas Explify analyses resulted in an initial detection frequency of 73.7% (84/114), the subsequent application of INSaFLU-TELEVIR(+), including taxonomic classification followed by confirmatory read mapping, enabled an overall detection proportion of 79.8% (91/114) of the PCR-positive hits. This translated into a detection rate increment from 54.3% (19/35) to 65.7% (23/35) for bacteria, and from 85.3% (58/68) to 89.7% (61/68) for viruses. The implemented workflow was also very satisfactory for samples with qPCR Ct values above 30, with an overall detection frequency of 71.8% (28/39) when compared with the 92.0% (46/50) observed for those with Ct ≤ 30. In summary, this study validated and established a pioneering approach at the Portuguese National Institute of Health to support clinicians in complex diagnosis, contributing to advance diagnostic capabilities toward a more informed clinical decision and potential improvement of infectious disease outcomes.},
}
@article {pmid41163852,
year = {2025},
author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H},
title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660970},
pmid = {41163852},
issn = {2235-2988},
mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.<br><br>METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.<br><br>RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.<br><br>DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.},
}
@article {pmid41163226,
year = {2025},
author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {350},
pmid = {41163226},
issn = {1743-422X},
support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; },
mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.<br><br>RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n&#x2009;=&#x2009;1), Paramyxoviridae (n&#x2009;=&#x2009;1), Polyomaviridae (n&#x2009;=&#x2009;1), Parvoviridae (n&#x2009;=&#x2009;7), Circoviridae (n&#x2009;=&#x2009;6), and Genomoviridae (n&#x2009;=&#x2009;1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.<br><br>CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.},
}
@article {pmid41163171,
year = {2025},
author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z},
title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {59},
pmid = {41163171},
issn = {1476-0711},
support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&amp;D Program of the China Ministry of Science and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.<br><br>METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.<br><br>RESULTS: No significant differences were observed in age (62.22&#x2009;&#xb1;&#x2009;5.74 vs. 58.23&#x2009;&#xb1;&#x2009;7.55, p&#x2009;=&#x2009;0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p&#x2009;=&#x2009;0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p&#x2009;<&#x2009;0.05) and distinct beta diversity clustering (p&#x2009;<&#x2009;0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p&#x2009;<&#x2009;0.0001). Neutral modeling indicated stochastic assembly (R&#xb2; >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.<br><br>CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.},
}
@article {pmid41163130,
year = {2025},
author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD},
title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {967},
pmid = {41163130},
issn = {1471-2164},
support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; },
abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.<br><br>RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.<br><br>CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.},
}
@article {pmid41163128,
year = {2025},
author = {Xiao, LF and Li, Y and Lian, H and Liu, X and Wen, Y and Chen, X and Huang, W and Li, B and Luo, L and Wang, X and Tutt, C and Zheng, J and Wang, VY and Shao, NY},
title = {Comprehensive metagenomic analysis of the giant panda's oral microbiome reveals distinct taxonomic and functional characteristics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {114},
pmid = {41163128},
issn = {2524-4671},
}
@article {pmid41162595,
year = {2025},
author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L},
title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37813},
pmid = {41162595},
issn = {2045-2322},
support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation &amp; purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; },
abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.},
}
@article {pmid41162426,
year = {2025},
author = {Zhao, Y and Yao, S and Umar, A and Huang, J and Chen, S and Yu, Z},
title = {Comprehensive multi omics explore the microbial function in metabolic pathway flow during altered diet.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {212},
pmid = {41162426},
issn = {2396-8370},
support = {82270564//National Natural Science Foundation of China/ ; 32170071//National Natural Science Foundation of China/ ; 2022JJ30916//Natural Science Foundation of Hunan Province/ ; 2022M713521//China Postdoctoral Science Foundation/ ; 2023CXQD059//Central South University Innovation-Driven Research Programme/ ; },
abstract = {High-protein diet (HPD) and high-fiber diet (HFiD) are two common types of diet, and the transition from HPD to HFiD frequently happens in people who perform diet control. Gut microbiota provide a bridge between diet and health. However, most of the research left out the metabolic landscape change and gut microbial influence under this kind of altered diet. Here, we examined gut microbiome and metabolites change using multi-omics (16S rRNA gene sequencing, shotgun metagenomics, LC-MS/MS metabolomics), and machine-learning methods were introduced to capture the response of gut microbiota to altered diet and associate the variable metabolites and microbial factors. The results suggest that the conversion from HPD to HFiD improves the gut microbial diversity and promotes the pathways of tryptophan, galactose, fructose, and mannose metabolism, which are associated with different gut microbiota and special metabolites. Among them, Faecalibacterium rodentium and Akkermansia muciniphila indicate potential roles in the multi-metabolism. Although these findings are exploratory and hypothesis-generating, they provide a foundation for future mechanistic investigations and emphasize the importance of diverse diets.},
}
@article {pmid41162178,
year = {2025},
author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H},
title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506012},
doi = {10.4014/jmb.2506.06012},
pmid = {41162178},
issn = {1738-8872},
mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.},
}
@article {pmid41162143,
year = {2025},
author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R},
title = {Taxonomy is a foundation of marine science, and it is in trouble.},
journal = {Advances in marine biology},
volume = {101},
number = {},
pages = {197-212},
doi = {10.1016/bs.amb.2025.08.003},
pmid = {41162143},
issn = {2162-5875},
mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; },
abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.},
}
@article {pmid41161821,
year = {2025},
author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L},
title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {10},
pages = {},
doi = {10.1136/jitc-2025-012444},
pmid = {41161821},
issn = {2051-1426},
mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.<br><br>METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.<br><br>RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).<br><br>CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.},
}
@article {pmid41161652,
year = {2025},
author = {Li, R and Qiu, C and Chen, X and Liu, N and Zhang, Y and Qi, L and Wang, S},
title = {Effects of thermal alkaline hydrolysis and biochar addition on anaerobic digestion of sewage sludge and fate of antibiotic resistance genes.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133569},
doi = {10.1016/j.biortech.2025.133569},
pmid = {41161652},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) has gained wide attention as a potential method to reduce the spread of antibiotic resistance genes (ARGs). This study systematically evaluated the impacts of thermal alkaline hydrolysis (TA), biochar addition (BA), and the combination of these two methods (TA-BA) on the efficiency of AD and the removal of ARGs in the sewage sludge AD process. Metagenomic sequencing and quantitative PCR were used to systematically analyze the dissemination of ARGs in different sludge samples. The results indicated that both TA and TA-BA could enhance the efficiency of sludge AD, and the cumulative biogas production was increased by 68.35 %-258.57 % compared to the control group. In addition, the absolute abundance of ARGs was significantly reduced by 59.31 %-74.67 % in the TA- and BA-treated groups compared to the control group. The combination of TA-BA exhibited a synergistic effect, achieving the most significant reduction in ARGs absolute abundance (up to 74.67 % removal), outperforming individual treatments. Both TA and BA could promote the generation of Anaerolinea and Longilinea. Meanwhile, TA significantly increased the relative abundance of Methanobacteriaceae, while BA enhanced the relative abundance of Methanothrix. The correlation analysis demonstrated a significant negative correlation between TOC and sul1 (P < 0.01), and revealing a significant positive correlation between intI1 and sul1 (P < 0.05). Moreover, a significant correlation was observed between the fate of ARGs and the succession of microbial community structure.},
}
@article {pmid41161648,
year = {2025},
author = {Kadam, R and Jo, S and Park, J},
title = {Importance of substrate mixture ratio optimization on efficient anaerobic co-digestion of organic wastes generated in livestock sector: Insights into process performances and metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133561},
doi = {10.1016/j.biortech.2025.133561},
pmid = {41161648},
issn = {1873-2976},
abstract = {Improving the efficiency of anaerobic co-digestion of livestock wastes, particularly through optimizing mixture ratios, is a key research focus. This study identifies an optimal substrate mixture ratio of 23 % cow manure, 22 % pig manure, and 55 % carcass waste, which significantly enhances the degradation of lignocellulose, protein, and lipids compared to equal ratios. In the optimal mixture, the methane (CH4) yield remained stable at 310-360 mL-CH4/g-VS (volatile solids) as the organic loading rate increased to 5 kg-VS/m[3]/d. In contrast, the equal substrate mixture ratio showed lower CH4 yield and less stability under increasing organic loads. Key bacterial genera in the optimal mixture included Cloacamonas, Pseudomonas, Geofilum, and Clostridium, with methanogenic archaea such as Methanosaeta and Methanosarcina. Metagenomic analysis showed enriched pathways for cellulose, hemicellulose, and lipid degradation, alongside enhanced metabolism of volatile fatty acids and ammonia. This study highlights the importance of optimizing substrate ratios for efficient CH4 yield and stability.},
}
@article {pmid41161351,
year = {2025},
author = {Rao, H and Gao, L and Zheng, X and Wei, J and Yue, M and Li, B and Wang, Z and Yang, M and Ren, X},
title = {Reducing environmental contamination during reprocessing of highly contaminated flexible bronchoscopes from the intensive care unit.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.10.006},
pmid = {41161351},
issn = {1532-2939},
abstract = {BACKGROUND: Flexible bronchoscopes (FBs) used in intensive care units (ICUs) frequently harbour pathogenic micro-organisms, creating early reprocessing risks for environmental contamination and staff exposure.<br><br>METHODS: In a six-month evaluation of 832 ICU FBs sampled immediately post-use with metagenomic next-generation sequencing, 55.4% carried one or more pathogens, including multi-drug-resistant bacteria, fungi and airborne agents. We instituted an enhanced reprocessing protocol centred on sealed transfer using double biohazard bags, a two-person dedicated handling method that separates contaminated-scope contact from support tasks, segregation of sinks and a dedicated automated endoscope reprocessor (AER) for ICU FBs, and rigorous terminal disinfection of equipment and work surfaces.<br><br>FINDINGS: Quality checks showed unchanged cleaning efficacy of FBs, whereas the environmental microbial burden on work surfaces after reprocessing was significantly reduced under the new protocol.<br><br>CONCLUSIONS: These findings identify ICU FBs as a high-load reservoir at the point of receipt and demonstrate that targeted, standardized controls during the earliest reprocessing steps can mitigate environmental contamination and enhance sterile-processing worker protection without compromising device reprocessing outcomes.},
}
@article {pmid41161274,
year = {2025},
author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W},
title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127802},
doi = {10.1016/j.jenvman.2025.127802},
pmid = {41161274},
issn = {1095-8630},
abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.},
}
@article {pmid41161238,
year = {2025},
author = {Chi, T and Liu, Z and Zhang, B and Zhu, L and Hu, B},
title = {Risk assessment of the spread of antibiotic resistance genes from hospitals to the receiving environment via wastewater treatment plants.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119264},
doi = {10.1016/j.ecoenv.2025.119264},
pmid = {41161238},
issn = {1090-2414},
abstract = {Antibiotics and antibiotic resistance genes (ARGs) enter the receiving environment from hospitals through wastewater treatment plants (WWTPs), increasing the presence of exogenous ARGs and conditional pathogens in the receiving environment, thereby elevating the risk of drug resistance. This study, based on metagenomics, investigated changes in risk across each node in the ARG transmission chain, from hospitals through WWTPs to downstream receiving water and sediments. The results showed that the total concentration of antibiotics decreased from 1467.80 ± 215.30 µg/L in hospital wastewater to 111.52 ± 18.70 µg/L in downstream receiving water, achieving a 92.40 % removal rate. However, the types of high ecological risk antibiotics in hospital wastewater were only reduced by 38.46 % after treatment by hospitals and sewage treatment plants. The abundance of Rank I ARGs was reduced by 37.03 % in hospital sewage treatment stations and 28.57 % in WWTPs, but these ARGs accounted for 81.8 % of the Rank I ARGs in receiving water. The potential host bacteria for these ARGs were mainly Proteobacteria, which carried bacitracin and multidrug resistance genes. While WWTPs removed 66.67 % of the conditional pathogens, bacteria such as Acinetobacter and Streptococcus still entered the receiving water. MetaCompare revealed that the potential transmission risk of ARGs decreased by 24.31 % after hospital wastewater treatment and by 20.71 % after WWTPs, with the risk of the receiving water being 7.01 times that in sediments. The potential risk assessment framework developed in this study for antibiotics and ARGs in the environment provides a theoretical guidance for antibiotic treatment and ARGs environmental risk control.},
}
@article {pmid41161021,
year = {2025},
author = {Sun, J and Tong, X and Liu, S and Zhang, S and Wang, L and Wang, D and Jia, Q and He, X and Lv, W and Abdo Qasem, MAA and Xiao, Y and Fan, H},
title = {Clinical characteristics and mortality risk factors of Streptococcus constellatus infection: A retrospective cohort study of 390 patients.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103023},
doi = {10.1016/j.jiph.2025.103023},
pmid = {41161021},
issn = {1876-035X},
abstract = {BACKGROUND: Few studies have investigated the clinical characteristics and mortality associated with Streptococcus constellatus (S.constellatus) infection. To identify the clinical features and mortality of patients with S. constellatus infection.<br><br>METHODS: This retrospective cohort study analyzed hospitalized patients with confirmed S.constellatus infection at West China Hospital of Sichuan University from January 2016 to April 2024. S. constellatus was identified using sterile body fluid culture or metagenomic next-generation sequencing (mNGS). Patients were categorized as monomicrobial or polymicrobial infection. Kaplan-Meier curve analysis was performed to compare the 30-day survival rates based on infection type and infection site, while multivariate Cox regression was conducted to identify independent risk factors for 30-day mortality.<br><br>RESULTS: Of the 390 patients, 301 (77.2&#x202f;%) were classified as monomicrobial S. constellatus infection. S. constellatus isolates were highly susceptible to penicillin (98.08&#x202f;%) and levofloxacin (98.90&#x202f;%).Overall 30- and 90-day mortality were 13.08&#x202f;% and 15.13&#x202f;%, higher in polymicrobial than monomicrobial infections (24.72&#x202f;% vs 8.97&#x202f;% at 30 days; 29.21&#x202f;% vs 10.96&#x202f;% at 90 days). Polymicrobial infection (adjusted hazard ratio [aHR] = 2.426, p&#x202f;=&#x202f;0.007) and brain abscess (aHR = 16.689, p&#x202f;<&#x202f;0.001) were identified as independent risk factors for 30-day mortality in patients with S. constellatus infection. In the subgroup of monomicrobial infection, mediastinal abscess (aHR = 6.738, p&#x202f;=&#x202f;0.002) and brain abscess (aHR = 13.933, p&#x202f;<&#x202f;0.001) were significantly associated with an increased risk of 30-day mortality.<br><br>CONCLUSIONS: Although S. constellatus was highly susceptible to antibiotics, short-term mortality remained substantial. Infection site and polymicrobial infection were key prognostic factors in patients with S. constellatus infection.},
}
@article {pmid41161015,
year = {2025},
author = {Ekman, M and Mahani, AN and Aralaguppe, SG and Normark, T and Stamouli, S and Andersson-Li, L and Sun, D and Broddesson, S and Wirta, V and Björkström, NK and Albert, J and Allander, T},
title = {Evaluation of a diagnostic metagenomic sequencing assay: Virus detection sensitivity and background nucleic acids in three different sample materials.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {181},
number = {},
pages = {105882},
doi = {10.1016/j.jcv.2025.105882},
pmid = {41161015},
issn = {1873-5967},
abstract = {BACKGROUND: Metagenomic sequencing has emerged as an attractive, general, and agnostic diagnostic method, in particular for detection of viruses. However, its application faces limitations, including reduced sensitivity due to background nucleic acid content of samples, and the search for an optimized protocol is still ongoing.<br><br>METHODS: We report the development of a metagenomic sequencing protocol for diagnostic use and its performance in detecting DNA and RNA viruses in three different sample materials: serum, cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS).<br><br>RESULTS: Sensitivity was higher for RNA viruses than for DNA viruses, and also higher in CSF than in serum and lowest in NPS. We characterized the background nucleic acids and found higher DNA than RNA levels in CSF and serum and overall highest nucleic acid levels in NPS, intermediate in serum and lowest in CSF. These differences largely explained the observed variability in sensitivity between sample preparations and sample materials.<br><br>CONCLUSIONS: Our results highlight the need to consider sample-type specific characteristics in efforts to improve the sensitivity of metagenomic assays e.g. via host depletion protocols.},
}
@article {pmid41160250,
year = {2025},
author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y},
title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {543},
pmid = {41160250},
issn = {1436-3771},
support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; },
mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; },
abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.<br><br>MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.<br><br>RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.<br><br>CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.<br><br>CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.<br><br>TRIAL REGISTRATION: ITMCTR2024000616.},
}
@article {pmid41160143,
year = {2025},
author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM},
title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {183},
pmid = {41160143},
issn = {1572-9699},
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.},
}
@article {pmid41160089,
year = {2025},
author = {Abuzahrah, SS},
title = {The microbiome of marine sponges located on the Saudi Arabia coast of the Red sea using high-throughput 16S amplicon sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {160},
pmid = {41160089},
issn = {2191-0855},
support = {PROJECT NO.: CRP/SAU24-02//International Centre for Genetic Engineering and Biotechnology (ICGEB)/ ; },
abstract = {Marine sponges (Porifera) from the Red Sea host diverse microbial communities that are integral to sponge health, nutrient cycling, and ecological resilience. Using high-throughput 16S rRNA amplicon sequencing, we characterized the bacterial diversity and functional potential across several Red Sea sponge species. Our findings revealed that these microbiomes are dominated by Alphaproteobacteria, Gammaproteobacteria, and Roseobacteraceae, with notable contributions from bacterial taxa involved in nitrogen fixation, organic matter degradation, and antimicrobial compound production. Functional predictions indicate that these symbionts support sponge nutrition, defense, and adaptation to the extreme Red Sea environment, including high salinity and temperature. Compared to sponge microbiomes from other marine regions, the Red Sea communities display unique taxonomic compositions and enhanced metabolic and defensive capacities. This highlights the essential ecological roles and potential biotechnological applications of these symbiotic assemblages. Our study underscores the significance of exploring sponge-associated microbiomes in understudied and extreme marine ecosystems. These results provide a foundation for future bioprospecting and work on adaptive mechanisms, emphasizing the value of Red Sea sponges and their microbiota for marine biotechnology and ecosystem resilience.},
}
@article {pmid41159973,
year = {2025},
author = {Anani, H and Destras, G and Regue, H and Bulteau, S and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Metagenome-assembled complete genome of Bohxovirus, a virulent bacteriophage involved in the prediction of hospital-acquired pneumonia in intubated critically ill patients.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059225},
doi = {10.1128/mra.00592-25},
pmid = {41159973},
issn = {2576-098X},
abstract = {We present the complete genome of a Bohxovirus species, a virulent phage targeting Prevotella jejuni, reconstructed from viral metagenomes in respiratory endotracheal aspirates of intubated critically ill patients. The 98-kbp bacteriophage, belonging to the Suoliviridae family, does not contain genes associated with antibiotic resistance or bacterial virulence.CLINICAL TRIALSClinicalTrials.gov numbers: NCT02003196 and NCT04793568.},
}
@article {pmid41159804,
year = {2025},
author = {Spottiswoode, N and Neyton, LPA and Calfee, CS and Langelier, CR},
title = {Reply to Liu et al. and Chen et al.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202509-2218LE},
pmid = {41159804},
issn = {1535-4970},
}
@article {pmid41159664,
year = {2025},
author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E},
title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70289},
doi = {10.1002/mnfr.70289},
pmid = {41159664},
issn = {1613-4133},
support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; },
abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.},
}
@article {pmid41159034,
year = {2025},
author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN},
title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655428},
pmid = {41159034},
issn = {1664-3224},
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.<br><br>METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.<br><br>RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.<br><br>DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.},
}
@article {pmid41158777,
year = {2025},
author = {Skoog, EJ and Cutts, E and Bosak, T},
title = {Linking microbial ecology to the cycling of neutral and acidic polysaccharides in pustular mats from Shark Bay, Western Australia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684648},
pmid = {41158777},
issn = {1664-302X},
abstract = {Cyanobacteria and other microbes in peritidal microbial mats have produced extracellular polymeric substances (EPS) for more than two billion years. The production and degradation of EPS contributes to the biogeochemical cycling of carbon and carbonate precipitation within modern microbial mats, but key microbes involved in the cycling of EPS remain unidentified. Here, we investigate the cycling of EPS in the peritidal pustular mats of Shark Bay, Western Australia. We characterize the chemical composition of EPS produced by cyanobacterial enrichment cultures under natural and UV-stress conditions and link these findings to the metabolic potential for EPS production and degradation encoded in 84 metagenome-assembled genomes (MAGs) from the mat community. We further identify the key microbial degraders of specific acidic and neutral polysaccharides in this community by cultivating enrichment cultures on seven commercially available polysaccharides representative of those present in the mats and assessing the dominant taxa. All sequenced Cyanobacteria MAGs have the potential to synthesize mannose, fucose, glucose, arabinose, rhamnose, galactose, xylose, N-acetylglucosamine, galacturonic acid and glucuronic acid. Biochemical analyses confirm the presence of nearly all these monosaccharides in the hydrolysates of EPS extracted from UV- and non-UV exposed cyanobacterial enrichments. Ultraviolet radiation influences the structure and composition of EPS by reducing the hydration, potentially due to cross-linking among polymers in EPS and increasing the relative abundances of uronic acids and xylose in polysaccharides. Analyses of carbohydrate-active enzymes (CAZymes) in the MAGs and of 16S rRNA sequences from experimental polysaccharide enrichments point to major roles for Bacteroidetes, Planctomycetes, and Verrucomicrobia in the cycling of acidic EPS. These experiments reveal a complex interplay among microbial community composition, CAZyme diversity, environmental stressors, and EPS cycling, which together shape carbon flow and biomineralization in pustular mats in Shark Bay.},
}
@article {pmid41158770,
year = {2025},
author = {Peng, Y and Huang, D and Li, J and Sun, X and Zhang, Q and Zhang, R and Yang, R and Li, B and Kong, T and Xiong, Z and Huang, Y and Chang, Z and Su, Y and Shang, Y and Ghani, MU and Wang, Y and Sun, W},
title = {Investigation of the role of sulfide oxidation in the gill-associated microbiota of freshwater mussel Limnoperna fortunei.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671425},
pmid = {41158770},
issn = {1664-302X},
abstract = {INTRODUCTION: Limnoperna fortunei is a notable invasive freshwater species, altering structure and function of natural and engineered aquatic ecosystems. The host-associated microbiomes play a critical role in the survival and thriving of L. fortunei, with the gill-associated microbiomes being particularly significant due to their involvement in filter feeding, nutrient metabolism, and symbiosis. However, research on microbiomes associated with L. fortunei remains limited, and studies specifically focusing on gill-associated microbiota are scarce, leaving a significant gap in our understanding of their ecological roles.<br><br>METHODS: In this study, gill-associated bacterial communities of the L. fortunei were compared with their surrounding water microbial populations in the largest water diversion projects (the Middle Route of the South-to-North Water Diversion Project) to elucidate their environmental adaptations and potential contribution to their hosts. Analyses included assessing bacterial diversity and composition, conducting Neutral Community Model (NCM) analysis to explore community assembly processes, constructing an environmental-microbial co-occurrence network to identify key environmental factors, and performing metagenomic analysis of gill samples to investigate functional genes.<br><br>RESULTS: Significant variations were observed in bacterial diversity and composition between gills and surrounding water. Sulfur oxidizing bacteria Pirellula, SM1A02, and Roseomonas were significantly enriched in gill-associated microbiota. Neutral community model (NCM) analysis unveiled that the assembly of gill microbial communities was primarily governed by stochastic processes, constrained by determined processes. Moreover, environmental-microbial co-occurrence network identified reduced sulfur as the key factor shaping the composition of bacterial communities. Metagenomic binning of gill samples further revealed that metagenome assembled genomes associated with Pirellula within the phylum Planctomycetota contained functional genes related to sulfide oxidation and resistant to oxidative stress.<br><br>DISCUSSION: This study provides systematic insights into the microbial community diversity, assembly patterns, and functional characteristics of L. fortunei gill-asscociated microbiota, contributing to a mechanistic understanding of their ecological roles.},
}
@article {pmid41158352,
year = {2025},
author = {Liu, J and Qian, H and Jin, J and Du, M and Wang, C and Yu, J and Pang, P and Shen, M and Mei, Z and Shi, Y and Wang, Z and Jiang, G and Guo, L and Zhong, C and Tang, P and Wang, Y and Shi, C and Ji, C},
title = {Use of metagenomic next-generation sequencing for accurate diagnosis of tuberculous pleurisy: a retrospective cohort study.},
journal = {Journal of thoracic disease},
volume = {17},
number = {9},
pages = {6771-6778},
pmid = {41158352},
issn = {2072-1439},
abstract = {BACKGROUND: Tuberculous pleurisy (TP) presents persistent diagnostic challenges owing to the suboptimal sensitivity of conventional microbiological assays. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in diagnosing TP using formalin-fixed paraffin-embedded (FFPE) pleural biopsy tissues.<br><br>METHODS: This retrospective study evaluated the diagnostic efficacy of mNGS in FFPE pleural samples of suspected TP patients at The First Affiliated Hospital of Soochow University between April 1, 2018 and February 1, 2023. Those patients with inadequate pleural specimens for mNGS analysis were excluded. Diagnosis of TP was established according to the WS 288-2017 Health Industry Standard of the People's Republic of China.<br><br>RESULTS: A total of 73 patients were enrolled in this study and divided into the TP group and non-tuberculous pleurisy (NTP) group. The TP group comprised 51 patients with a median age of 52 years, including 33 (64.7%) males. The NTP group consisted of 22 patients with a median age of 64 years, including 13 (59.1%) males. Our results showed that mNGS assay on FFPE in pleural biopsies had a sensitivity of 78.43% [95% confidence interval (CI): 0.667-0.901] and a specificity of 100% (95% CI: 1.000-1.000) in diagnosing TP. In the 51 TP cases, mNGS detected Mycobacterium tuberculosis complex (MTBC) in 40 (78.43%) cases and non-tuberculous mycobacteria (NTM) in 31 (60.78%) cases. Of these, 16 cases were MTBC infections alone and 7 cases were NTM infections alone, while 24 were mixed MTBC and NTM infections.<br><br>CONCLUSIONS: mNGS of FFPE of pleural biopsy tissues not only improves the diagnostic efficiency of TP, but also potential accurately distinguishes between MTBC and NTM, providing molecular and microbial basis for the diagnosis of TP, which is helpful for the rapid diagnosis and precise treatment of TP.},
}
@article {pmid41158324,
year = {2025},
author = {Fatemi, S and Kriefall, NG and Yogi, D and Weber, D and Hynson, NA and Medeiros, MCI and Sadowski, P and Amend, AS},
title = {Microbial composition and function are nested and shaped by food web topologies.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf175},
pmid = {41158324},
issn = {2730-6151},
abstract = {Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.},
}
@article {pmid41157632,
year = {2025},
author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K},
title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101362},
pmid = {41157632},
issn = {1999-4915},
support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; },
mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; },
abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.},
}
@article {pmid41157620,
year = {2025},
author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ},
title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101349},
pmid = {41157620},
issn = {1999-4915},
support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation &amp; purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; },
abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.},
}
@article {pmid41157605,
year = {2025},
author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J},
title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101334},
pmid = {41157605},
issn = {1999-4915},
support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; },
mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genotype ; Genetic Variation ; },
abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.},
}
@article {pmid41157584,
year = {2025},
author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS},
title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101312},
pmid = {41157584},
issn = {1999-4915},
support = {202271250010//Parliamentary Amendment from the S&#xe3;o Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; },
mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; },
abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.},
}
@article {pmid41157271,
year = {2025},
author = {Al-Khalaifah, H and Rahman, MH and Al-Surrayai, T and Al-Dhumair, A and Al-Hasan, M},
title = {A One-Health Perspective of Antimicrobial Resistance (AMR): Human, Animals and Environmental Health.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/life15101598},
pmid = {41157271},
issn = {2075-1729},
abstract = {Antibiotics are essential for treating bacterial and fungal infections in plants, animals, and humans. Their widespread use in agriculture and the food industry has significantly enhanced animal health and productivity. However, extensive and often inappropriate antibiotic use has driven the emergence and spread of antimicrobial resistance (AMR), a global health crisis marked by the reduced efficacy of antimicrobial treatments. Recognized by the World Health Organization (WHO) as one of the top ten global public health threats, AMR arises when certain bacteria harbor antimicrobial resistance genes (ARGs) that confer resistance that can be horizontally transferred to other bacteria, accelerating resistance spread in the environment. AMR poses a significant global health challenge, affecting humans, animals, and the environment alike. A One-Health perspective highlights the interconnected nature of these domains, emphasizing that resistant microorganisms spread across healthcare, agriculture, and the environment. Recent scientific advances such as metagenomic sequencing for resistance surveillance, innovative wastewater treatment technologies (e.g., ozonation, UV, membrane filtration), and the development of vaccines and probiotics as alternatives to antibiotics in livestock are helping to mitigate resistance. At the policy level, global initiatives including the WHO Global Action Plan on AMR, coordinated efforts by (Food and Agriculture Organization) FAO and World Organisation for Animal Health (WOAH), and recommendations from the O'Neill Report underscore the urgent need for international collaboration and sustainable interventions. By integrating these scientific and policy responses within the One-Health framework, stakeholders can improve antibiotic stewardship, reduce environmental contamination, and safeguard effective treatments for the future.},
}
@article {pmid41156846,
year = {2025},
author = {Liu, Y and Shang, Y and Wang, X and Li, X and Yu, Z and Zeng, Z and Chen, Z and Wang, L and Xiang, T and Huang, X},
title = {Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102387},
pmid = {41156846},
issn = {2076-2607},
support = {31872181//National Natural Science Foundation of China/ ; 2021QDL062//Research Start-up Funds from the Hangzhou Normal University/ ; 2025JCXK01//Interdisciplinary Research Project of Hangzhou Normal University/ ; },
abstract = {In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.},
}
@article {pmid41156834,
year = {2025},
author = {Kakumyan, P and Yang, L and Liu, S and Saninjuk, K and Dong, Q and Pan, X and Yu, C and Zhao, Y},
title = {Sustainable Recycling of Mushroom Residue as an Effective Substitute for Cotton Hull Waste in Volvariella volvacea Cultivation: Evidence from Physicochemical and Microbiome Analyses.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102372},
pmid = {41156834},
issn = {2076-2607},
support = {2024YFD1200204//National Key R&amp;D Program of China/ ; 19390743000//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; },
abstract = {Mushroom residue (MR) is extensively produced during the industrialized cultivation of mushrooms, and its utilization is environmentally sustainable. Cotton hull waste (CW) serves as a common raw material for the cultivation of Volvariella volvacea in China. This study compared MR- and CW-based cultivation formulas with respect to their physicochemical characteristics, bacterial communities, and functional dynamics during substrate fermentation (composting). Xylanase production was greater in the MR formula than in the CW formula. Conversely, cellulase (CMCase) was generated at higher levels in the CW formula compared to the MR formula. Interestingly, the biological efficiency of MR was found to be comparable to that of CW, but the cost of MR was much lower. The dynamics of bacterial communities and their associated metabolic functions during substrate fermentation were monitored using 16S rRNA metagenomics techniques. Significant alterations in bacterial community structure were observed within both formulas throughout the preparation phase. Indicator species analysis revealed distinct patterns of bacterial diversity development between MR- and CW-based composts during fermentation. Metabolic function analysis indicated that carbohydrate and amino acid metabolism remained relatively active throughout this process. These results suggest that the MR formula is equally effective as conventional CW compost for supporting V. volvacea cultivation, while also offering a lower raw material cost.},
}
@article {pmid41156833,
year = {2025},
author = {Xing, L and Niu, S and Wu, D and Zhang, Z and Xu, M},
title = {Sodium Butyrate Supplementation in Whole Milk Modulates the Gastrointestinal Microbiota Without Altering the Resistome and Virulome in Preweaned Calves.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102375},
pmid = {41156833},
issn = {2076-2607},
support = {BR221506//Universitiy Basic Research Fund Project of Inner Mongolia Autonomous Region/ ; 2023LHMS03048//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; },
abstract = {This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM without SB (CON) and (2) WM supplemented with SB (8.8 g/d; SB). At 74 days of age, all calves were slaughtered to collect ruminal and cecal digesta. Metagenomic analysis was used to characterize the microbial composition, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs). SB supplementation altered the ruminal microbial composition and increased the abundance of beneficial bacteria, including Actinobacteria, Bifidobacterium, and Olsenella (p < 0.05). Although SB did not significantly affect the overall microbial composition or diversity in the cecum (p > 0.05), it promoted the growth of beneficial genera such as Flavonifractor and Subdoligranulum (p < 0.05). Furthermore, SB supplementation did not significantly alter the composition of VFGs or ARGs in either the rumen or the cecum (p > 0.05). However, significant differences in VFGs and ARGs were observed between the rumen and the cecum, with a greater diversity of both VFGs and ARGs detected in the cecum compared to that in the rumen (p < 0.05). In summary, supplementing whole milk with sodium butyrate modulates gastrointestinal health in preweaned calves by favorably shaping the microbial community without significantly altering the antibiotic resistome or virulome.},
}
@article {pmid41156832,
year = {2025},
author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P},
title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102373},
pmid = {41156832},
issn = {2076-2607},
support = {1671/22-03-2023//Green Fund/ ; },
abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.},
}
@article {pmid41156828,
year = {2025},
author = {Stock, EK and Rota, K and Dunn, B and Vasquez, M and Hernandez-Velazquez, D and Lespes, A and Bosmans, S and Smith, JC and Kyndt, JA},
title = {Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102369},
pmid = {41156828},
issn = {2076-2607},
support = {NSF OIA-2044049//EPSCoR NE/ ; },
abstract = {The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.},
}
@article {pmid41156825,
year = {2025},
author = {Lorenzin, G and Carlin, M},
title = {Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102366},
pmid = {41156825},
issn = {2076-2607},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely defined. For this systematic review, a search was conducted in PubMed, Embase, Scopus, Web of Science, and Google Scholar to identify studies directly comparing long-read (e.g., Oxford Nanopore, PacBio) and short-read (e.g., Illumina, Ion Torrent, BGISEQ) metagenomic sequencing for the diagnosis of LRTI. Eligible studies reported diagnostic accuracy or comparative performance between platforms. Risk of bias was evaluated using the QUADAS-2 tool. Thirteen studies met inclusion criteria. Reported platforms included Illumina, Oxford Nanopore, PacBio, Ion Torrent, and BGISEQ-500. A total of 13 studies met inclusion criteria. Across studies reporting sensitivity, average sensitivity was similar for Illumina (71.8%) and Nanopore (71.9%). Specificity varied substantially, ranging from 42.9 to 95% for Illumina and 28.6 to 100% for Nanopore. Concordance between platforms ranged from 56 to 100%. Illumina consistently produced superior genome coverage (approaching 100% in most reports) and higher per-base accuracy, whereas Nanopore demonstrated faster turnaround times (<24 h), greater flexibility in pathogen detection, and superior sensitivity for Mycobacterium species. Risk of bias was frequently high or unclear, particularly in patient selection (6 studies), index test interpretation (5), and flow and timing (4), limiting the robustness of pooled estimates. Long-read and short-read mNGS platforms exhibit comparable strengths in the diagnosis of LRTIs. Illumina remains optimal for applications requiring maximal accuracy and genome coverage, whereas Nanopore offers rapid, versatile pathogen detection, particularly for difficult-to-detect organisms such as Mycobacterium. However, there are certain limitations of the review, including a lack of comparable outcomes reported in all studies; therefore, further research is warranted to address this.},
}
@article {pmid41156813,
year = {2025},
author = {Mollova, D and Baev, V and Iliev, I},
title = {In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102352},
pmid = {41156813},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual's health and well-being across all stages of life. Breastfeeding, the introduction of solid food at a certain stage after birth, and the type of food largely determine the composition of the developing microbiome. The influence of probiotics on the early development of the microbiome is gaining increasing interest. The method of in vitro co-cultivation with probiotic strains provides a clearer picture of the influence of these microorganisms on the community and the functional changes that the infant's microbiome undergoes. We used fecal samples to study this influence by conducting metagenomic sequencing to determine the composition of the microbiome and a series of cultivations to determine the absorption of various fibers and prebiotic sugars from breast milk. We found statistically significant differences in the absorption of prebiotic sugars isolated from breast milk, as well as better absorption of several substrates in the presence of a probiotic strain.},
}
@article {pmid41156808,
year = {2025},
author = {Mqambalala, A and Maleke, M and Deysel, LM and Osman, JR and Gomez-Arias, A and Valverde, A and Hernandez, JC},
title = {First Insight into the Natural Attenuation of Emerging Contaminants Using a Metagenomics Approach from Drinking Water Sources in the Free State.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102349},
pmid = {41156808},
issn = {2076-2607},
support = {PMDS230718136664//National Research Foundation/ ; },
abstract = {Emerging contaminants have gained interest over the years due to their adverse effects on the aquatic environment. Therefore, it is essential to improve the current strategies for their removal. Biodegradation has emerged as an efficient strategy driven by microorganisms through metabolism and co-metabolism pathways. Enzymes encoded by specific genes facilitate these processes. This study aimed to identify and quantify the genes involved in these pathways. The research identified bacterial species belonging to the genera Pseudomonas, Nitrosomonas, Nitrosospira, and Methylotenera, which are associated with the degradation of emerging contaminants. Additionally, it successfully identified genes linked to metabolism and co-metabolism processes within the indigenous bacteria (MAGs). The findings suggest that the native bacteria in the samples may have the natural potential to mitigate emerging contaminants in aquatic environments through the combined actions of metabolism and co-metabolism.},
}
@article {pmid41156764,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Jiang, F and Song, P and Liu, Y and Fan, Q and Xu, Y and Zhang, R},
title = {Insights into Cold-Season Adaptation of Mongolian Wild Asses Revealed by Gut Microbiome Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102304},
pmid = {41156764},
issn = {2076-2607},
support = {32360139//National Natural Science Foundation of China/ ; 2023LHMS03067//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; LHZX-2023-02//Joint Grant from Chinese Academy of Sciences -People's Government of Qinghai Province on San-jiangyuan National Park/ ; },
abstract = {The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g-h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass.},
}
@article {pmid41156729,
year = {2025},
author = {Carnaggio, AA and Barthet, MM},
title = {It's a Question at the 'Root' of the Problem: Fungal Associations of Dionaea muscipula (Venus' Flytrap) Roots in Its Native Habitat.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102269},
pmid = {41156729},
issn = {2076-2607},
support = {//US Fish &amp; Wildlife Services; Coastal Carolina University Coastal Marine and Wetlands Science Master's program; the Coastal Carolina University Graduate Student Research Incentive Grant; Savannah Presbytery's M.K. Pentecost Ecology Fund Grant/ ; },
abstract = {Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in nutrient acquisition influencing plant vigor and overall success. Dionaea muscipula, commonly known as the Venus' flytrap, is endemic to rims of the Carolina Bays located in southeast North Carolina and northeast South Carolina, where D. muscipula survives in nutrient poor soils with a vestigial root system. We utilized a combination of microscopy, plating, and metagenomics, to investigate the presence/absence of fungal partners that may contribute to success and vigor of D. muscipula in its native habitat in order to further conservation of this carnivorous plant. Results support that D. muscipula forms both mycorrhizal and fungal endophytic associations, most likely to aid nutrient uptake from otherwise nutrient-poor soils, as well as aid in stress defense. Several ectomycorrhizal, endophytic, and saprophytic fungal species were identified from the surrounding rhizosphere of D. muscipula roots presenting a first glimpse into fungal communities that may influence D. muscipula physiology and compose the microbiome of the Carolina Bays ecosystem.},
}
@article {pmid41156696,
year = {2025},
author = {Wang, Y and Shi, F and Lang, F and Wang, G and Mao, Y and Xiao, Y and Yin, L and He, G and Liao, Y},
title = {Ecological Imprint of Rare Earth Mining on Microbial Communities and Water Quality Across Depth and Distance Gradients in Ganzhou, China.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102236},
pmid = {41156696},
issn = {2076-2607},
support = {42167014//National Natural Science Foundation of China/ ; GJJ2401516//Jiangxi Provincial Department of Education Science and Technology research-youth project/ ; S202510419008//Innovation and Entrepreneurship Project for College Students in Jiangxi Province/ ; JZB1915//the Research Project of Jinggangshan University (Natural Sciences)/ ; },
abstract = {Rare earth element (REE) mining exerts profound impacts on aquatic ecosystems, yet the microbial community responses and water quality under such stress remain underexplored. In this study, the surface (0.2 m) and subsurface (1.0 m) water along a spatial transect from proximal to distal points was investigated in a REE-mining area of Ganzhou, China. Physicochemical analyses revealed pronounced gradients of nitrogen (e.g., NH4[+]-N, NO3[-]-N), heavy metals (e.g., Mn, Zn, Pb), and REEs (e.g., La, Nd, Ce), with higher accumulation near mining sources and partial attenuation downstream. Dissolved oxygen and redox potential indicated mildly reducing conditions at contaminated points, potentially promoting denitrification and altering nitrogen cycling. Metagenomic sequencing showed significant shifts in microbial community composition, with enrichment of metal- and nitrogen-tolerant taxa, and key denitrifiers (e.g., Acidovorax, Bradyrhizobium, Rhodanobacter), particularly at upstream polluted points. KEGG-based gene annotation highlighted dynamic nitrogen transformations mediated by multiple pathways, including nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation. Notably, genes associated with nitrite and nitrate reduction (e.g., nir, nar, nrf) were enriched near mining sources, indicating enhanced nitrogen conversion potential, while downstream activation of nitrogen-fixing genes suggested partial ecosystem recovery. Meanwhile, some microbial such as Variovorax carried metal tolerant genes (e.g., ars, chr, cnr). These findings demonstrate that REE and heavy metal contamination restructure microbial networks, modulate nitrogen cycling, and create localized ecological stress gradients. This study provides a comprehensive assessment of mining-related water pollution, microbial responses, and ecological risks, offering valuable insights for monitoring, restoration, and sustainable management of REE-impacted aquatic environments.},
}
@article {pmid41156619,
year = {2025},
author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB},
title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101008},
pmid = {41156619},
issn = {2076-0817},
mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; },
abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.},
}
@article {pmid41156596,
year = {2025},
author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH},
title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14100985},
pmid = {41156596},
issn = {2076-0817},
support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology, Vietnam/ ; },
mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; },
abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.},
}
@article {pmid41156563,
year = {2025},
author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M},
title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203312},
pmid = {41156563},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.},
}
@article {pmid41155945,
year = {2025},
author = {Bodnár, K and Fehér, P and Ujhelyi, Z and Haimhoffer, &#xc1; and Papp, B and Sinka, D and Freytag, C and Fidrus, E and Szarka, K and Kardos, G and Nacsa, F and Bácskay, I and Józsa, L},
title = {Formulation and Testing of Alginate Microbeads Containing Salvia officinalis Extract and Prebiotics.},
journal = {Pharmaceutics},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/pharmaceutics17101308},
pmid = {41155945},
issn = {1999-4923},
support = {ek&#xf6;p-24-3-I//university research scholarship program of the ministry for culture and innovation from the source of the national research, development and innovation fund/ ; TKP2021-EGA-18//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; 2022-1.2.2-T&#xc9;T-IPARI-UZ-2022-00006//National Research, Development and Innovation Fund/ ; },
abstract = {Background/Objectives: This study aimed to develop an advanced oral delivery platform for Salvia officinalis (S. officinalis) extract by co-encapsulating it with inulin and pectin in alginate-based microbeads, formulated via ionic gelation. Methods: The microbeads were comprehensively characterized, including the assessment of morphology, particle size, encapsulation efficiency, swelling behavior, in vitro dissolution, and enzymatic stability, and Caco-2 cell-based assays for cytocompatibility, permeability, and transepithelial electrical resistance. Antioxidant capacity and anti-inflammatory effects were also evaluated. Results: The resulting microbeads (~275 µm) achieved > 90% encapsulation efficiency and exhibited pronounced swelling (~90%). The release of S. officinalis constituents displayed pH sensitivity, with sustained release in simulated intestinal fluid, alongside significant enhancement of enzymatic stability. Encapsulation led to markedly improved permeability of bioactive compounds across Caco-2 monolayers, attributable to reversible modulation of tight junctions. Encapsulated extract retained potent antioxidant activity and significantly reduced pro-inflammatory cytokines. The formulation, across various concentrations, further promoted the growth and viability of Lactobacillus strains. Conclusions: Collectively, these findings demonstrate that alginate-inulin-pectin microbeads provide a multifunctional system for stabilizing S. officinalis extract, enabling controlled release, enhanced intestinal absorption, and maintained bioefficacy. Importantly, the formulation also promoted Lactobacillus viability, indicating a prebiotic effect and offering considerable potential for improved oral therapeutic applications.},
}
@article {pmid41155696,
year = {2025},
author = {Ji, M and Ma, B and Dong, J and Liu, S and Shi, Y and Bu, M and Wang, L and Liu, L},
title = {Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/ph18101583},
pmid = {41155696},
issn = {1424-8247},
support = {2022YFC2303100, 32472320, 32022002 and 32270083//National Key Research and Development Program of China, National Natural Science Foundation of China/ ; },
abstract = {The vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell genomics, and synthetic biology, have opened new avenues for accessing and harnessing bioactive natural products from these previously inaccessible microorganisms. This review highlights recent methodological and technological advancements in the cultivation and identification of novel microorganisms, and showcases the resulting discoveries of new natural products, demonstrating their potential for drug development.},
}
@article {pmid41155464,
year = {2025},
author = {Usui, M and Miyagi, S and Yamanaka, R and Oka, Y and Kobayashi, K and Sato, T and Sano, K and Onizuka, S and Inoue, M and Fujii, W and Iwasaki, M and Ariyoshi, W and Nakashima, K and Nishihara, T},
title = {Measuring the Invisible: Microbial Diagnostics for Periodontitis-A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010172},
pmid = {41155464},
issn = {1422-0067},
mesh = {Humans ; *Periodontitis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Porphyromonas gingivalis/isolation &amp; purification/genetics ; },
abstract = {Periodontitis is a biofilm-driven inflammatory disease in which conventional indices (probing depth, clinical attachment level, and radiographs) quantify tissue destruction without capturing the biology of infection. In this review, we synthesized microbiological diagnostics, from chairside tools to omics. We outline sampling strategies and emphasize the quantitative monitoring of bacterial load. Enzymatic assays (e.g., N-benzoyl-DL-arginine-2-naphthylamide hydrolysis assay test) measure functional activity at the point of care. Immunological methods include rapid immunochromatography for Porphyromonas gingivalis and enzyme-linked immunosorbent assay for the high-throughput measurement of bacterial antigens. Molecular platforms encompass quantitative polymerase chain reaction (qPCR) (TaqMan, SYBR, multiplex panels; propidium monoazide quantitative-qPCR for viable cells), checkerboard DNA-DNA hybridization for semi-quantitative community profiling, loop-mediated isothermal amplification (LAMP)/molecular beacon-LAMP for portable isothermal detection, and microarrays. Complementary modalities such as fluorescent in situ hybridization, next-generation sequencing, and Fourier transform infrared spectroscopy provide spatial, ecological, and biochemical resolutions. We discuss the limitations of current approaches, including sampling bias, presence-activity discordance, semi-quantitation, method biases, limited strain/function resolution, low-biomass artifacts, and lack of validated cutoffs. To address these challenges, we propose a pragmatic hybrid strategy: site-specific quantitative panels combined with activity and host-response markers interpreted alongside clinical metrics under standardized quality assurance/quality control. Priorities include outcome-linked thresholds, strain-aware/functional panels, robust point-of-care chemistry, and harmonized protocols to enable personalized periodontal care.},
}
@article {pmid41155136,
year = {2025},
author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T},
title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209841},
pmid = {41155136},
issn = {1422-0067},
support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; },
mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation &amp; purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; },
abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.},
}
@article {pmid41154862,
year = {2025},
author = {Yin, R and Chen, B and He, X and Cai, C and Zhai, T and Shi, H and Li, N and Ma, X},
title = {Enhanced Phosphorus Removal by Iron-Carbon in Constructed Wetlands Across Salinity Gradients: Mechanisms and Microbial Insights for Aquaculture Tailwater Treatment.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101459},
pmid = {41154862},
issn = {2079-7737},
support = {No. BK20220682//Natural Science Foundation of Jiangsu Province/ ; LYG20230005//Postdoctoral Science Foundation of Lianyungang/ ; KYCX24-3671//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 2025SNJF008//Zhejiang Province 'San Nong Jiu Fang' Science and Technology Collaboration Project/ ; },
abstract = {Saline aquaculture tailwater challenges conventional constructed wetlands (CWs) with their limited phosphorus (P) removal capacity. To address this, iron-carbon constructed wetlands (IC-CWs) were developed and operated under four salinity gradients (0, 10, 20, and 30) for 155 days to investigate the effects of salinity on P removal and associated microbial mechanisms. The results showed that salinity critically influenced long-term P removal, with the system at salinity 20 (S20) achieving the highest total phosphorus (TP) removal efficiency (78.80 ± 6.01%). Enhanced P removal was primarily attributed to the upregulation of phosphate transport genes (pstS, 14.25-fold increase) and elevated activity of key enzymes (AKP and ACP) in phosphorus-accumulating organisms (PAOs). However, high salinity (30) suppressed microbial metabolic functions. Metagenomic analysis revealed that salinity stress reshaped microbial community structure, with Bacteroidota abundance increasing 10-fold in S20 compared to S0 (control). This phylum harbored the phnE gene, significantly promoting organic phosphorus mineralization. Additionally, iron release increased with rising salinity, and the relative abundance of the phnE gene in Bacteroidota was highest in the S20 group, indicating a close association between iron release and PAOs as well as organic P mineralization genes. The quadratic polynomial model revealed that iron release under high salinity followed nonlinear kinetics, with passivation layer rupture promoting iron-phosphorus precipitate desorption in later stages. These findings provide a theoretical basis for optimizing salinity parameters to enhance chemical-biological P removal synergy, offering a promising strategy for saline aquaculture wastewater treatment.},
}
@article {pmid41154799,
year = {2025},
author = {Promariya, A and Treenarat, S and Akrimajirachoote, N and Sricharern, W and Raksajit, W},
title = {Cultivation of Arthrospira platensis in Veterinary Hospital Wastewater Enhances Pigment Production and Reduces Antibiotic Resistance Genes.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101396},
pmid = {41154799},
issn = {2079-7737},
support = {FF(KU)18.66 and FF(KU)50.67//Kasetsart University Research and Development (KURDI)/ ; The 80th Anniversary of Kasetsart University's Establishment//Graduate School, Kasetsart University/ ; High Quality Research Graduate Development Cooperation Project//Kasetsart University and the National Science and Technology Development Agency (NSTDA)/ ; },
abstract = {Veterinary hospital wastewater (VHW) is a significant environmental concern due to its high nutrient content, organic pollutants, and antibiotic resistance genes (ARGs). This study evaluated the physicochemical properties of VHW, its potential to support Arthrospira platensis cultivation, and its effects on microbial and resistome profiles. VHW contained high levels of ammonia nitrogen, total Kjeldahl nitrogen, biological oxygen demand (BOD), and chemical oxygen demand (COD), indicating substantial contamination. A. platensis was cultivated for 8 days in Zarrouk medium supplemented with 0-100% VHW. Biomass production peaked in 25% VHW (0.78 ± 0.05 g/L), while growth was strongly suppressed at concentrations ≥75%. Pigment levels in 25% VHW increased significantly compared to the control: 1.3-fold for chlorophyll-a (12.0 μg/mL), 1.5-fold for carotenoids (4.4 μg/mL), 1.7-fold for phycocyanin (120 μg/mL), and 2.3-fold for allophycocyanin (54 μg/mL). Shotgun metagenomic analysis revealed that A. platensis cultivation markedly altered the microbial community and reduced the prevalence of ARGs. In 25% VHW, Proteobacteria dominated the community (97.0%), but their abundance declined to 11.6% when co-cultivated with A. platensis. Likewise, Acinetobacter sp. carrying high levels of the aph gene, along with Methylophaga sp. and Pseudomonas_E sp. harboring oqxB, decreased substantially, suggesting that A. platensis effectively suppressed ARG-rich genera. These findings highlight the dual potential of A. platensis for sustainable pigment-rich biomass production and efficient wastewater treatment.},
}
@article {pmid41154019,
year = {2025},
author = {Zhang, S and Wang, Q and Gong, S and Li, M and Zhang, Y and Sun, L and Sun, L},
title = {The Effect of Cucumaria frondosa Tentacles Hydrolysates on Dextran Sulfate Sodium-Induced Colitis: Integrated Metagenomics and Metabolomics Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/foods14203483},
pmid = {41154019},
issn = {2304-8158},
support = {42106111//National Natural Science Foundation of China/ ; 2023JCYJ088//The Yantai Science and Technology Innovation Development Program/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; QSCDP202304//Fund of Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food/ ; },
abstract = {Inflammatory bowel disease continues to pose substantial therapeutic challenges in modern gastroenterology. This study systematically evaluated the anti-colitis efficacy of Cucumaria frondosa tentacles hydrolysates (CFTHs) using a dextran sulfate sodium (DSS)-induced murine colitis model. Characterized by enhanced stability and solubility with molecular weights below 1000 Da, administration of CFTHs demonstrated a significant mitigation in colitis pathology. Therapeutic outcomes included an improved splenic index, attenuated colonic mucosal damage, and substantial decreases in serum pro-inflammatory cytokines. Relative to the DSS group, the MPO value in the CFTHs-H group decreased by 27.6%, and the IL-6 value exhibited a reduction of 33%. Metagenomic profiling revealed that CFTHs mediated gut microbiota modulation, particularly the enrichment of beneficial Bacteroidetes and suppression of pro-inflammatory Proteobacteria. Metabolomic analysis identified elevated colonic concentrations of anti-inflammatory metabolites such as gamma-linolenic acid and prostaglandin I2, suggesting a microbiome-metabolome crosstalk in the therapeutic mechanism. These multi-omics findings in a murine model suggest that CFTHs may represent a promising candidate for future studies as a nutraceutical intervention for inflammatory bowel disorder. This intervention may operate through mechanisms that include simultaneous immunomodulation, microbiota restoration, and metabolic reprogramming.},
}
@article {pmid41153961,
year = {2025},
author = {Xiang, R and Chen, J and Wang, J and Song, H and Jiang, J and Wu, F and Luo, J and Duan, M and Zhu, G},
title = {Characteristics of the Gut Microbiota in Different Segments of the Gastrointestinal Tract of Big-Eyed Bamboo Snake (Pseudoxenodon macrops).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/ani15203035},
pmid = {41153961},
issn = {2076-2615},
abstract = {Snakes are model animals to study energy balance, but studies on the gut microbiota of the animals are rather scarce. To fill the gap, we used metagenome sequencing to investigate the microbial community composition and adaptability in the stomach, small intestine, and large intestine of Big-eyed Bamboo Snake. The results showed that there was no significant differences in α-diversity among different gastrointestinal segments. Pseudomonadota, Bacteroidota, and Bacillota were the most abundant phyla. The dominant genera in the stomach and small intestine were similar, while those in the large intestine were distinct. The abundance of Bacteroides, Citrobacter and Clostridium was significantly higher in the large intestine than in the small intestine. The LEfSe analysis revealed that the small intestine had the most characteristic bacteria, with a total of 20 species, while the stomach and large intestine each had two species. Additionally, in the current study, we also focused on the impact of the microbial community structure on functions through functional annotations in the KEGG and CAZy. There were significant differences in the KEGG level 2 between the stomach and the small intestine. The LEfSe analysis revealed the differences in the CAZy level 2 between the large intestine and the small intestine. Overall, our study provided a comparative and contrastive analysis of the gut microbiota in different gastrointestinal segments of Big-eyed Bamboo Snake, offering valuable insights for the co-evolution mechanism of the host and the gut microbiota.},
}
@article {pmid41153865,
year = {2025},
author = {Wei, J and Wei, L and Ullah, A and Geng, M and Zhang, X and Wang, C and Khan, MZ and Wang, C and Zhang, Z},
title = {Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/ani15202938},
pmid = {41153865},
issn = {2076-2615},
support = {2022YFD1600103; 2023YFD1302004//the National Key R&amp;D Program of China/ ; },
abstract = {Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host-microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including Prevotella, Fibrobacter, and Ruminococcus, correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production.},
}
@article {pmid41153262,
year = {2025},
author = {Feng, Y and Feng, H and Yu, X and Zhao, J and Zhou, H and Li, J and Chen, P and Feng, L},
title = {Next-Generation Sequencing for Diagnosis of Fatal Balamuthia Amoebic Encephalitis: A Case Report.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/diagnostics15202590},
pmid = {41153262},
issn = {2075-4418},
support = {Z20200307//The scientific research project of Guangxi Health Commission/ ; },
abstract = {Background:Balamuthia mandrillaris is a free-living amoebic parasite that primarily causes rare opportunistic infections in immunocompromised hosts. Balamuthia amoebic encephalitis (BAE) is a rare yet severe parasitic infection affecting the central nervous system. It has an extremely low incidence in China but can have a mortality rate as high as 98%. The clinical manifestations of amebic infections are similar to those of bacterial and tuberculous meningitis, lacking specificity, which makes accurate diagnosis challenging in the clinical setting. Case Presentation: A 61-year-old immunocompetent woman experienced worsening headache and a moderate fever over the course of five days, initially treated as a common cold. On 25 February 2025, she exhibited behavioral abnormalities, dysphagia, and a high fever of 40.2 °C, which progressed to a coma. On 26 February, her cranial CT scan revealed multifocal hemorrhagic lesions in the right frontotemporoparietal lobes. The MRI revealed similar lesions with slight enhancement and herniation. She underwent an emergency decompressive craniectomy, yet her condition continued to deteriorate following the surgery. On 27 February, serum targeted next-generation sequencing (tNGS) detected B. mandrillaris. Additionally, metagenomic NGS (mNGS) of the cerebrospinal fluid (CSF) sample confirmed the presence on 28 February. Finally, B. mandrillaris was identified through a brain tissue biopsy on 3 March. However, due to the delayed diagnosis and lack of effective drugs, her condition rapidly deteriorated and became irreversible. Her family ultimately chose to withdraw treatment. Conclusions: This study highlights the application of NGS for early diagnosis of patients with severe CNS infection. Both tNGS and mNGS can be considered for the rapid detection of rare or novel pathogens and for facilitating diagnosis.},
}
@article {pmid41152730,
year = {2025},
author = {Su, Y and Xiao, Q and Ye, S and Qiu, F and Guo, Q and Chen, Q and Chen, P and You, Y and Huang, S and Wu, Z},
title = {Metagenomic next-generation sequencing (mNGS) guides targeted antibiotic therapy and reduces mortality in sepsis: a propensity-matched retrospective cohort study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1430},
pmid = {41152730},
issn = {1471-2334},
support = {A2024130//Guangdong Medical Research Foundation/ ; A2023198//Guangdong Medical Research Foundation/ ; 82374216//National Natural Science Foundation of China/ ; 20251363//Traditional Chinese Medicine Bureau of Guangdong Province/ ; 2320001006680//Foshan Science and Technology Bureau/ ; 2320001006896//Foshan Science and Technology Bureau/ ; 2220001005576//Foshan Science and Technology Bureau/ ; YN2022QN01//Guangdong Hospital of Traditional Chinese Medicine Special Research Project on Traditional Chinese Medicine Science and Technology/ ; SL2025A04J4201//Planned Science Technology Project of Guangzhou/ ; 20210001//Foshan Medical Research Project/ ; },
}
@article {pmid41152727,
year = {2025},
author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S},
title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {691},
pmid = {41152727},
issn = {1471-2180},
support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Thyroid Cancer, Papillary/microbiology ; *Butyrates/metabolism ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Feces/microbiology ; *Thyroid Nodule/microbiology ; Adult ; *Thyroid Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.<br><br>METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16&#xa0;S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.<br><br>RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.<br><br>CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.},
}
@article {pmid41152726,
year = {2025},
author = {Zou, Y and Zou, Q and Wang, Y and Han, C},
title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {693},
pmid = {41152726},
issn = {1471-2180},
support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; China ; Feces/microbiology ; },
abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.<br><br>RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of &#x3b1;-galactosidase and &#x3b2;-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.<br><br>CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.},
}
@article {pmid41152332,
year = {2025},
author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L},
title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1702},
pmid = {41152332},
issn = {2052-4463},
support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; },
mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; },
abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.},
}
@article {pmid41152293,
year = {2025},
author = {Pold, G and Saghaï, A and Jones, CM and Hallin, S},
title = {Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9495},
pmid = {41152293},
issn = {2041-1723},
support = {2016-03551//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2023-03627//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Senior Career Grant 2019//Sveriges Lantbruksuniversitet (Swedish University of Agricultural Sciences)/ ; },
mesh = {*Denitrification/genetics ; *Bacteria/genetics/metabolism/classification ; Nitrates/metabolism ; *Genome, Bacterial ; *Genome, Microbial ; Metagenome ; Nitrites/metabolism ; Metabolic Networks and Pathways/genetics ; },
abstract = {Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.},
}
@article {pmid41152000,
year = {2025},
author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, &#xc4; and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H},
title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70222},
doi = {10.1111/1758-2229.70222},
pmid = {41152000},
issn = {1758-2229},
support = {2020-02710//Svenska Forskningsr&#xe5;det Formas/ ; 20-102//Svenskt Vatten/ ; },
mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.},
}
@article {pmid41151807,
year = {2025},
author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M},
title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70112},
doi = {10.1111/1758-2229.70112},
pmid = {41151807},
issn = {1758-2229},
support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; },
mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; },
abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.},
}
@article {pmid41151605,
year = {2025},
author = {Burillo, A and Serrano-Lobo, J and Bouza, E and Muñoz, P},
title = {Is it possible to identify genotypes underlying resistant phenotypes in Gram-negative pathogens?.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001158},
pmid = {41151605},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review explores the relationship between genotypes and resistant phenotypes in Gram-negative pathogens. We analyse to what extent conventional phenotypic methods predict genetic mechanisms of resistance, the reliability of genotypic approaches, and how integrated strategies may improve diagnostic accuracy and clinical utility.<br><br>RECENT FINDINGS: Traditional AST remains the clinical reference standard due to its correlation with therapeutic outcomes, yet it often fails to identify the molecular basis of resistance. Molecular methods such as PCR, microarrays, and targeted sequencing allow rapid detection of known genes but cannot reliably predict expression or functionality. Whole-genome sequencing provides the most comprehensive overview, capturing both known and novel resistance determinants as well as mobile genetic elements. Nevertheless, genotype-phenotype discordance persists, driven by regulatory mutations, inducible expression, or synergistic mechanisms. Emerging technologies - including real-time sequencing, metagenomics, and machine learning-based predictive models - are enhancing our ability to infer phenotypes from genomic data. Still, these approaches face challenges of standardization, validation, and integration into clinical workflows.<br><br>SUMMARY: Linking genotypes to resistant phenotypes in Gram-negative pathogens remains complex. While phenotypic AST ensures reliability for therapy, genotypic methods provide unprecedented insight into resistance mechanisms and epidemiology. Discrepancies between the two highlight the need for integrated diagnostic platforms that combine functional and genomic perspectives. Artificial intelligence-driven predictive models and curated resistance databases hold promise for improving accuracy, but widespread adoption requires robust datasets, clinical validation, and harmonized interpretative frameworks. Ultimately, integrating phenotypic and genotypic data represents the most effective strategy to provide mechanism-informed, clinically actionable diagnostics for antimicrobial resistance management.},
}
@article {pmid41151513,
year = {2025},
author = {Qin, C and Xie, X and Wang, H and Ma, L and Lu, X},
title = {Metagenomic investigation of antibiotic resistance genes and assessment of their health risk in antimony-mining area.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140278},
doi = {10.1016/j.jhazmat.2025.140278},
pmid = {41151513},
issn = {1873-3336},
abstract = {Here, we conducted a metagenomic investigation of antibiotic resistance genes (ARGs) from soil, surface water, and groundwater samples collected in Xikuangshan antimony (Sb)-mine area in China. Overall, 1737 subtypes of ARGs were detected which collectively conferred resistance to 27 classes of antibiotics. The health risk of the ARGs to humans were quantitatively evaluated by integrating human accessibility, mobility, pathogenicity, and clinical availability. A total of 6706 ARGs were identified within metagenome-assembled genomes (MAGs), with 44 of these ARGs posing a health risk, particularly those that confer multidrug resistance. Soil served as a potential reservoir of ARGs, harboring a greater variety of ARGs. In contrast, aquatic environments were hotspots for high-risk ARGs, with groundwater containing the most numerous risk-associated ARGs but surface waters posing the greatest health risks. Remediated soils showed significantly reduced ARG abundance and health risk, indicating that ecological restoration effectively mitigates ARG-related health risks. Pseudomonadota persisted as the dominant functional phylum in Sb mining area, exhibiting significant positive correlations with ARGs abundance. Acinetobacter, Achromobacter, and Stenotrophomonas, were identified as opportunistic pathogens carrying high-risk ARGs. Our analysis suggested that mining activities may amplify public health risks of ARGs, highlighting the importance for ecological remediation of mining areas.},
}
@article {pmid41151484,
year = {2025},
author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J},
title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.},
journal = {International immunopharmacology},
volume = {167},
number = {},
pages = {115730},
doi = {10.1016/j.intimp.2025.115730},
pmid = {41151484},
issn = {1878-1705},
abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).<br><br>METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-&#x3ba;B signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.<br><br>RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-&#x3ba;B pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-&#x3ba;B pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-&#x3ba;B activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-&#x3ba;B and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.<br><br>CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-&#x3ba;B pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.},
}
@article {pmid41151425,
year = {2025},
author = {Lv, J and Zhao, Q and Jiang, J and Ding, J and Wei, L and Liang, J},
title = {Electron transfer performance and mechanism in twin microbial fuel cell powered electro-Fenton system with waste activated sludge as substrate.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {168},
number = {},
pages = {109154},
doi = {10.1016/j.bioelechem.2025.109154},
pmid = {41151425},
issn = {1878-562X},
abstract = {The twin microbial fuel cell powered electro-Fenton system (twin-MFCⓅEFs), combining active oxygen component and microbial metabolism, was constructed to improve the treatment process of waste activated sludge (WAS). Nevertheless, the performance and mechanism of electron transfer underlying this enhancement remain poorly understood. This study investigated the performance and mechanism of electron generation and utilization in twin-MFCⓅEFs with WAS as substrate. The higher electron generation and recovery efficiency (8.25 % of coulombic efficiency) was attributed to the higher content of amino acids (such as tryptophan), humic substances and their aromatic groups and unsaturated conjugated double bonds in the soluble organic matter, which facilitated biodegradation and electron transfer. The higher electron utilization performance (52.76 % of faraday efficiency) relied on the superior electron supply system that exhibited greater free radical oxidation. Metagenomic analysis indicated that an increased secretory capacity of glycosyltransferases (including glucosyltransferases and β-glucosidases) and a reduced activity of acetate kinase and methyl-coenzyme M reductase alpha subunit in cellular metabolic processes favored signaling and electricity production. The study focused on electron flow in twin-MFCⓅEFs and offered a promising strategy for improving the sludge treatment process.},
}
@article {pmid41151197,
year = {2025},
author = {Ortiz-López, G and Sánchez-Reyes, A and Téllez-Galván, A and Bustamante, VH and Breton-Deval, L},
title = {Influence of anthropogenic inputs on microbial risks and resistance genes in a riverine environment.},
journal = {International journal of hygiene and environmental health},
volume = {271},
number = {},
pages = {114699},
doi = {10.1016/j.ijheh.2025.114699},
pmid = {41151197},
issn = {1618-131X},
abstract = {Rivers face significant anthropogenic pressures due to diverse water discharges, which alter microbial community structures and may facilitate the dissemination of potentially pathogenic microorganisms and antibiotic-resistance genes (ARGs). This study used metagenomic analysis to characterize microbial and viral communities, determine antibiotic resistance profiles, and evaluate potential public health risks associated with different discharges sources. Water samples were collected from agricultural, hospital, untreated domestic wastewater, treated wastewater, and environmental inputs. Results revealed that hospital wastewater (HW) had microbial genera associated with the wastewater treatment plant; however, we were able to isolate a multidrug-resistant Klebsiella aerogenes, Enterobacter spp. and Staphylococcus spp. Untreated domestic wastewater (UW) was dominated by species such as Arcobacter cryaerophilus, Acinetobacter johnsonii, Escherichia coli, and Acinetobacter lwoffii, while treated wastewater (TW) showed the presence of Arcobacter cryaerophilus, Aeromonas caviae, Prevotella copri, Arcobacter butzleri, Acinetobacter johnsonii, Escherichia coli, and Pseudomonas stutzeri. Regarding ARGs, HW contributed significantly to ARGs diversity, particularly genes conferring resistance to critical antibiotics such as meropenem and vancomycin. TW exhibits the highest ARG diversity, including genes for broad-spectrum resistance to aminoglycosides, penicillins, and cephalosporins, suggesting cumulative contamination from multiple sources. These findings emphasize the importance of advancing efforts to tackle this challenge in wastewater treatment practices and stricter regulations to mitigate the spread of antibiotic resistance and pathogenic microorganisms in aquatic environments.},
}
@article {pmid41150814,
year = {2025},
author = {Jiang, L and Qing, Y and Huang, K and Huang, H and Li, C and Mei, Q and Wu, Q},
title = {Comparison of Gut Microbial Structure and Function Changes in Sichuan-Tibetan Black Pigs at Different Growth Stages Based on Metagenomic Analysis.},
journal = {Current issues in molecular biology},
volume = {47},
number = {10},
pages = {},
doi = {10.3390/cimb47100866},
pmid = {41150814},
issn = {1467-3045},
support = {2023NSFSC0206//the Natural Science Foundation Project of Science and Technology Department of Sichuan Province/ ; },
abstract = {The gut microbiota plays a crucial role in maintaining swine health and understanding its stage-specific variations provides a scientific basis for health assessment. This study investigated the structural changes in intestinal microbiota during the development of Sichuan-Tibetan black pigs (n = 15) by collecting fecal samples at three growth stages: the nursery period (1 month), growing period (3 months), and finishing period (10 months). Microbial profiling was performed using 16S rRNA sequencing. Results showed no significant difference in the Shannon index between the nursery and growing periods, while the finishing period exhibited distinct ACE and Chao 1 indices compared to other stages. PCoA and NMDS analyses revealed significant structural divergence in the finishing period microbiota, with greater intra-group variability observed in the nursery and growing periods. At the phylum level, Firmicutes abundance increased progressively with growth, becoming the absolute dominant phylum, whereas Bacteroidota showed a declining trend. These characteristics are particularly prominent during the finishing period. At the family level, Lactobacillaceae abundance increased continuously. Oscillospiraceae remained stable during the early stages but decreased significantly in the finishing period. Genus-level analysis shows that Lactobacillus, especially L. amylovorus and L. reuteri, become dominant bacterial species during the finishing period. A total of 84 differentially abundant core microbiota were identified, with the finishing period containing the highest number. Functional annotation revealed 19 significantly different metabolic pathways across the three stages. The most significant is the enhanced activity of microorganisms during the finishing period in pathogen-related metabolism and exogenous degradation, reflecting their adaptability to complex feed. These findings demonstrate stage-dependent variations in the gut microbiota of Sichuan-Tibetan black pigs, providing valuable references for nutritional regulation and feeding management practices.},
}
@article {pmid41150726,
year = {2025},
author = {Ma, M and Li, Q and Wu, F and Zhu, B and Lu, H and Zhang, D and Łukasik, P and Hu, Y},
title = {Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch of Tetraponera ants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2514882122},
doi = {10.1073/pnas.2514882122},
pmid = {41150726},
issn = {1091-6490},
support = {32370448//MOST | National Natural Science Foundation of China (NSFC)/ ; 2243200009//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
mesh = {*Ants/microbiology/physiology/metabolism ; Animals ; *Symbiosis/physiology ; *Nitrogen/metabolism ; Microbiota/physiology ; Larva/microbiology/growth &amp; development ; Amino Acids/metabolism ; *Bacteria/metabolism/genetics ; Urea/metabolism ; },
abstract = {While microbial symbioses are fundamental to the nutrition of many animal groups, current paradigms focus on symbiont functions at the host individual level. It remains unclear whether microbial symbioses can sustain colony-level fitness in social insects, whose ecological success depends on nutrient coordination across castes. Here, we investigate the specialized bacterial pouch, a symbiont-containing organ present exclusively in adult workers of Tetraponera nigra-group ants, revealing its crucial role in colony-wide nutrient provisioning. Using a combination of microscopy, amplicon and metagenomic sequencing, and [15]N-urea feeding experiments on four species in the group, we show that its adult-specific pouch-associated microbiota, primarily Tokpelaia, recycle nitrogen from urea and convert it into amino acids which are provisioned to adult workers and developing larvae. Disruption of this nitrogen-recycling symbiosis severely impairs larval growth and overall colony fitness. Our results show how caste-restricted microbial organs can centralize metabolic functions at the colony level, challenging individual-centric paradigms of host-microbe mutualism and providing insights into the pivotal role of microbial symbionts in superorganismal adaptation to nutritional constraints.},
}
@article {pmid41150505,
year = {2025},
author = {Zong, C and Gao, S and Wei, Q and Yin, Y and Shi, Y},
title = {Impact of Chromium Exposure on Potato Farming Systems and Plant Responses.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09289},
pmid = {41150505},
issn = {1520-5118},
abstract = {Chromium (Cr) is a major source of heavy metal pollution, posing a significant threat to agricultural production. This study investigated the impact of chromium on potato farmland and explored integrated control strategies using the potato cultivar Dongnong 310 as the research subject. Transcriptomic and rhizosphere microbial metagenomic sequencing methods were employed. The main findings were as follows: (1) chromium stress downregulated genes encoding photosystem II, thereby inhibiting photosynthesis in potatoes. (2) Chromium stress altered the diversity of rhizosphere soil microorganisms, reduced the abundance of nitrous oxide reductase, and increased emissions of the greenhouse gas N2O. (3) The rhizosphere microorganism Bacillus strain C5 and potato gene LOC102599109 exhibited chromium resistance. This study provides theoretical guidance for the integrated management of chromium pollution in potato farmland.},
}
@article {pmid41149776,
year = {2025},
author = {Tana, C and Moffa, S and Tana, M and Ucciferri, C and Moffa, L},
title = {Gut Microbiota, Mild Cognitive Impairment and Dementia: A Systematic Review.},
journal = {Neurology international},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/neurolint17100155},
pmid = {41149776},
issn = {2035-8385},
abstract = {BACKGROUND: Alterations of the gut microbiota have been increasingly implicated in the pathogenesis of dementia through mechanisms involving systemic inflammation, immune dysregulation, and gut-brain axis disruption. Clinical evidence, however, remains fragmented.<br><br>OBJECTIVES: This systematic review aimed to characterize gut microbiota profiles in individuals with mild cognitive impairment (MCI) or Alzheimer's dementia (AD), explore mechanistic associations with neurodegeneration, and evaluate the impact of microbiota-targeted interventions on cognitive outcomes.<br><br>METHODS: Following PRISMA 2020 guidelines and a registered protocol (PROSPERO CRD420251074832), PubMed/Medline was searched through May 2025. Eligible studies included randomized controlled trials (RCTs) and cohort and case-control studies assessing microbiota composition or interventions in participants with MCI or AD.<br><br>RESULTS: Twenty-one studies were included (1 RCT, 20 observational; sample size 22-302). Most used 16S rRNA sequencing; one used shotgun metagenomics. Across cohorts, MCI and AD patients consistently showed reduced short-chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcaceae, Lachnospiraceae) and increased pro-inflammatory taxa (Escherichia/Shigella, Enterobacteriaceae, Bacteroides). Several studies reported reduced microbial diversity. Specific taxa, including Akkermansia muciniphila and Faecalibacterium, were associated with amyloid burden, hippocampal atrophy, and cognitive decline. Environmental and dietary factors influenced microbial composition and cognition. The RCT reported that probiotic supplementation improved inflammatory markers and BDNF levels, although changes in microbiota composition were inconsistent.<br><br>CONCLUSIONS: Gut dysbiosis is strongly associated with cognitive impairment and markers of neurodegeneration. Modulation of the microbiota through diet and probiotics emerges as a promising avenue for dementia prevention and management, though robust longitudinal and interventional studies are needed to confirm causality and therapeutic efficacy.},
}
@article {pmid41149107,
year = {2025},
author = {Matsumoto, R and Takahashi, M and Hosomichi, K and Okuwaki, S and Koizumi, S and Hikita, Y and Hatanaka, R and Yamaguchi, T},
title = {Comparison of Long-Term Oral Bacterial Flora Before and After Orthognathic Surgery in Surgical Orthodontic Treatment.},
journal = {Dentistry journal},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/dj13100458},
pmid = {41149107},
issn = {2304-6767},
support = {24K20091//Yu Hikita/ ; 24K13185//Tetsutaro Yamaguchi/ ; },
abstract = {Background/Objectives: Multi-bracket appliances are essential in surgical orthodontic treatment, and perioperative oral management during orthognathic surgery is critical. Thorough plaque control, appropriate use of antibiotics, and shortening of operative time have been reported to be effective in preventing postoperative infections and ensuring surgical success. As highly invasive orthognathic surgery involving osteotomy may influence the postoperative oral microbiota, this study aimed to investigate the characteristics of and clarify the changes occurring in the salivary oral microbiota after orthognathic surgery. Methods: The study included 14 patients (Group S; mean age 29.3 ± 9.8 years) who underwent surgical orthodontic treatment and 15 control patients (Group C; mean age 27.1 ± 8.7 years) who received orthodontic treatment alone. Salivary samples were analyzed via 16S rRNA gene sequencing, and the relative abundances of bacteria were evaluated using the Linear Discriminant Analysis Effect Size. Results: The prevalence of Neisseria, which is associated with early biofilm formation, decreased over time in both groups. In contrast, Streptococcus exhibited an increase in prevalence. In Group S, members of Pseudomonas, the family Saccharimonadaceae, and the order Rhizobiales showed increases at 5-8 months post-surgery. Conclusions: Surgical orthodontic treatment may influence the oral microbiota and promote colonization by opportunistic pathogens. Instructions regarding oral hygiene and appropriately timed professional cleaning interventions are critical in preventing such colonization. Longitudinal monitoring of the microbiota using metagenomic analysis may be useful for future perioperative management and guidance of oral hygiene.},
}
@article {pmid41149072,
year = {2025},
author = {Amorim Filho, AG and Martins, RCR and Franco, LAM and Marinelli, JVC and Peres, SV and Francisco, RPV and Carvalho, MHB},
title = {Vaginal Microbiota in Short Cervix Pregnancy: Secondary Analysis of Pessary vs. Progesterone Trial.},
journal = {Diseases (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/diseases13100338},
pmid = {41149072},
issn = {2079-9721},
abstract = {BACKGROUND/OBJECTIVES: Preterm birth (PTB) is a leading cause of neonatal mortality, particularly in women with a short cervix. Vaginal dysbiosis has been associated with increased PTB risk. Progesterone (PR) and Arabin pessary (PE) are commonly used for PTB prevention, but their impact on vaginal microbiome composition is unclear. This study aimed to compare the effects of these interventions on the vaginal microbiome in women at risk of PTB.<br><br>METHODS: In a secondary analysis of a randomized trial at Hospital das Cl&#xed;nicas, Universidade de S&#xe3;o Paulo, 203 women with singleton pregnancies and cervical length &#x2264; 25 mm at the second trimester were assigned to daily vaginal PR (200 mg) or PE. Vaginal swabs from 44 participants (n = 22 per group) were collected at baseline and 4 weeks post-treatment and analyzed via 16S rRNA gene sequencing.<br><br>RESULTS: From 88 samples analyzed, 80 showed a low-diversity, Lactobacillus-dominated microbiota, 42 classified into Lactobacillus iners-dominated community state type (CST-III), and 38 presented other Lactobacillus species dominance (termed CST-I/II/V). The remaining eight samples presented non-Lactobacillus dominance (CST-IV). Comparing the two groups, no significant changes in CST were observed between sampling timepoints (PE group, p = 0.368; PR group, p = 0.223). Similarly, Shannon alpha diversity did not change (PE group, p = 0.62; PR group, p = 0.30), and Bray-Curtis dissimilarity also did not change after treatment (p = 0.96, before; p = 0.87, after treatment).<br><br>CONCLUSIONS: Arabin pessary and vaginal progesterone maintain vaginal microbiome stability in women at high PTB risk, supporting the microbiological safety of both interventions.},
}
@article {pmid41148745,
year = {2025},
author = {Tewolde, R and Thombre, R and Farley, C and Nadarajah, S and Khan, I and Sewell, M and Spiller, OB and Afshar, B},
title = {Comparison of Phenotypic and Whole-Genome Sequencing-Derived Antimicrobial Resistance Profiles of Legionella pneumophila Isolated in England and Wales from 2020 to 2023.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101053},
pmid = {41148745},
issn = {2079-6382},
abstract = {Background: Antimicrobial resistance (AMR) in Legionella pneumophila is emerging as a concern, particularly with resistance to macrolides and fluoroquinolones. Although clinically significant resistance in Legionella pneumophila remains uncommon, systematic genomic surveillance using whole-genome sequencing (WGS) is needed to anticipate treatment failure as metagenomic diagnostics move toward routine use. Objectives: We assessed the UK Health Security Agency AMR pipeline for predicting resistance in L. pneumophila by analysing 522 L. pneumophila isolates from England and Wales (2020-2023) together with nine database sequences that carry confirmed 23S rRNA mutations conferring high-level azithromycin resistance. The objective of the present study was to examine the presence of antimicrobial resistance genes (ARGs) in L. pneumophila isolates and to determine whether they exhibited phenotypic resistance through minimum inhibitory concentration (MIC) testing. Methods: Serogroups (sgs) were determined using an in-house qPCR assay, and L. pneumophila non-sg1 isolates were serogrouped using the Dresden monoclonal antibody (mAb) typing method. Sequence types were determined using the standard sequence-based typing method by Sanger sequencing. WGS reads were screened against standard AMR databases to identify resistance genes and resistance-mediating mutations. Agar dilution measured MICs for azithromycin, erythromycin, ampicillin, levofloxacin, tetracycline and spectinomycin in isolates possessing the blaOXA-29, lpeAB or aph(9)-Ia gene. Results: AMR screening detected lpeAB, two allelic β-lactamase variants (blaOXA-29 and blaLoxA) and aph(9)-Ia in 165 of the 522 L. pneumophila isolates, while all high-azithromycin MIC reference sequences contained the expected 23S mutation. Only lpeAB was associated with a significant twofold elevation in macrolide MICs. Neither β-lactamase variant increased ampicillin MICs, and aph(9)-Ia carriage did not correlate with higher spectinomycin MICs. Conclusions: Advanced genomic analytics can now deliver timely therapeutic guidance, yet database-flagged genes may not translate into phenotypic resistance. Continuous pairing of curated mutation catalogues with confirmatory testing remains essential for distinguishing clinically actionable determinants such as 23S mutations and lpeAB from silent markers like blaOXA-29 and aph (9)-Ia.},
}
@article {pmid41148714,
year = {2025},
author = {Lertcanawanichakul, M and Bhoopong, P and Horpet, P},
title = {Mangrove Ecosystems as Reservoirs of Antibiotic Resistance Genes: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101022},
pmid = {41148714},
issn = {2079-6382},
support = {The official grant number has not yet been assigned.//Plant Genetic Conservation Project Unde&#xe1e; the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn - RSPG/ ; },
abstract = {Background: Mangrove ecosystems are critical coastal environments providing ecological services and acting as buffers between terrestrial and marine systems. Rising antibiotic use in aquaculture and coastal agriculture has led to the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in these habitats. Aim: This narrative review aims to synthesize current knowledge on the prevalence, diversity, and environmental drivers of ARGs in mangrove ecosystems, highlighting their role as reservoirs and the potential for horizontal gene transfer. Methods: Studies published up to September 2024 were identified through PubMed, Scopus, Web of Science, and Google Scholar. Inclusion criteria focused on ARGs and ARB in mangrove sediments, water, and associated biota. Data on ARG prevalence, microbial community composition, detection methods, and environmental factors were extracted and narratively synthesized. Results: Seventeen studies from Asia, South America, and Africa were included. ARGs conferring resistance to tetracyclines, sulfonamides, β-lactams, and multidrug resistance were found to be widespread, particularly near aquaculture and urban-influenced areas. Metagenomic analyses revealed diverse resistomes with frequent mobile genetic elements, indicating high potential for horizontal gene transfer. Environmental factors, including sediment type, organic matter, and salinity, influenced ARG abundance and distribution. Conclusions: Mangrove ecosystems act as both reservoirs and natural buffers for ARGs. Sustainable aquaculture practices, continuous environmental monitoring, and integrated One Health approaches are essential to mitigate ARG dissemination in these sensitive coastal habitats.},
}
@article {pmid41148708,
year = {2025},
author = {Lynch, S and Thomson, P and Santibañez, R and Avendaño-Herrera, R},
title = {Influence of Florfenicol Treatments on Marine-Sediment Microbiomes: A Metagenomic Study of Bacterial Communities in Proximity to Salmon Aquaculture in Southern Chile.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101016},
pmid = {41148708},
issn = {2079-6382},
support = {FONDAP No. 1523A0007//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {Background/Objectives: Metagenomic analyses are an important tool for understanding ecological effects, particularly in sites exposed to antimicrobial treatments. Marine sediments host diverse microbial communities and may serve as reservoirs for microbial resistance. Although it is known that antimicrobials can alter microbial composition, specific impacts on sediments surrounding salmon farms remain poorly understood. This study analyzed bacterial community structure in marine sediments subjected to florfenicol treatment from salmon farms in the Los Lagos Region of southern Chile. Methods: Sediment samples were collected and examined through DNA extraction and PCR amplification of the 16S rRNA gene (V3-V4 region). Sequences were analyzed using a bioinformatics pipeline, and amplicon sequence variants (ASVs) were taxonomically classified with a Naïve Bayesian classifier. The resulting ASV abundance were then used to predict metabolic functions and pathways via PICRUSt2, referencing the MetaCyc database. Results: Significant differences in bacterial phyla were observed between the control farm and two farms treated with florfenicol (17 mg kg[-1] body weight per day) for 33 and 20 days, respectively. Farm 1 showed notable differences in phyla such as Bacteroidota, Bdellovibrionota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fibrobacterota, Firmicutes, and Fusobacteriota, while Farm 2 exhibited differences in the phyla Bdellovibrionota, Calditrichota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fusobacteriota, Nanoarchaeota, and Nitrospirota. Shannon Index analysis revealed a reduction in alpha diversity in the treated farms. Comparative analysis between the control and the treated farms showed pronounced shifts in the relative abundance of several bacterial phyla, including statistically significant differences in Chloroflexi and Firmicutes. Predicted functional pathways revealed a notable enrichment of L-methionine biosynthesis III in Farm 2, suggesting a shift in sulfur metabolism potentially driven by antimicrobial treatment. Additionally, increased activity in fatty acid oxidation pathways indicates a higher microbial potential for lipid degradation at this site. Conclusions: These findings highlight the considerable influence of florfenicol on sediment microbial communities and reinforce the need for sustainable management strategies to minimize ecological disruption and the spread of antimicrobial resistance.},
}
@article {pmid41148701,
year = {2025},
author = {Ramsay, DE and McDonald, W and Gow, SP and McLeod, L and Otto, SJG and Osgood, ND and Waldner, CL},
title = {The Potential for Sample Testing at the Pen Level to Inform Prudent Antimicrobial Selection for Bovine Respiratory Disease Treatment: Investigations Using a Feedlot Simulation Tool.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101009},
pmid = {41148701},
issn = {2079-6382},
support = {N/A//Genome Canada/ ; N/A//Saskatchewan Agriculture Development Fund/ ; N/A//Beef Cattle Research Council (BCRC)/ ; N/A//National Sciences and Engineering Research Council (NSERC)/ ; N/A//University of Saskatchewan/ ; N/A//University of Alberta/ ; },
abstract = {Background: Antimicrobial drugs are used to treat bacterial diseases in livestock production systems, including bovine respiratory disease (BRD) in feedlot cattle. It is recommended that therapeutic antimicrobial use (AMU) in food animals be informed by diagnostic tests to limit the emergence of antimicrobial resistance (AMR) and preserve the effectiveness of available drugs. Recent evidence demonstrates preliminary support for the pen as a prospective target for AMR testing-based interventions in higher-risk cattle. Methods: A previously reported agent-based model (ABM) was modified and then used in this study to investigate the potential for different pen-level sampling and laboratory testing-informed BRD treatment strategies to favorably impact selected antimicrobial stewardship and management outcomes in the western Canadian context. The incorporation of sample testing to guide treatment choice was hypothesized to reduce BRD relapses, subsequent AMU treatments and resultant AMR in sentinel pathogen Mannheimia haemolytica. The ABM was extended to include a discrete event simulation (DES) workflow that models the testing process, including the time at sample collection (0 or 13 days on feed) and the type of AMR diagnostic test (antimicrobial susceptibility testing or long-read metagenomic sequencing). Candidate testing scenarios were simulated for both a test-only control and testing-informed treatment (TI) setting (n = 52 total experiments). Key model outputs were generated for both the pen and feedlot levels and extracted to data repositories. Results: There was no effect of the TI strategy on the stewardship or economic outcomes of interest under baseline ecological and treatment conditions. Changes in the type and number of uses by antimicrobial class were observed when baseline AMR in M. haemolytica was assumed to be higher at feedlot arrival, but there was no corresponding impact on subsequent resistance or morbidity measures. The impacts of sample timing and diagnostic test accuracy on AMR test positivity and other outputs were subsequently explored with a theoretical "extreme" BRD treatment protocol that maximized selection pressure for AMR. Conclusions: The successful implementation of a pen-level sampling and diagnostic strategy would be critically dependent on many interrelated factors, including the BRD treatment protocol, the prevalences of resistance to the treatment classes, the accuracy of available AMR diagnostic tests, and the selected "treatment change" thresholds. This study demonstrates how the hybrid ABM-DES model can be used for future experimentation with interventions proposed to limit AMR risk in the context of BRD management.},
}
@article {pmid41148456,
year = {2025},
author = {Loera, MY and de Figueras, CG and Sánchez-Costa, M and Martínez-Rodríguez, P and Mirete, S and Lamprecht-Grandío, M and Díaz, S and González-Pastor, JE and Díaz-Rullo, J},
title = {Co-expression of environmental extremophilic genes strongly enhances Escherichia coli cross-protection to abiotic stress.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {39},
pmid = {41148456},
issn = {1433-4909},
support = {PID2021-126114NB-C43//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Escherichia coli/genetics/physiology/metabolism/radiation effects ; *Extremophiles/genetics ; *Stress, Physiological ; Oxidative Stress ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Nature is home to a wide range of species that thrive in extreme conditions. Despite the identification and study of many extremophilic organisms, significant questions remain regarding the limits of life and the potential for enhancing, combining, or transferring extreme characteristics to other organisms. In previous works of our group, several genes retrieved from environmental extremophiles using functional metagenomics were shown to increase the tolerance of the model bacterium Escherichia coli towards different stress conditions. Here, we proposed to evaluate whether the rational combination of those resistance genes isolated from environmental extremophiles and involved in different molecular mechanisms enhanced the cross-protection of E. coli to extreme conditions. Data revealed that the simultaneous introduction in E. coli of environmental extremophilic resistance genes involved in protein degradation, biofilm formation, oxidative stress, and DNA protection resulted in strongly enhanced, non-additive effects, significantly increasing survival rate under perchlorate exposure, UV radiation, and low pH compared to the individual introduction of these genes. Our findings supports that the introduction of multiple resistance genes isolated from environmental extremophiles that belong to diverse biological processes of stress adaptation may be crucial for engineering of multi-resistant species of interest in biomanufacturing and astrobiology.},
}
@article {pmid41148396,
year = {2025},
author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q},
title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.},
journal = {International ophthalmology},
volume = {45},
number = {1},
pages = {447},
pmid = {41148396},
issn = {1573-2630},
support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical &amp; Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; },
abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.<br><br>METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n&#x2009;=&#x2009;5959), 233 blood metabolites (n&#x2009;=&#x2009;136,016), and RVO cases and controls from the FinnGen consortium (cases, n&#x2009;=&#x2009;775; controls, n&#x2009;=&#x2009;308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.<br><br>RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.<br><br>CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.},
}
@article {pmid41148302,
year = {2025},
author = {Hirayama, M and Maeda, T and Kashihara, K and Tsuboi, Y and Ito, M and Nishiwaki, H and Ohno, K and Ueyama, J},
title = {Linking diet, gut microbiota, and metabolites to Parkinson's disease risk: a shotgun metagenomic comparison of Japanese and Taiwanese cohorts.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {},
number = {},
pages = {},
pmid = {41148302},
issn = {1435-1463},
support = {24K10657//Japan Society for the Promotion of Science/ ; 23H02794//Japan Society for the Promotion of Science/ ; 2022G025//Smoking Research Foundation/ ; },
abstract = {Emerging evidence suggests that gut microbiota and its metabolites play pivotal roles in the pathogenesis of Parkinson's disease (PD). However, cross-national differences in diet and microbial composition may account for the striking variability in PD prevalence worldwide. To address this, we performed a comparative shotgun metagenomic analysis between Japanese and Taiwanese individuals, two genetically similar East Asian populations with distinct dietary habits and differing PD incidence rates. Our analysis revealed marked differences in dietary intake: Taiwanese individuals consumed higher amounts of animal fats and tropical fruits, whereas the Japanese diet was characterized by greater intake of seafood, root vegetables, and traditional fermented foods such as natto. These dietary patterns were reflected in gut microbiota profiles. Japanese individuals exhibited a higher abundance of Blautia, Faecalibacterium, and Bifidobacterium, while Taiwanese samples were enriched in Bacteroides and Alistipes. Functionally, genes involved in short-chain fatty acid (SCFA), vitamin, and polyamine biosynthesis were significantly reduced in PD patients and in the Taiwanese cohort. Metabolomic analyses corroborated these findings, showing decreased levels of SCFAs, polyamines, and key vitamins such as nicotinate and pantothenate in PD patients. Notably, Blautia abundance correlated positively with a broad range of beneficial metabolites, highlighting its potential role as a central modulator of host-microbe metabolic interactions. Our findings suggest that traditional Japanese dietary practices may shape a gut microbial environment that confers resistance to PD, underscoring the need for future interventional studies targeting diet-microbiota interactions in PD prevention and treatment.},
}
@article {pmid41148242,
year = {2025},
author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R},
title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02725},
pmid = {41148242},
issn = {1588-2640},
abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.},
}
@article {pmid41147939,
year = {2025},
author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F},
title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03604f},
pmid = {41147939},
issn = {2042-650X},
abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.},
}
@article {pmid41147782,
year = {2025},
author = {Zhang, L and Yang, G and Zhang, C and Ji, B and Wu, D},
title = {Symbiotic nitrogen fixation and recycling in xylophagous insects: insights from gut microbiota of Apriona swainsoni larvae.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70323},
pmid = {41147782},
issn = {1526-4998},
support = {81503115//National Natural Science Foundation of China/ ; JNFX2025192//Domestic Visiting Program for Young Key Teachers of Anhui Province/ ; BK2012816//Natural Science Foundation of Jiangsu Province/ ; 201409/WT_/Wellcome Trust/United Kingdom ; CX (16)1005//Jiangsu Agricultural Science and Technology Independent Innovation Project/ ; 2023AH050727//Natural Science Foundation (Key project) of the University in Anhui Province/ ; 2024AH050921//Natural Science Foundation (Key project) of the University in Anhui Province/ ; HZR2436//Hefei Municipal Natural Science Foundation/ ; 2024A755//Anhui Postdoctoral Scientific Research Program Foundation/ ; },
abstract = {BACKGROUND: Xylophagous insects, as nitrogen-limited organisms, face severe nutritional constraints due to the inherently low nitrogen content of lignocellulosic substrates-insufficient for growth. To alleviate this limitation, they rely on gut microbiota-mediated symbiotic nitrogen fixation and nitrogenous waste recycling. Apriona swainsoni, a model wood-boring cerambycid, exemplifies this adaptation: under extreme nitrogen scarcity in its xylem diet. While gut symbionts are hypothesized to overcome nitrogen limitation, the underlying mechanisms remain unclear.<br><br>RESULTS: First, metagenomic sequencing and functional gene analysis revealed enrichment of nitrogenase and urease genes in the posterior hindgut (PHG). Metaproteomics detected the nitrogenase gene nifU but no urease proteins, identifying nitrogen fixation as the primary nitrogen limitation mitigation strategy in A. swainsoni larvae. Subsequently, in vivo/in vitro [15]N isotope tracing showed peak [15]N in the PHG (105.02% higher than the natural environment) and&#x2009;~&#x2009;25-fold greater [15]N incorporation in cultured Klebsiella oxytoca versus controls. Targeted amino acid profiling further demonstrated [15]N enrichment in both essential and non-essential amino acids, with a spatial gradient (intestinal tissues > extra-intestinal tissues > frass)-indicating efficient microbial conversion of nitrogen into host-utilizable amino acids. Importantly, we identified that intestinal microbiota primarily mediate ammonia-to-amino acid conversion via the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the PHG. This is the first reported GS/GOGAT-mediated nitrogen fixation pathway in cerambycids.<br><br>CONCLUSIONS: Our comprehensive analysis of gut microbial nitrogen metabolism might elucidate a set of mechanisms by which some xylophagous insects may overcome nutritional constraints in nitrogen-deficient niches, via evolutionarily optimized host-microbe metabolic interactions. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid41147731,
year = {2025},
author = {Jones, JA and Moczek, AP and Newton, ILG},
title = {The dung beetle microbiome complements host metabolism and nutrition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117225},
doi = {10.1128/msystems.01172-25},
pmid = {41147731},
issn = {2379-5077},
abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.},
}
@article {pmid41147494,
year = {2025},
author = {Naureckas Li, C and Jhaveri, R and Huston, S},
title = {Results of a local modified Delphi consensus on use of plasma metagenomic next-generation sequencing.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10334},
pmid = {41147494},
issn = {1559-6834},
abstract = {Molecular tests without well-defined test performance characteristics are increasingly available for diagnosis of infectious diseases. These tests present a diagnostic stewardship challenge for institutions. We share the results of a local modified Delphi consensus undertaken to define appropriate scenarios for use of plasma metagenomic next-generation sequencing.},
}
@article {pmid41147490,
year = {2025},
author = {Qin, X and Liu, P and Lu, D and Lu, T and Li, C and Deng, Z and Liu, Z},
title = {The clinical value of metagenomic next-generation sequencing for diagnosing pulmonary infections in kidney transplant recipients.},
journal = {Laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/labmed/lmaf035},
pmid = {41147490},
issn = {1943-7730},
abstract = {INTRODUCTION: Rapid and accurate identification of pathogens is essential for managing lung infections in patients following kidney transplantation. This study aimed to compare the diagnostic performance and clinical utility of conventional detection methods and metagenomic next-generation sequencing (NGS) in kidney transplant recipients with respiratory infections.<br><br>METHODS: We conducted a retrospective analysis of metagenomic NGS and conventional detection method results in 71 patients, examining the spectrum of pathogen detection characteristics between the 2 methods.<br><br>RESULTS: The overall positivity rate of conventional detection methods was statistically significantly lower than that of metagenomic NGS (61.97% vs 84.51%, P&#x2005;=&#x2005;.004). Among the 38 participants who tested positive by both methods, metagenomic NGS identified a greater number of pathogens than conventional detection methods. Following metagenomic NGS results, antibiotic therapy was modified in 71.83% of participants, leading to improved prognoses in 33.33% of patients. In additionally, metagenomic NGS demonstrated a shorter turnaround time than conventional detection methods. The most prevalent bacteria identified in pulmonary infections among kidney transplant recipients were Klebsiella pneumoniae, while cytomegalovirus was the most common virus and Pneumocystis jirovecii was the predominant fungus.<br><br>DISCUSSION: This study offers preliminary insights into the spectrum of pathogens responsible for pulmonary infections following kidney transplantation, laying the foundation for better understanding their clinical characteristics. In patients with post-transplant pulmonary infections, metagenomic NGS outperforms conventional detection methods in terms of pathogen detection, speed, positivity rate, sensitivity, and ability to diagnose mixed infections.},
}
@article {pmid41147138,
year = {2025},
author = {Lee, YL and Hsueh, PR},
title = {An update on antimicrobial selection and duration for intra-abdominal infections.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2025.2580451},
pmid = {41147138},
issn = {1744-8336},
abstract = {INTRODUCTION: Intra-abdominal infections (IAIs) pose significant challenges to clinicians. The increasing prevalence of multidrug-resistant (MDR) organisms with evolving resistance patterns adds to the difficulty in managing IAIs.<br><br>AREAS COVERED: This review synthesizes the latest evidence and recommendations from major global guidelines. Key topics include novel antimicrobial agents, empirical and targeted therapy strategies, and the role of antimicrobial stewardship in optimizing antibiotic use. Furthermore, advances in diagnostic tools, such as metagenomic next-generation sequencing and rapid resistance detection assays, are highlighted. Updates in therapy duration, emphasizing shorter courses guided by biomarkers and source control, are critically analyzed.<br><br>EXPERT OPINION: The management of IAIs has advanced significantly, with updated guidelines highlighting the importance of early and appropriate antimicrobial therapy tailored to the infection's severity and resistance patterns, along with effective source control. Novel antibiotics such as ceftolozane-tazobactam, ceftazidime-avibactam, imipenem-relebactam, eravacycline, and cefiderocol have broadened treatment options for MDR pathogens. Shorter antibiotic courses, guided by source control and biomarkers, have shown to be as effective as traditional longer regimens. Future research should focus on understanding of global resistance patterns, expanding real-world evidence for novel antibiotics, refining biomarker-guided strategies, enhancing rapid diagnostics, and applying artificial intelligence for more personalized and precise management of IAIs.},
}
@article {pmid41146816,
year = {2025},
author = {Wang, N and Wu, J and Xiang, X and Zhao, Q and Yao, L},
title = {Endogenous Fungal Endophthalmitis Following Eyebrow Tattooing: A Case Report.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e93246},
pmid = {41146816},
issn = {2168-8184},
abstract = {This case report describes a rare instance of bilateral endogenous fungal endophthalmitis in a 50-year-old healthy female patient, following a facial tattooing procedure. Initially misdiagnosed as iritis in the right eye due to presenting symptoms of blurred vision and ocular pain, the patient's condition worsened following treatment with corticosteroids. Ophthalmic examination revealed severe vitreous opacity in the right eye and a yellowish-white lesion in the inferonasal retina of the left eye. Metagenomic sequencing of the vitreous fluid confirmed infection with Aspergillus fumigatus. The patient underwent pars plana vitrectomy with silicone oil tamponade, retinal laser photocoagulation, and intravitreal voriconazole injection in the right eye. Both eyes received multiple intravitreal voriconazole injections, supplemented with systemic antifungal therapy. Postoperatively, the visual acuity in the right eye improved, and the left eye gradually recovered to 20/35. Serial optical coherence tomography follow-up of the left eye documented the progressive detachment of the fungal embolus from the retinal lesion into the vitreous cavity. This case highlights that traumatic cosmetic procedures, such as eyebrow tattooing, can be a potential risk factor for endogenous fungal infection. In cases of atypical uveitis, early etiological investigation is crucial to avoid misdiagnosis and inappropriate treatment. Dynamic imaging provides valuable evidence for assessing the efficacy of antifungal therapy and determining prognosis.},
}
@article {pmid41146290,
year = {2025},
author = {Kraft, L and Söding, J and Steinegger, M and Jochheim, A and Wad Sackett, P and Fernandez-Guerra, A and Renaud, G},
title = {CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {372},
pmid = {41146290},
issn = {1474-760X},
support = {NNF20OC0062491//Novo Nordisk Fonden/ ; NNF20OC0062491//Novo Nordisk Fonden/ ; 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B//German Network for Bioinformatics Infrastructure (de.NBI)/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Software ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Humans ; },
abstract = {De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.},
}
@article {pmid41145643,
year = {2025},
author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K},
title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37529},
pmid = {41145643},
issn = {2045-2322},
support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; },
abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.},
}
@article {pmid41145216,
year = {2025},
author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM},
title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280550.125},
pmid = {41145216},
issn = {1549-5469},
abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.},
}
@article {pmid41145088,
year = {2025},
author = {Dan Guan, and Chen, C and Zheng, Y and Shen, W and Huang, Y and Ge, M and Jiang, T and Zhang, J and Liu, R and Xiong, L},
title = {Chlorination-driven selection of resistant pathogens and mobile genetic elements exacerbates antibiotic resistance risks in drinking water treatment.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119281},
doi = {10.1016/j.ecoenv.2025.119281},
pmid = {41145088},
issn = {1090-2414},
abstract = {The dissemination of Antibiotic resistance genes (ARGs) in drinking water systems poses public health risks; treatment impacts on pathogen dynamics remain unclear. In this study, two treatment trains-PK (sand filtration, ozonation-activated carbon, 5 % NaClO)and CX(ozonation-activated carbon, ultrafiltration, and 10 % NaClO) were compared through metagenomics analysis. Chlorination reduced microbial α-diversity but selected for divergent pathogens: CX-Treated Water (TW) was enriched with Salmonella enterica, Escherichia coli, and Erwinia amylovora, while PK retained Xanthomonas oryzae and Mycobacterium tuberculosis. Virulence gene tufA persisted, with 43 human-associated virulence factors being differentially expressed after disinfection. ARG analysis revealed high abundances of bacitracin and multidrug resistance gene (MRG) in early treatment stages for both lines. Chlorination paradoxically enriched these ARGs in TW, particularly MRG, which increased by 5.99 and 126.12 times in PK and CX, respectively. Mobile genetic elements (MGEs), particularly IS91, rebounded after disinfection and strongly correlated with the dissemination of ARGs (R > 0.9, p < 0.05). Higher concentrations of hypochlorite doses in CX-DWTP amplified plasmid associated Rep7/IS91 abundances, increasing ARG transmission risks. These findings revealed that aggressive disinfection selected resistant pathogens, enriches virulence determinants, and facilitated the dissemination of ARGs via MGEs, highlighting the need for optimized disinfection strategies to safeguard water biosafety.},
}
@article {pmid41145028,
year = {2025},
author = {Zhu, F and Penha, FM and Cetecioglu, Z},
title = {Functional microbial enrichment and chelation-enhanced phosphorus release from marine sediments: Toward sustainable phosphorus management.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124842},
doi = {10.1016/j.watres.2025.124842},
pmid = {41145028},
issn = {1879-2448},
abstract = {To improve the efficiency of phosphorus (P) release from marine sediments and contribute to P loop closure, this study proposed a novel strategy combining bio-inoculation with polyphosphate-accumulating organisms (PAOs) and chemical enhancement via chelating agents. Based on prior findings, two-stage experiments were conducted. In Stage 1, anaerobic batch tests assessed the effect of different chelating agents for P release. While citrate showed no promoting effect, the addition of ethylenediaminetetraacetic acid (EDTA) significantly enhanced total P release, reaching 48.5 % within 15 days. In Stage 2, PAO-acclimated sediments were introduced into the system, followed by alternating anaerobic-aerobic fed-batch operation for 7 days, and subsequent EDTA addition with anaerobic incubation for another 6 days. This combined approach achieved a total P release efficiency 83.4 %, with final soluble P concentrations reaching 145.9 mg/L. During this process, PAOs were rapidly enriched, with their relative abundance increasing from 12.9 % to 65.0 %. Metagenomic analysis revealed that EDTA promoted environmental filtering, selectively enriching PAOs (Candidatus Accumulibacter) and thereby reinforcing their specific contributions to P functional genes. The resulting P-rich supernatant was then subjected to precipitation. PHREEQC simulations guided the prediction of optimal precipitation conditions, and laboratory experiments confirmed that most soluble P, especially Fe-bound forms, could be efficiently recovered, with maximum precipitation efficiencies of 98.8 %.},
}
@article {pmid41144667,
year = {2025},
author = {Xu, JY and Yu, YT and Du, S and Shen, LQ and Zhang, Q and Qian, H and Cai, TG and Wang, YF and Zhao, J and Li, HZ and Zhang, C and Zhu, D},
title = {Discarded cigarette butts as overlooked reservoirs and amplifiers of antibiotic resistance genes and pathogens in urban green spaces.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2525377122},
doi = {10.1073/pnas.2525377122},
pmid = {41144667},
issn = {1091-6490},
support = {42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22125601//MOST | NSFC | National Science Fund for Distinguished Young Scholars (NSF for Distinguished Young Scholars)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; China ; *Tobacco Products/microbiology ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Biofilms/growth &amp; development ; },
abstract = {Cigarette butts are widely discarded in urban green spaces, yet their microbial health risks remain poorly understood. In a nationwide survey across China, we investigated the presence, sources, health risks, and drivers of antibiotic resistance genes (ARGs) and potential pathogens in discarded cigarette butts. Shotgun metagenomic and full-length 16S ribosomal rRNA (rRNA) sequencing revealed that cigarette butts harbored significantly higher abundances of ARGs and bacterial pathogens than plant litter or soil. Health risk assessment further showed that cigarette butts carried ARGs with greater mobility, clinical relevance, and pathogenic potential. Genomic analyses highlighted enrichment of ARG-carrying pathogens, particularly Enterobacteriaceae and Pseudomonas, with mobile genetic elements and oxidative stress responses as key contributors. Functional assays, including plasmid transfer, transcriptomic profiling, and single-cell Raman spectroscopy, demonstrated that cigarette butts promoted horizontal gene transfer and upregulated key ARGs (e.g., mexE, mexF, cfrC) under stress conditions. Scanning electron microscopy confirmed biofilm formation on cigarette fibers, supporting enhanced bacterial persistence. Source-tracking analyses identified both human oral and environmental sources of the enriched ARGs and pathogens in cigarette butts. Finally, socioeconomic factors such as lower gross domestic product (GDP), reduced education, and poor sanitation were strongly associated with elevated ARG and pathogen risks. Collectively, our findings identify cigarette butts as overlooked yet potent vectors of ARG and pathogen dissemination in urban green spaces, underscoring the need for targeted interventions within a One Health framework.},
}
@article {pmid41144656,
year = {2025},
author = {Myburgh, DA and da Silva, NA and Haller-Caskie, M and Colominas, L and Castanyer, P and Frigola, J and Tremoleda, J and Hölzel, C and Unterweger, D and Nebel, A and Krause-Kyora, B},
title = {Detection of Clostridium sporogenes in a Roman-era cattle mass grave at Vilauba.},
journal = {Virulence},
volume = {},
number = {},
pages = {2580731},
doi = {10.1080/21505594.2025.2580731},
pmid = {41144656},
issn = {2150-5608},
abstract = {In the ancient Roman world, cattle played an integral role in daily agricultural tasks, providing the means necessary to plow fields, mill grains, and transport goods. The research presented here deals with the remains of 14 cattle discovered in a mass grave at the Roman villa of Vilauba in Catalonia, Spain. According to the archeological record, it can be ruled out that the animals were slaughtered for consumption, banqueting, or sacrificial purposes. By investigating the metagenomic sequences generated from the bovine remains, we identified in three individuals a group I Clostridium strain, phylogenetically related to known producers of botulinum neurotoxins - suggesting that the Vilauba strain may have had toxigenic potential. Moreover, we discovered a Mycolicibacterium species phylogenetically related to known opportunistic pathogens. While no definitive conclusions can be drawn about disease, the phylogenetic placement of these taxa and the detection of Clostridium virulence-associated genes suggest a possible role beyond postmortem contamination. Collectively, these findings draw attention to atypical bacterial species, such as C. sporogenes, which are often overlooked in palaeogenomic studies due to their ambiguous status as environmental microbes, commensals, or potential pathogens. Their detection in animal remains highlights that they may represent a blind spot in our current understanding of livestock health. More broadly, this study underscores the current complexity of investigating such taxa and emphasizes the need for novel methods to disentangle the roles of these bacterial species.},
}
@article {pmid41144256,
year = {2025},
author = {Dziegiel, AH and Duong, VT and Bloomfield, SJ and Thomson, NR and Maskell, DJ and Wain, J and Janecko, N and Baker, S and Mather, AE},
title = {Metagenomic identification of disease-causing Salmonella enterica serovars and antimicrobial resistance genes from paediatric faecal samples.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001547},
pmid = {41144256},
issn = {2057-5858},
mesh = {Humans ; *Feces/microbiology ; *Salmonella enterica/genetics/isolation &amp; purification/drug effects/classification ; *Metagenomics/methods ; *Salmonella Infections/microbiology ; Child, Preschool ; *Drug Resistance, Bacterial/genetics ; Infant ; Child ; Serogroup ; Metagenome ; Vietnam ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; },
abstract = {Background. Nontyphoidal Salmonella (NTS) is a common cause of enterocolitis and a major cause of death in children in low- and middle-income countries (LMICs). High antimicrobial resistance (AMR) prevalence in LMICs reduces treatment options for individuals at risk of severe infections.Methods. We investigated the use of metagenomics to identify NTS and associated AMR genes in 28 faecal metagenomes from children with culture-confirmed salmonellosis in Vietnam, using accompanying NTS genomes from isolated serovars (one per metagenome). Read-based and assembly-based methods were utilised for NTS and AMR detection. Case metagenomes were compared to healthy control metagenomes (n=21) with respect to the microbiome composition, NTS relative abundances, number of unique AMR genes and antimicrobial classes to which the genes confer resistance, including classes used in Salmonella treatment.Results. Salmonellosis cases displayed significantly higher relative abundances of Enterobacteriaceae than controls. Bracken and Centrifuge analysis facilitated the identification of Salmonella enterica sequences in case metagenomes at varying relative abundances (0.00259-27.7 % of total reads), which were significantly higher than controls. MetaPhlAn4 did not detect S. enterica in any control metagenomes, though 12 case metagenomes were also negative. The isolated serovars were identified in 78.6% of the associated case metagenomes with Centrifuge, suggesting this method is the most sensitive; however, the isolated genome serovar was the most abundant in only six case metagenomes, and serovar sequences were also identified in control metagenomes. Alignment to a Salmonella reference database, followed by local assembly and realignment, predicted the isolated serovar as the most likely serovar present in 35.7% of metagenomes, whereas Salmonella in silico typing resource classification of the local assembly was concordant with the isolate genome in 28.6% of cases. Metagenome-assembled genomes produced using two tools following de novo assembly identified the isolated serovar in 17.8-21.4% of cases. The percentage of NTS AMR genes identified in each case metagenome ranged between 0.00 and 100%. There was no significant difference in the number of unique AMR genes or antimicrobial classes between cases and controls, indicating comparable resistomes between cohorts.Conclusions. This study highlights the potential of metagenomics for NTS identification in faecal samples, although overlap in S. enterica relative abundance between cohorts calls for further work to identify a diagnostic cutoff. Reliable characterisation of the organism to the serovar and AMR genotype level is affected by the complexity of the microbiome, sequencing and analysis approaches. Increased sequencing depth, for example through improved host DNA depletion, may facilitate enhanced characterisation. Detection of multiple serovars within individual samples with the Centrifuge suggests inaccurate classification or the presence of multiple serovars, making characterisation difficult.},
}
@article {pmid41143690,
year = {2025},
author = {Kim, KJ and Garcia, M and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY},
title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfaf145},
pmid = {41143690},
issn = {1096-0929},
abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1162 bacterial species and 1437 metabolites were evaluated for downstream analysis. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes. Our study demonstrates that microplastics dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.},
}
@article {pmid41143557,
year = {2025},
author = {Shi, Z and Liu, Q and Zhou, M and Xu, W and Luo, G},
title = {Persistent Risks in the Effluents of Wastewater Treatment Plants: Mobile Genetic Elements and Viral-Mediated Dissemination of Pathogenic Antibiotic-Resistant Bacteria.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08352},
pmid = {41143557},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are recognized as reservoirs of pathogenic antibiotic-resistant bacteria (PARB), yet their genomic risk dynamics remain unclear. This study recovered PARB genomes from 102 influent and effluent metagenomes from six countries; their activity and risk potential were then experimentally validated with metatranscriptomics on samples from a Shanghai WWTP. A total of 44 PARB genomes were reconstructed, which carried both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and they persisted in the effluent. Mobile genetic elements might mediate ARG transfer in 13 PARB genomes. Moreover, bacteriophages infecting PARB harbored and were transcribing ARGs/VFGs, and antiviral defense systems of PARB correlated with horizontal gene transfer (HGT). Evolutionary analyses indicated that influent PARB maintained high microdiversity via homologous recombination, while effluent populations underwent purifying selection, suggesting that wastewater treatment reduced the genetic diversity of PARB through purifying selection. However, the persistent accumulation of PARB as well as HGT might maintain the dissemination of ARGs. This study emphasized the necessity of selecting the PARB genomes for wastewater monitoring, thereby optimizing treatment strategies and mitigating the potential health risks posed by pathogenic bacteria.},
}
@article {pmid41143534,
year = {2025},
author = {Conrad, R and Gerhardt, K and Konstantinidis, KT and Williams-Newkirk, AJ and Huang, AD},
title = {ROCker models for reliable detection and typing of short-read sequences carrying mcr, erm, mph, and lnu antibiotic resistance genes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0241325},
doi = {10.1128/spectrum.02413-25},
pmid = {41143534},
issn = {2165-0497},
abstract = {Quantitative monitoring of emerging antimicrobial resistance genes (ARGs) using short-read sequences remains challenging due to the high frequency of amino acid functional domains and motifs shared with related but functionally distinct (non-target) proteins. To facilitate ARG monitoring efforts using unassembled short reads, we present novel ROCker models for mcr, mph, erm, and lnu ARG families, as well as models for variants of special public health concern within these families, including mcr-1, mphA, ermB, lnuF, lnuB, and lnuG genes. For this, we curated target gene sequence sets for model training and built these models using the recently updated ROCker V2 pipeline (Gerhardt et al., in review). To validate our models, we simulated reads from the whole genome of ARG-carrying isolates spanning a range of common read lengths and used them to challenge the filtering efficacy of ROCker versus common static filtering approaches, such as similarity searches using BLASTx with various e-value thresholds or hidden Markov models. ROCker models consistently showed F1 scores up to 10× higher (31% higher on average) and lower false-positive (by 30%, on average) and false-negative (by 16%, on average) rates based on 250 bp reads compared to alternative methods. The ROCker models and all related reference materials and data are freely available through http://enve-omics.ce.gatech.edu/rocker/models, further expanding the available model collection previously developed for other genes. Their application to short-read metagenomes, metatranscriptomes, and PCR amplicon data should facilitate more accurate classification and quantification of unassembled short-read sequences for these ARG families and specific genes.IMPORTANCEAntimicrobial resistance gene families encoding erm and mph genes confer resistance to the macrolide class of antimicrobials, which are used to treat a wide range of infections. Similarly, the mcr gene family confers resistance to polymyxin E (colistin), a drug of last resort for many serious drug-resistant bacterial infections, and the lnu gene family confers resistance to lincomycin, which is reserved for patients allergic to penicillin or where bacteria have developed resistance to other antimicrobials. Assessing the prevalence of these genes in clinical or environmental samples and monitoring their spread to new pathogens are thus important for quantifying the associated public health risk. However, detecting these and other resistance genes in short-read sequence data is technically challenging. Our ROCker bioinformatic pipeline achieves reliable detection and typing of broad-range target gene sequences in complex data sets, thus contributing toward solving an important problem in ongoing surveillance efforts of antimicrobial resistance.},
}
@article {pmid41143528,
year = {2025},
author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW},
title = {Evaluating the use of biobanked urine specimens for human urobiome studies.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0216424},
doi = {10.1128/spectrum.02164-24},
pmid = {41143528},
issn = {2165-0497},
abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.},
}
@article {pmid41143408,
year = {2025},
author = {Liao, Y and Cheng, J and Xiong, S and Liu, Y and Qian, J and Shi, M and Guo, Y and Kang, Y-J},
title = {Dynamics of the respiratory infectome in children with community-acquired pneumonia: insights from large and short time-scale analyses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145025},
doi = {10.1128/spectrum.01450-25},
pmid = {41143408},
issn = {2165-0497},
abstract = {UNLABELLED: Community-acquired pneumonia (CAP) has emerged as a significant health challenge for young children, especially after the relaxation of COVID-19 restrictions, which coincided with a sharp increase in CAP cases. While pathogen profiling is commonly performed, comprehensive studies examining the total infectome and its dynamic changes during disease progression and in relation to the pandemic remain scarce. To address this gap, we conducted a prospective cohort study involving 58 children hospitalized with CAP in Wuxi, China, during and after COVID-19 control measures. Sputum samples were analyzed using metagenomic and metatranscriptomic sequencing to characterize the total infectome. Results showed that RNA sequencing offers a more comprehensive view of the infectome, while DNA sequencing excels in detecting DNA viruses with greater sensitivity. Notable increases in Mycoplasma pneumoniae, human respiratory syncytial virus (RSV), and Haemophilus influenzae were observed after COVID-19 restrictions were lifted. During disease progression, some patients exhibited a decline in pathogen abundance, while others developed secondary infections, frequently involving co-infections, which might contribute to prolonged pneumonia or complicated disease course. Viral-bacterial co-infections were common, with M. pneumoniae and RSV being the most prevalent combination. In summary, this study highlights the shifting respiratory infectome in children with CAP, both after the relaxation of COVID-19 control measures and throughout hospitalization. It emphasizes the need for comprehensive infectome monitoring to track dynamic changes across broader timeframes and during disease progression, offering insights for improved clinical management and future research.<br><br>IMPORTANCE: Community-acquired pneumonia (CAP) remains a leading threat to children's health globally, with shifting pathogen dynamics post-COVID-19 posing new challenges. This study reveals how pandemic control measures and their relaxation influenced the respiratory "infectome"-the full spectrum of pathogens-in children with CAP. By integrating multi-sequencing technologies, we uncovered critical trends: a resurgence of virulent pathogens like Mycoplasma pneumoniae and respiratory syncytial virus after restrictions eased, frequent viral-bacterial co-infections linked to prolonged pneumonia, and distinct infection patterns during hospitalization that predict recovery or complications. These findings highlight the need for dynamic, multi-pathogen surveillance to guide clinical decisions, particularly in managing co-infections and preventing secondary infections. Our work provides actionable insights for pediatricians and public health experts to anticipate post-pandemic pathogen behavior, tailor treatments, and mitigate risks during future outbreaks, ultimately improving care for vulnerable young patients.},
}
@article {pmid41142817,
year = {2025},
author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER},
title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1610360},
pmid = {41142817},
issn = {1664-3224},
mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; },
abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.<br><br>METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).<br><br>RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 &#xb1; 13.19 years, and the mean BMI was 25.25 &#xb1; 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (&#x3b2;=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (&#x3b2;=0.32; p<0.01) and Faecalicatena fissicatena (&#x3b2;= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.<br><br>CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.},
}
@article {pmid41142066,
year = {2025},
author = {Kyrychenko, A},
title = {Molecular architecture of giant viruses infecting microbial eukaryotes (protists).},
journal = {Biotechnologia},
volume = {106},
number = {3},
pages = {361-376},
pmid = {41142066},
issn = {2353-9461},
abstract = {In this review, I describe recent findings on the molecular architecture and genomic characterization of giant viruses that infect microbial eukaryotes (protists) across diverse ecosystems and ecological niches. Giant viruses are distinguished by their large and complex genomes, which encode a wide range of functions, including protein translation, carbohydrate and lipid metabolism, nitrogen cycling, light assimilation, and key metabolic pathways such as glycolysis and the tricarboxylic acid cycle. Additionally, these genomes feature unique genes, often acquired through horizontal gene transfer, that are not found in other viruses and contribute to the viruses' ability to manipulate host metabolism and evade host defenses. A core set of genes conserved across different families of giant viruses is highlighted, serving as essential components for key life-cycle processes and providing valuable phylogenetic markers. The review also discusses the role of ORFans and virophages in contributing to the genetic diversity and evolutionary adaptation of these viruses. These findings are crucial for understanding the diversity, evolutionary mechanisms, and complex virus-host interactions of giant viruses, as well as for developing more advanced classification systems. Furthermore, the potential biotechnological applications of unique viral genes and pathways are explored, underscoring the importance of ongoing research in this field.},
}
@article {pmid41140871,
year = {2025},
author = {Talamantes-Becerra, B and Chang, WS and Michie, M and Hodda, M and Hopper, M and Caron, V},
title = {RNA-seq dataset of land snails collected in Australia.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112122},
pmid = {41140871},
issn = {2352-3409},
abstract = {Snails are known to be host of pathogens and parasites and they can play an important role in the transmission of some parasites and pathogens, including nematodes and trematodes of medical and veterinary importance. They have a diverse diet, and can be classified as detritivores, plant feeders, or carnivores. The datasets presented here include raw RNA-seq data of 10 terrestrial land snails collected in three locations in Australia, including Northern Territory, Queensland and South Australia. The snails were identified morphologically, and RNA was extracted from whole organisms using a modified version of the Maxwell ® RSC simplyRNA Tissue Kit. The sequencing was performed in all samples and generated an average of at least 56 million paired-end reads per sample. RNA-seq raw reads and assembled transcripts including both host-derived and non-host sequences were deposited into a DRYAD repository. Assembled transcripts including only host data are also provided in this project. The dataset has reuse potential for environmental studies related to conservation biology, invasive species surveillance, disease research, educational purposes, development of bioinformatic tools for environmental transcriptomics or host-pathogen interactions. Moreover, the dataset can be used for benchmarking metatranscriptomic classification tools in non-model invertebrates.},
}
@article {pmid41140851,
year = {2025},
author = {Tran, SH and Restrepo-Ortiz, CX and Vu, DQ and Troussellier, M and Bettarel, Y and Bouvier, T and Bui, VN and Minh, NH and Hoang, TD and Nguyen, QH and Auguet, JC},
title = {NEMESISdb: A full length 16S rRNA gene dataset for the detection of human, fish, and crustacean potentially pathogenic bacteria.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112135},
pmid = {41140851},
issn = {2352-3409},
abstract = {NEMESISdb is a 16S rRNA full length sequence curated dataset designed to enable the identification and tracking of potentially pathogenic bacteria (PPB) for human, fish, and crustacean hosts. It addresses the limited focus on marine and coastal environments as key reservoirs for PPB, where bacteria from diverse sources-terrestrial, marine, and animal-can coexist. Leveraging recent advances in high-throughput sequencing, NEMESISdb provides a robust resource for the detection of PPB in 16S rRNA gene metabarcoding or metagenomic data. The database comprises three datasets corresponding to human, fish, and crustacean hosts, containing 1703, 222, and 64 PPB species, respectively, with a total of over 150,000 16S rRNA full length sequences curated for accuracy. This resource was constructed by extracting sequences from the SILVA 138.2 SSU Ref NR99 database, refining them through a rigorous curation pipeline to ensure taxonomic consistency and eliminate misclassifications. The resulting datasets are optimized for use with popular tools such as BLAST and classifier software, enabling rapid and accurate detection of PPB in metabarcoding and metagenomic data. NEMESISdb supports diverse applications, including pathogen surveillance in aquatic ecosystems, studies on environmental factors influencing PPB dynamics, and the development of targeted strategies for mitigating pathogen impacts in aquaculture. Additionally, it facilitates research within the One Health framework by linking the circulation of PPB across environmental, animal, and human compartments.},
}
@article {pmid41140834,
year = {2025},
author = {Van Uffelen, A and Posadas, A and Fraiture, MA and Roosens, NHC and De Keersmaecker, SCJ and Marchal, K and Vanneste, K},
title = {Detection of Bacillus production strains and contaminants in food enzyme products.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100309},
pmid = {41140834},
issn = {2666-5662},
abstract = {Shotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, especially for low-abundance or taxonomically complex genera like Bacillus, where closely related species may differ in safety and function, and their co-occurrence increases misclassification risk. This study presents a bioinformatics framework for defining detection thresholds of biological contaminations in samples using nanopore shotgun metagenomics data, demonstrated through a case study on Bacillus subtilis sensu lato (s.l.) and Bacillus cereus s.l. contaminations in food enzyme (FE) products. The framework was developed by employing in silico mixes of isolate sequencing data of different B. subtilis and B. cereus species, and uses the tool KMA for taxonomic classification with post-processing steps based on template identity to differentiate true positives from false positives, coupled with curation of the underlying reference genomic database. The performance of the developed framework was afterwards validated with five in vitro mixes mimicking potential FE contaminations. Finally, the applicability of the validated framework was evaluated with six real and well-characterized commercial contaminated FE samples, confirming its ability to accurately detect B. subtilis and B. cereus contaminants, even at low abundances up to a relative abundance of 1 %. In conclusion, we present a bioinformatics framework allowing reliable species-level detection of challenging low-level contaminants in samples using nanopore shotgun metagenomics sequencing, which was successfully applied to identify B. subtilis and B. cereus contaminations in FE products.},
}
@article {pmid41140673,
year = {2025},
author = {Ao, D and Li, X and Zhang, G and Ma, H and Yang, L and Tian, H and Ao, S and Feng, J and Geng, W},
title = {Diagnostic value of metagenomic next-generation sequencing in atypical brucellosis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1652671},
pmid = {41140673},
issn = {2296-858X},
abstract = {BACKGROUND: Brucellosis with atypical presentations, such as submandibular abscess without fever, is frequently misdiagnosed.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was applied to pus samples from a 47-year-old female with a treatment-refractory submandibular abscess and a history of livestock exposure; results were confirmed serologically.<br><br>RESULTS: Within 48&#x202f;h, mNGS identified Brucella suis-representing, to our knowledge, the first reported afebrile submandibular infection caused by this pathogen. Targeted therapy with doxycycline and rifamycin led to symptom resolution within 6&#x202f;days.<br><br>CONCLUSION: This case highlights that mNGS, combined with a thorough epidemiological history, can resolve diagnostic dilemmas in atypical brucellosis, guide precise treatment, and mitigate antibiotic misuse.},
}
@article {pmid41140651,
year = {2025},
author = {Wang, X and Chen, S and Yang, C},
title = {Coexistence of cat scratch disease lymphadenitis and active pulmonary tuberculosis in an immunocompetent host - a case report with metagenomic diagnosis and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1667171},
pmid = {41140651},
issn = {2296-858X},
abstract = {Cat scratch disease (CSD), caused by Bartonella henselae (B. henselae), typically presents as localized swelling of lymph nodes following a scratch or bite from a cat. It is crucial to differentiate CSD from tuberculosis (TB), particularly in regions where TB is prevalent. This report describes a 56-year-old man who exhibited bilateral swelling of the cervical lymph nodes. Initially, he was suspected to have tuberculous lymphadenitis due to the granulomatous changes observed in a biopsy of the lymph nodes, typical signs of TB on a chest CT scan, and a positive result from an interferon-gamma release assay (IGRA). He was subsequently referred to our hospital for TB treatment. Testing of bronchoalveolar lavage fluid confirmed the presence of TB-DNA, indicating active pulmonary tuberculosis (PTB). However, further investigation revealed recent cat contact. This led to the identification of a B. henselae infection using metagenomic pathogen detection workflow (MetaPath™) on formalin-fixed paraffin-embedded (FFPE) histopathological sections from a cervical lymph node specimen obtained at an external hospital, which confirmed the diagnosis of CSD and ruled out TB. Through a review of the literature, we found that this represents the first documented case of concurrent active PTB and CSD-related lymphadenitis in an immunocompetent individual. It highlights the diagnostic challenges in distinguishing CSD from TB in cases of granulomatous lymphadenitis and emphasizes the need to consider CSD in patients with a history of cat exposure, showcasing the pivotal role of advanced metagenomic diagnostics in accurately diagnosing CSD.},
}
@article {pmid41140474,
year = {2025},
author = {Chen, Y and Li, X and Bi, C and Yang, Y and Xiong, S and Tian, X and Zhong, D and Gan, Y and Gao, A},
title = {Cutaneous Talaromyces marneffei Infection in an Immunocompetent Adolescent: A Case Report.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {2701-2706},
pmid = {41140474},
issn = {1178-7015},
abstract = {Talaromyces marneffei (TM) infection is a rare but potentially fatal deep fungal disease that typically affects immunocompromised individuals in endemic regions. However, an increasing number of cases have been reported in HIV-negative, immunocompetent patients without classical risk factors. We report the case of a 15-year-old girl residing in urban southern China who presented with chronic cutaneous plaques and cervical lymphadenopathy, initially misdiagnosed as tuberculous lymphadenitis. Despite one year of anti-tuberculosis therapy, her condition worsened and liver dysfunction developed. Subsequent skin biopsy, fungal culture, and metagenomic next-generation sequencing (mNGS) confirmed localized cutaneous TM infection. The patient responded well to oral itraconazole, and lesions resolved after four months of treatment, with no recurrence during an 18-month follow-up. This case highlights the importance of considering deep fungal infections in the differential diagnosis of chronic granulomatous skin lesions, even in immunocompetent hosts, and emphasizes the diagnostic utility of mNGS in atypical presentations.},
}
@article {pmid41140407,
year = {2025},
author = {Li, D and Li, Z and Liu, W},
title = {The gut-kidney axis in urolithiasis: roles of gut microbiota, metabolites, and therapeutic implications.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1655808},
pmid = {41140407},
issn = {1664-302X},
abstract = {Urolithiasis affects 2-20% of the global population and recurs frequently. Emerging evidence positions the gut-kidney axis as a central driver of stone formation. This review synthesizes epidemiological data, comparative metagenomic analyzes, and mechanistic studies to demonstrate that stone formers exhibit reduced α-diversity, depletion of oxalate-degrading taxa (e.g., Oxalobacter, Lactobacillus, Bifidobacterium), and enrichment of pro-inflammatory genera (Escherichia, Bacteroides). Microbial metabolites-oxalate, short-chain fatty acids, p-cresol, and secondary bile acids-modulate intestinal oxalate transport, systemic inflammation, and renal crystal nucleation. Therapeutic modulation via targeted probiotics, prebiotics, engineered Lactobacillus, or fecal microbiota transplantation restores oxalate homeostasis and attenuates nephrolithiasis in rodent models; however, human efficacy remains preliminary. Large-scale multi-omics cohorts and randomized controlled intervention trials are imperative to translate gut-centric strategies into precision urology.},
}
@article {pmid41140401,
year = {2025},
author = {Rozmiarek, KS and Yang, J and Schambach, J and Bennett, H and Caro, TA and Sammon, J and Whiting, JJ and Miller, PR and Ricken, B and Bigler, L and Jayne, RS and Fukuyama, D and Jones, TR and Smallwood, CR},
title = {Microbial and chemical predictors of methane release from a stratified thermokarst permafrost hotspot.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1657143},
pmid = {41140401},
issn = {1664-302X},
abstract = {Soils are dynamic interfaces that can act as both sources and sinks of methane (CH4), yet the microbial processes underlying these fluxes remain poorly constrained in current Earth system models-particularly in thawing permafrost regions. Accurately quantifying subsurface microbial activity and its response to environmental variation is essential for improving predictions of CH4 emissions under shifting temperature regimes. Here, we explore the potential of volatile organic compounds (VOCs) as early chemical indicators of microbial processes driving CH4 production within a thermokarst-associated CH4 hotspot. Field surveys at Big Trail Lake, a young thermokarst feature in central Alaska, identified localized CH4 emission zones. Anaerobic soil laboratory microcosms from 50, 200, and 400 cm depths were incubated at -4 °C, 5 °C, and 12 °C to simulate freeze-thaw transitions. Methane flux increased markedly with temperature, and microbial community shifts revealed Methanosarcina spp. as the dominant methanogen, particularly at 200 cm. VOC profiling showed strong depth- and temperature-dependent patterns, with the 50 cm layer exhibiting the greatest chemical diversity. Notably, 200 cm soils produced VOC signatures overlapping with those from pure Methanosarcina acetivorans C2A cultures, supporting the identification of shared metabolites linked to active methanogenesis. Extended 60-day incubations confirmed temperature-sensitive CH4 production. Carbon isotopic enrichment in CH4 was unexpectedly strong with warming, and metagenomic detection of ANME-associated markers-including multiheme cytochromes and formate dehydrogenases-supports temperature-sensitive anaerobic oxidation of methane as a significant control on isotopic signatures. Calculated Q10 values for methanogenesis exceeded typical values for boreal soils, highlighting an underappreciated temperature responsiveness of Arctic methanogens. Together, these results demonstrate that VOCs can serve as informative biomarkers of subsurface microbial activation and offer a novel diagnostic tool for detecting early-stage CH4 hotspot formation. Incorporating such chemically and biologically resolved metrics into process-based models will be critical for improving forecasts of CH4 release from thawing permafrost landscapes.},
}
@article {pmid41140397,
year = {2025},
author = {Mudoor Sooresh, M and Jayawickrama, A and Silva, A and Nguyen, S and Schmidt, S and Sebastian, J and Carey, S and Harynuk, J and Willing, BP and Bourrie, BCT},
title = {Fermentation of kefir with traditional freeze-dried starter cultures successfully recreates fresh culture fermented kefir.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1655390},
pmid = {41140397},
issn = {1664-302X},
abstract = {INTRODUCTION: Interest in fermented foods and their purported health benefits has led to increased scientific research investigating the development of starter cultures which maintain the characteristics of traditional products while allowing for industrial scale production. One such fermented food that is gaining steady attention for industrial production is kefir. To improve the ease of use and maintenance of starter cultures without compromising desirable fermentation characteristics and potential health benefits, this study investigated the impact of freeze-drying a previously described reconstituted kefir consortia with two lyoprotectants trehalose and milk.<br><br>METHODS: 5 bacterial species (Lentilactobacillus kefiri, Lactobacillus kefiranofaciens, Lactococcus cremoris, Leuconostoc mesenteroides, and Acetobacter pasteurianus) and 4 yeast species (Saccharomyces cerevisiae, Pichia fermentans, Monosporozyma unispora, and Kluyveromyces marxianus) underwent freeze-drying prior to viability testing and use as starter cultures in kefir fermentations. Completed kefir fermentations were analyzed for pH, microbial composition, volatile compounds, organic acids, and sugar consumption. Freeze-dried starter culture fermentations were compared to kefir made with fresh starter cultures of the same species and pitching rate.<br><br>RESULTS: All starter cultures were able to ferment milk to a similar pH, however the freeze-dried cultures prepared with milk took a longer time to complete fermentation. The total bacterial and yeast counts were comparable across the fermentations performed as was the composition of bacteria and yeast present as determined by shotgun metagenomic sequencing. High performance liquid chromatography (HPLC) analysis showed no difference in the levels of lactic acid, acetic acid, ethanol, glucose, and galactose. Additionally, solid-phase microextraction followed by two-dimensional gas chromatography-time-of-flight mass spectrometry (SPME-GC &#xd7; GC-TOFMS) showed that kefir fermented with freeze-dried starter cultures did not change the volatile profile compared to fresh cultures.<br><br>CONCLUSION: These findings indicate that freeze-dried starter cultures consisting of traditional kefir microorganisms are able to recreate the fresh starter culture version of this product. This provides encouraging evidence for the development of commercially viable starter cultures that are capable of recreating traditional functional fermented foods.},
}
@article {pmid41140395,
year = {2025},
author = {Li, G and Lao, J and Jiang, Y and Tang, P and Huang, H and He, L and Yuan, K and Lai, X},
title = {Exploring drug resistance genes in Acinetobacter baumannii using metagenomic next-generation sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669208},
pmid = {41140395},
issn = {1664-302X},
abstract = {INTRODUCTION: With the rising incidence of infectious diseases, the overuse of antibiotics has become a serious problem in clinical practice. In recent years, metagenomic next-generation sequencing (mNGS) has emerged as a promising alternative, offering advantages such as rapid turnaround, broad-spectrum detection, and comprehensive coverage. However, its clinical utility for antimicrobial resistance testing remains to be fully established.<br><br>METHODS: In this study, we evaluated the effectiveness of mNGS in detecting antimicrobial resistance in Acinetobacter baumannii using 53 clinical samples. The performance of mNGS was compared with conventional culture-based methods. In addition, clinical judgment of drug resistance was used as a reference to assess concordance between sequencing results and patient treatment.<br><br>RESULTS: Metagenomic sequencing produced an average of 8.4 &#xd7; 10&#x2077; reads per sample and identified 61 resistance loci-20 of which appeared in at least five isolates. Among the A. baumannii-positive samples, class-specific accuracy of mNGS exceeded 80% for &#x3b2;-lactams, aminoglycosides, quinolones, and minocycline, underscoring its strong performance in comprehensive resistome profiling. We further investigated resistance-associated genes in A. baumannii that appeared with high frequency, including enzymatic inactivation mechanisms (ADC-type cephalosporinases and OXA-type oxacillinases), efflux systems (AbaQ, AbeM), and RND-type efflux pumps (adeIJK/adeN and adeFGH/adeL).<br><br>DISCUSSION: Our findings demonstrate a high concordance between mNGS results, culture-based methods, and clinical evaluations, highlighting the potential of mNGS as a reliable tool for assessing antimicrobial resistance in A. baumannii.},
}
@article {pmid41140172,
year = {2025},
author = {Negri, T and Vitale, GA and Adamek, M and Bağcı, C and Hegemann, JD and Petras, D and Hughes, CC and Ziemert, N},
title = {Discovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring Structure.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c00970},
pmid = {41140172},
issn = {1520-6025},
abstract = {Culture-independent metagenomic approaches have proven to be effective tools for identifying previously hidden biosynthetic gene clusters (BGCs) encoding novel natural products with potential medical relevance. However, producing these compounds remains challenging as metagenomic BGCs often originate from organisms phylogenetically distant from available heterologous hosts. Lasso peptides, a subclass of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, exhibit diverse bioactivities, yet no lasso peptide has previously been discovered directly from a metagenome. Here, we report the discovery and heterologous expression of the first soil metagenome-derived lasso peptide. Expression of its biosynthetic gene cluster in Escherichia coli, followed by mass spectrometry analysis, strongly supported the predicted amino acid sequence and lasso structure of the peptide. Notably, this lasso peptide is the first to feature asparagine as the ring-forming residue at position one. Taxonomic analysis of the corresponding BGC identified an uncultivated member of the Steroidobacterales family (Gammaproteobacteria) as the closest known relative of the potential native host. These findings underscore the potential of metagenomic genome mining to reveal structurally novel RiPPs and to expand our understanding of the natural diversity of lasso peptides.},
}
@article {pmid41140047,
year = {2025},
author = {Wang, Y and Zhang, B and Han, G and Bartlam, M and Wang, Y},
title = {Chiral Pesticides Stereoselectively Stimulate N2O Emissions: An Overlooked Environmental Risk in Agricultural Soils.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09622},
pmid = {41140047},
issn = {1520-5851},
abstract = {Agricultural soil is a major source of N2O emissions due to soil denitrification. However, the influence of pesticides, particularly chiral pesticides, on soil denitrification has often been overlooked. In this study, we investigated the effects and regulatory mechanisms of the widely used chiral pesticide cis-epoxiconazole on denitrification and N2O emissions. The 2R, 3S-(+)-cis-epoxiconazole ((+)-EPO) enantiomer reduced nitrate removal efficiency by 15.04%-54.49% after 3 days and increased N2O emissions by 109.27%-163.68% after 35 days of exposure in a microcosm system, whereas the 2S, 3R-(-)-cis-epoxiconazole ((-)-EPO) enantiomer had minimal impact. At a concentration of 0.5 mg/kg, (+)-EPO inhibited β-glucosidase activity by 34.80% and decreased electron transport system activity by 43.70%, thereby impairing electron generation and transfer during denitrification. Expression of the nosZ gene was suppressed by 53.34%, while nitric oxide reductase and nitrous oxide reductase activities were upregulated by 118.89% and downregulated by 46.70%, respectively. These key regulatory changes directly contribute to the increased N2O emissions observed with (+)-EPO treatment. Additionally, although (+)-EPO caused only minor changes in denitrifying microbial taxa, it increased the relative abundance of Nitrososphaerota and Euryarchaeota by 0.08%-0.10% and 0.40%-0.45%, respectively, after 35 days, enhancing nitrification and indirectly stimulating N2O emissions. Overall, this study deepens our understanding of how cis-epoxiconazole disrupts denitrification in agricultural soils through microbial, genetic, electronic, and enzymatic pathways.},
}
@article {pmid41139867,
year = {2025},
author = {Cao, X and Yan, Z and Ma, X and Yang, X and Liu, Z and Yang, L and Cui, Z and Xu, L and Jiang, X and Xiao, M},
title = {Discovery of Sialidases with Transglycosylation Activity and Rational Engineering of Their Catalytic Pockets for Efficient Synthesis of 6'-Sialyllactose.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10966},
pmid = {41139867},
issn = {1520-5118},
abstract = {Sialyloligosaccharides are essential components of human milk oligosaccharides. Sialidases with transglycosylation activity have shown great potential for industrial production of sialyloligosaccharides using cheaper glycosyl donors. Herein, five novel sialidases with transglycosylation activity were identified from human gut metagenomic DNA, among which BiS47 synthesized 6'-sialyllactose with the highest yield of 1.32 g/L. Molecular dynamics simulations revealed that BiS47 possessed an open conformation of the catalytic pocket which was then remodeled to narrow, a more favorable near-attack conformation, by site-directed mutagenesis and combinatorial mutations based on the design of entrance loops flexibility and bottom residues side chains. Two mutants G185C and G398H were obtained with 6'-sialyllactose yields increased 2.43-fold and 2.45-fold, respectively. "Property grafting" of G185C and G398H onto other four sialidases improved their transglycosylation activities, and eight mutants generated also exhibited narrowed catalytic pockets. This work provides efficient enzymatic tools for sialyloligosaccharide synthesis and important guidance for rational design of glycosidases.},
}
@article {pmid41139486,
year = {2025},
author = {Tran, T and Duong, DV and Le, TD and Bui, XT},
title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {10},
pages = {e70072},
doi = {10.1111/apm.70072},
pmid = {41139486},
issn = {1600-0463},
mesh = {*Biofilms/growth &amp; development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; },
abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.},
}
@article {pmid41139468,
year = {2025},
author = {Yang, Q and Kang, KL and Zhao, B and Feng, K and Feng, YS and Ye, J and Deng, Y and Wang, L},
title = {Geographical inference of dust from typical Chinese cities based on metagenomic shotgun sequencing.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {10},
pages = {1156-1168},
doi = {10.16288/j.yczz.25-009},
pmid = {41139468},
issn = {0253-9772},
mesh = {*Dust/analysis ; *Metagenomics/methods ; China ; Cities ; Bacteria/genetics/classification/isolation &amp; purification ; Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; Shotgun Sequencing ; },
abstract = {Microbial profiles in dust are closely correlated with geographical locations and provide valuable clues for criminal investigation, demonstrating significant potential in forensic use. However, the feasibility of using microbial profiles from metagenomics datasets to infer the geographical locations remains underexplored. In this study, we collect 170 dust samples from resident communities in four cities across northern, eastern, southwestern, and northwestern China. All samples are subjected to shotgun metagenomic sequencing to reveal variations in microbial composition. In total, 41,029 species are annotated, including 93.39% bacteria, 6.37% eukaryotes, 0.21% viruses, and 0.03% archaea. Clear clustering patterns are observed among the four cities (R[2]=0.870, P<0.001). Further filtering of species with detection rates below 10% across all samples strengthens city-level clustering (R[2]=0.948, P<0.001). Additionally, 127 biomarkers are identified using linear discriminant analysis effect size (LEfSe) to distinguish between the cities. Each city harbors a distinct microbial community, with unique species and relatively abundant taxa that contribute to its differentiated microbial profile. All samples are randomly split into training and testing sets in a 7:3 ratio. Five machine learning models including SourceTracker, FEAST, LightGBM, Random Forest and Support Vector Machine are applied to 51 randomly sample data and achieve average accuracies of 88.89%, 92.16%, 98.04%, 99.35% and 69.28%, respectively. These results constitute a microbial genetic map of four cities in China that highlights distinct microbial taxonomic signatures and provides an approach for city-scale source tracking of dust samples.},
}
@article {pmid41139156,
year = {2025},
author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K},
title = {Metagenomic next-generation sequencing: a game-changer in the diagnosis of unique intraocular infections.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {41139156},
issn = {1476-5454},
abstract = {OBJECTIVE: To thoroughly describe unique intraocular infections diagnosed by metagenomic next-generation sequencing (mNGS).<br><br>METHODS: A retrospective case series of patients presenting with challenging atypical intraocular infections at Tel Aviv Sourasky Medical Center during 2024. Clinical and demographic data, as well as mNGS results were extracted from patient records. mNGS was performed on the Illumina NextSeq500 platform using a custom bioinformatics pipeline. The following parameters were examined: Reads Per Million, Reads Per Million-ratio to negative control and E-index (K-mers*coverage/reads).<br><br>RESULTS: The study included three patients with novel presentations of intraocular infections, manifesting with atypical clinical manifestations and negative routine diagnostic workups. mNGS allowed the identification of Cytomegalovirus in a 43-year-old male with a history of autosomal dominant hyper-IgE syndrome, Bartonella henselae infection manifesting with photoreceptoritis, retinal vasculitis and global retinal dysfunction in a healthy 28-year-old female, and polymicrobial endophthalmitis with Rothia mucilaginosa and Pantoea agglomerans following intravitreal faricimab injection for neovascular age-related macular degeneration in an 81-year-old male. Treatment regimens were adjusted based on mNGS results.<br><br>CONCLUSIONS: Metagenomic next-generation sequencing has an important role in the diagnosis of challenging intraocular infections. It enables comprehensive pathogen identification and enhances the precision of treatment strategies.},
}
@article {pmid41139029,
year = {2025},
author = {Guo, Z and Li, YG and Liu, XL and Teng, ZJ and Qin, QL and Cha, QQ and Wang, ZB and Ni, SQ},
title = {Bulk metagenomics and machine learning unravels nitrogen metabolism patterns in extreme-temperature marine environments.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133551},
doi = {10.1016/j.biortech.2025.133551},
pmid = {41139029},
issn = {1873-2976},
abstract = {The nitrogen metabolism genes and associated microorganisms in polar oceans and hydrothermal vents remain insufficiently studied. In this study, metagenomic data were analyzed to characterize the geographical and biological features of 16 key nitrogen-cycling genes. NasA/B, narG, and nxrB were consistently abundant in both environments. Polar oceans were dominated by common nitrogen-cycling taxa, whereas hydrothermal vents hosted species linked to sulfur and methane metabolism. Environmental extremes exerted a stronger influence on nitrogen cycling than depth. Distinct co-occurrence networks (centralized vs. redundant) and accurate habitat classification (>95 %) highlighted strong environmental shaping. Differences in amino acid preferences and enzyme thermal stability reflected evolutionary divergence and adaptation to extreme temperatures. Overall, depth and environmental conditions structured community networks, while genetic variation supported ecological adaptation. These findings reveal contrasting nitrogen-cycling strategies and adaptations, with potential implications for biotechnological applications.},
}
@article {pmid41138869,
year = {2025},
author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M},
title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148387},
doi = {10.1016/j.ijbiomac.2025.148387},
pmid = {41138869},
issn = {1879-0003},
abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.},
}
@article {pmid41138860,
year = {2025},
author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S},
title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107295},
doi = {10.1016/j.mimet.2025.107295},
pmid = {41138860},
issn = {1872-8359},
abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.},
}
@article {pmid41138814,
year = {2025},
author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K},
title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.10.015},
pmid = {41138814},
issn = {2405-4577},
abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.<br><br>METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4 years; 55.8% male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9% of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (&#x3b2; = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (&#x3b2; = -0.159, p = 0.067) and Faith's PD (&#x3b2; = -0.38, p = 0.111).<br><br>CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.},
}
@article {pmid41138407,
year = {2025},
author = {Zhao, Q and Zhao, Y and Liu, W and Wang, J and Xie, H and Wu, H and Hu, Z},
title = {Nitrogen-transforming bacteria as key hosts and disseminators of antibiotic resistance genes in constructed wetlands: Metagenomic and metatranscriptomic evidence.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140220},
doi = {10.1016/j.jhazmat.2025.140220},
pmid = {41138407},
issn = {1873-3336},
abstract = {Given global concerns over antibiotic resistance genes (ARGs), constructed wetlands (CWs) have emerged as a cost-effective strategy to remove nitrogen (N) and mitigate ARG-related ecological risks. The occurrence and dissemination of ARGs are mainly driven by microorganisms. Although nitrogen transformation is a key process in CWs, the relationship between nitrogen-transforming bacteria (NTB) and ARG dynamics remains unclear. In this study, metagenomic and metatranscriptomic analyses were employed to comprehensively examine the associations between N transformation and the abundance, hosts, and ecological risks of ARGs in full-scale CWs. NTB, particularly dissimilatory nitrate reducers and bacteria involved in N organic degradation and synthesis, were identified as the primary hosts of ARGs. Furthermore, CWs substantially reduced ARG-related ecological risks, achieving decreases of 79.5 % in ARG expression, 94.9 % in mobile genetic elements, and 88.0 % in antibiotic-resistant pathogens, and identified NTB as key contributors to these risks. Both the decline in NTB abundance and adaptive fitness costs were identified as key mechanisms driving ARG reduction and mitigating ecological risk. This study highlights the critical role of N transformation in shaping ARG dynamics from a microbial perspective, providing a theoretical foundation for engineering practice in the co-control of ARGs and nitrogen removal in CWs.},
}
@article {pmid41138387,
year = {2025},
author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T},
title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127698},
doi = {10.1016/j.jenvman.2025.127698},
pmid = {41138387},
issn = {1095-8630},
abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.},
}
@article {pmid41138382,
year = {2025},
author = {Chen, C and Zhang, L and Tong, C and Ding, B and Li, A and Ji, B},
title = {Intermittent nighttime lighting enhances microalgal-bacterial granular sludge in synthetic wastewater treatment.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127689},
doi = {10.1016/j.jenvman.2025.127689},
pmid = {41138382},
issn = {1095-8630},
abstract = {The microalgal-bacterial granular sludge (MBGS) system is a promising technology due to its low energy demand and high treatment efficiency under illumination. However, its performance declines at night owing to the absence of light, reducing dissolved oxygen and microbial activity. This study proposes and evaluates an intermittent nighttime lighting strategy (12 h-light/3 h-dark/6 h-light/3 h-dark using LEDs) to enhance MBGS performance for treating synthetic wastewater. Supplemental lighting improved removal efficiencies of chemical oxygen demand, ammonia nitrogen, and phosphate by 7.5 %, 27.7 %, and 27.1 %, respectively. Metagenomic analysis revealed an increased genetic potential for pollutant degradation, evidenced by a higher abundance of genes involved in key metabolic pathways (e.g., GLU, ppa). Microbial community structure shifted, with increased abundances of Cyanobacteria and Verrucomicrobia and a decreased abundance of Proteobacteria. Genetic potential analysis suggested enhanced nitrogen assimilation, ATP cycling, and glycogen synthesis, alongside reduced lactate metabolism, indicating a shift toward aerobic pathways. These results demonstrate that intermittent nighttime lighting enables sustainable round-the-clock wastewater treatment.},
}
@article {pmid41138328,
year = {2025},
author = {Bai, X and Bi, J and Li, A and Deng, X and Zhao, Z and Hu, H and Pan, H},
title = {Walnut cake meal improves amino acids, fatty acid composition and flavor of egg yolk via the microbiota-yolk metabolites crosstalk in Jingfen-1 laying hens.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105981},
doi = {10.1016/j.psj.2025.105981},
pmid = {41138328},
issn = {1525-3171},
abstract = {Egg production is important for both human nutrition and its economic contribution. However, regions with a shortage of soybean meal (SM) may not meet the nutritional needs of the laying hen industry. Walnut cake meal (WM), a by-product of walnut processing, can be reused in laying hen production. In this study, we evaluated the feasibility of using WM to reduce the demand for SM in the laying hen industry. A total of 144 47-week laying hens (with similar performance) were randomly assigned to two groups (12 hens in each replicate and six replicates for each group). One group was fed a maize-SM diet (SM group), and the other was fad a maize-WM diet (WM group). The diets of both groups had similar crude protein and ME contents. After replacing SM with WM, the laying rate, egg weight, and feed efficiency did not significantly change (P > 0.05). WM increased (P < 0.05) the polyunsaturated fatty acids content, particularly linoleic acid, as well as umami and essential amino acids, in the eggs. WM diet also enhanced the flavor of eggs by enriching multiple volatile organic compounds that smell of sweet and herb-like foods. In addition, probiotic bacteria such as Cyanobacteriota and Prevotella, were enriched in the cecal microbiota of laying hens fed WM. Moreover, targeted metabolomics revealed the enrichment of butyric acid, 4-methylvaleric acid, isoleucine, and valine in the cecal digesta of laying hens fed with WM. Metagenomic sequencing revealed genes in the cecal microbiota associated with the synthesis of these enriched metabolites. Increased isoleucine and 4-methylvaleric acid in the digestive system contributed to the enrichment of fatty acids and amino acids in the yolks, whereas elevated flavor substances in the yolk could be associated with more amino acids in the intestine of laying hens. In conclusion, WM can reduce the need for soybean meal, improve cecal metabolism and egg quality, and ultimately achieve sustainable agriculture.},
}
@article {pmid41138271,
year = {2025},
author = {Mishra, R and Singh, R and Goel, R and Hasmi, RR and Malik, M and Gaur, PK and Lata, K},
title = {Biologically Active Molecules from Marine Brown Algae: A Review of Their Potential and Applications.},
journal = {Chemistry &amp; biodiversity},
volume = {},
number = {},
pages = {e01813},
doi = {10.1002/cbdv.202501813},
pmid = {41138271},
issn = {1612-1880},
abstract = {The highly bioactive secondary metabolites present in marine flora may prove to be abundant sources for producing innovative pharmaceuticals. Numerous brown algae species are being researched extensively because of their commercial relevance in nutraceuticals and medication discovery. The difficult environments that these creatures live in aid in the synthesis of special and powerful bioactive substances such as fucoidans, polysaccharides, hentriacontane, sterols like fucosterol, 24-ketocholesterol, and so forth. Despite its promising characteristics, additional in vivo studies are needed to validate algae's efficacy in a variety of applications. Effective extraction techniques must also be known to inexpensively isolate these chemicals, permit industrial application, and facilitate large-scale manufacturing. A comprehensive study of the genomes, metagenomics, transcriptomics metagenomics, transcriptomics, and metabolomics of marine algae is also necessary to elaborate on the underlying genetic and metabolic pathways involved in the manufacture of algal chemicals; these topics are covered in detail in this review. Brown algae are a major source of numerous secondary metabolites as evidenced by their phytoconstituents. This review elucidates the bioactive substance found in marine brown algae and their major pharmacological role so as to pave the way for maximum utilization of these underused resources.},
}
@article {pmid41138185,
year = {2025},
author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C},
title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116431},
doi = {10.1016/j.celrep.2025.116431},
pmid = {41138185},
issn = {2211-1247},
abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.},
}
@article {pmid41138182,
year = {2025},
author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF},
title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116477},
doi = {10.1016/j.celrep.2025.116477},
pmid = {41138182},
issn = {2211-1247},
abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.},
}
@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}
@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
doi = {10.1080/19490976.2025.2569739},
pmid = {41137523},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}
@article {pmid41137517,
year = {2025},
author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S},
title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2568706},
doi = {10.1080/19490976.2025.2568706},
pmid = {41137517},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation &amp; purification ; Models, Animal ; Disease Models, Animal ; },
abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.},
}
@article {pmid41137451,
year = {2025},
author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J},
title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70156},
doi = {10.1111/mec.70156},
pmid = {41137451},
issn = {1365-294X},
support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; },
abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.},
}
@article {pmid41137177,
year = {2025},
author = {Correa, F and Luise, D and Palladino, G and Estellé, J and Turroni, S and Scicchitano, D and Babbi, G and Rampelli, S and Candela, M and Martelli, PL and Stefanelli, C and Perez-Calvo, E and Trevisi, P},
title = {Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {110},
pmid = {41137177},
issn = {2524-4671},
support = {818290//Horizon 2020 Framework Programme/ ; },
}
@article {pmid41137068,
year = {2025},
author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM},
title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {426},
pmid = {41137068},
issn = {1756-3305},
mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.<br><br>METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Ba&#xf1;os, Laguna, Philippines, that differ in topography and land use transformations.<br><br>RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.<br><br>CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.},
}
@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert R&#xfc;f Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.<br><br>RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.<br><br>CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}
@article {pmid41136619,
year = {2025},
author = {Fujikawa, K and Saito, T and Kawashima, A and Jingushi, K and Motooka, D and Nakai, S and Hagi, T and Momose, K and Yamashita, K and Tanaka, K and Makino, T and Takahashi, T and Kurokawa, Y and Tsujikawa, K and Wada, H and Eguchi, H and Doki, Y},
title = {Bacteria-derived DNA in serum extracellular vesicles as a biomarker for gastric cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {11},
pages = {346},
pmid = {41136619},
issn = {1432-0851},
mesh = {Humans ; *Stomach Neoplasms/blood/microbiology/diagnosis ; *Extracellular Vesicles/genetics/microbiology ; *Biomarkers, Tumor/blood/genetics ; Male ; *DNA, Bacterial/genetics/blood ; Middle Aged ; Female ; RNA, Ribosomal, 16S/genetics ; Prognosis ; Aged ; Adult ; Case-Control Studies ; Tumor Microenvironment/immunology ; },
abstract = {Bacterial flora is present in various parts of the human body, and bacterial 16S rRNA genes have been detected in the bloodstream. Distinct blood microbiomes have been identified in various diseases, including cancer, and are thought to play a role in disease pathogenesis. In this study, we conducted a 16S rRNA metagenomic analysis of serum extracellular vesicles from 89 patients with gastric cancer (GC) and 25 healthy donors. We identified lower levels of Bacteroidetes and Actinobacteria and higher levels of Firmicutes in patients with GC than in healthy donors. By integrating this characteristic bacterial DNA profile, we developed a BAF index, defined as the ratio of Bacteroidetes and Actinobacteria to Firmicutes, which exhibited high sensitivity for detecting GC in both the discovery and validation cohorts, suggesting its potential utility as a screening tool. A high BAF index was significantly associated with an advanced tumor stage and poor prognosis. Moreover, a high BAF index was linked to an immunosuppressive tumor microenvironment, which may contribute to the unfavorable outcomes observed in these patients. These findings indicate that circulating bacterial signatures may serve as promising biomarkers for GC.},
}
@article {pmid41136439,
year = {2025},
author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z},
title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9353},
pmid = {41136439},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; },
abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.},
}
@article {pmid41136135,
year = {2026},
author = {Du, R and Li, X and Xu, Y and Jing, K and Ao, L and Deng, B and Xu, Q and Song, P and Yu, J},
title = {Metagenomics reveals potential antimicrobial peptides in Chinese baijiu fermentation.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104918},
doi = {10.1016/j.fm.2025.104918},
pmid = {41136135},
issn = {1095-9998},
mesh = {Humans ; Fermentation ; Metagenomics ; *Antimicrobial Peptides/pharmacology/chemistry/metabolism ; Bacteria/genetics/drug effects/metabolism/classification/isolation &amp; purification ; Molecular Docking Simulation ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; *Fermented Foods/microbiology ; Escherichia coli/drug effects ; A549 Cells ; China ; Hep G2 Cells ; Food Microbiology ; },
abstract = {Antimicrobial peptides (AMPs) from food fermentation microbiota hold promise for food preservation and as potential antimicrobial agents. However, the biosynthetic potential of AMPs in food fermentations remains largely unclear. Here, using Chinese baijiu fermentation as a model, we provided a workflow for AMP mining by combining metagenomics and machine learning. We recovered 389 metagenome-assembled genomes (MAGs) spanning both bacteria and archaea from 18 fermented samples. In total, 414 AMPs, including 290 novel AMPs, were predicted in 59.38 % of these MAGs using a machine learning model. Correlation network analysis showed that AMP-producing microorganisms potentially mediated negative microbial interactions. We selected ten AMPs for experimental validation, and eight AMPs exhibited antimicrobial activity against five human pathogens and two food spoilage microorganisms. One peptide, AMP_22, showed a broad-spectrum activity (all seven test strains) with high potency (MIC = 3.06-200 μg/mL) and cytotoxicity was not observed below 25 μg/mL using HepG2 and A549 cell lines. We further investigated the antimicrobial mechanism of AMP_22 using Escherichia coli as a model. Treatment with AMP_22 caused severe damage to the bacterial cell membrane, inhibited intracellular protein synthesis, and led to a significant accumulation of reactive oxygen species (ROS). Furthermore, molecular docking analysis indicated that AMP_22 can bind to DNA gyrase and dihydrofolate reductase via hydrogen bonding. This study highlights the potential of food-derived AMPs for application as preservatives and antimicrobial agents.},
}
@article {pmid41135804,
year = {2025},
author = {Dang, H and Zhang, Y and Zhang, L and Liu, Y},
title = {Transitional role of granular activated carbon for potentially promoting the expression of conductive pili and quorum sensing during anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133544},
doi = {10.1016/j.biortech.2025.133544},
pmid = {41135804},
issn = {1873-2976},
abstract = {Granular activated carbon (GAC) amendment mediated the microorganisms to significantly enhances methane production in anaerobic digestion. To elucidate the underlying microbial mechanisms, a genome-centric metagenomic analysis was conducted on DNA extracted from lab-scale anaerobic digesters treated with GAC. A total of 431 non-redundant metagenome-assembled genomes (MAGs) were recovered. Co-occurrence network analysis demonstrated that methanogens exhibit a distinct preference for associating with syntrophic partners that harboring potential pilA (e-pilA) producing conductive pili. Analysis revealed a potential temporal succession of key enhancement mechanisms: in the less developed community, QS facilitates biofilm formation and granulation, particularly for that of methanogens and MAGs with e-pilA. As the community became more developed, this QS-mediated influence weakens, concurrently e-pilA enrichment signifying established conductive pili connections. These connections optimize interspecies electron transfer for sustained methane yield enhancement. These results realved GAC sequentially promoting biofilm assembly via QS and optimizing electron flux for enhanced AD performance.},
}
@article {pmid41135729,
year = {2025},
author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J},
title = {Deciphering Microbial Dynamics in Coastal Ecosystems Under Polycyclic Aromatic Hydrocarbon Stress: Community Assembly, Interaction Networks, and Metabolic Adaptations.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123179},
doi = {10.1016/j.envres.2025.123179},
pmid = {41135729},
issn = {1096-0953},
abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.},
}
@article {pmid41135463,
year = {2025},
author = {Zhang, A and Pan, P and Zhou, NY and Li, T},
title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140176},
doi = {10.1016/j.jhazmat.2025.140176},
pmid = {41135463},
issn = {1873-3336},
abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.},
}
@article {pmid41135184,
year = {2025},
author = {Meng, J and Yang, C and Jing, M and Huang, J and Wang, W and Li, X and Zhao, P},
title = {Metagenomic sequencing of bronchoalveolar lavage fluid in pediatric pneumonia: A single-center study in Gansu province.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117153},
doi = {10.1016/j.diagmicrobio.2025.117153},
pmid = {41135184},
issn = {1879-0070},
abstract = {BACKGROUND: Pneumonia is one of the important causes of death in children. Conventional detection methods such as bacterial culture and polymerase chain reaction (PCR) are very limited for the detection of pathogens. Metagenomic next generation sequencing (mNGS) has shown strong coverage in nucleic acid detection, but its research in lower respiratory tract samples of children with pneumonia is still quite limited, especially in northwest China.<br><br>AIM: To characterize the pathogenic microbial spectrum in bronchoalveolar lavage fluid (BALF) of pediatric pneumonia patients in Gansu Province, China, using mNGS, and to demonstrate the advantages of mNGS in pediatric pneumonia diagnostics.<br><br>METHODS: A total of 128 pediatric pneumonia patients admitted to Gansu Provincial Maternal and Child Health Hospital (Gansu Central Hospital) between March 1, 2023 and February 5, 2025 were enrolled. BALF data, including bacterial culture, Polymerase chain reaction (PCR), and mNGS results, were collected from each patient for comprehensive analysis.<br><br>RESULTS: A total of 128 patients were enrolled in this retrospective study. Out of all patients, 68(53 %) were male and the median age was 3 years. A total of 31 patients had underlying diseases. mNGS demonstrated a significantly higher pathogen detection rate compared to conventional testing. Through mNGS analysis, viruses were identified as the predominant pathogenic microorganisms in children with pneumonia, and the most common infection pattern was a combination of viral and bacterial infections. Additionally, mNGS detected three types of difficult-to-culture bacteria, namely Tropheryma whipplei, Legionella pneumophila, and Mycobacterium tuberculosis complex, in the BALF from pediatric pneumonia patients in this study.<br><br>CONCLUSIONS: mNGS has shown obvious advantages in the detection of pathogenic microorganisms in children with pneumonia. Its universality helps to identify the pathogen as soon as possible and make up for the shortcomings of conventional testing, which is particularly important for the accurate treatment of patients with unclear infection or no obvious curative effect.},
}
@article {pmid41134432,
year = {2025},
author = {Kumar, A and Kumar, T and Batra, K and Dhania, NK and Jangir, BL and Budania, S and Maan, S},
title = {Detection, isolation, and complete genome sequencing of pigeon torque teno virus in Indian racing pigeons with pock-like lesions.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41134432},
issn = {1572-994X},
support = {State scheme//LUVAS, Hisar/ ; },
abstract = {This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.},
}
@article {pmid41134295,
year = {2025},
author = {Muralidhar, M and Naseem, MN and Mesa, JRB and Omaleki, L and Turni, C},
title = {Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001532},
pmid = {41134295},
issn = {2057-5858},
mesh = {Animals ; Swine ; *Wastewater/microbiology/virology ; *Metagenomics/methods ; Farms ; DNA, Bacterial/isolation &amp; purification/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Wastewater can be a useful sample to monitor disease outbreaks in the community, as it was demonstrated during the recent Severe acute respiratory syndrome coronavirus 2 pandemic. Due to housing conditions, diseases can rapidly spread within pig herds, resulting in high mortalities and significant economic losses. Monitoring piggery wastewater using Oxford Nanopore Technology's (ONT) sequencing platform combined with metagenomic analysis can provide early disease detection to deploy preventative measures. Nevertheless, obtaining DNA of the required purity and integrity from piggery wastewater is a major challenge. This study aims to identify and optimize the most effective method for obtaining high-quality and quantity DNA, which can be used in downstream applications for pathogen detection. Six DNA extraction protocols were tested on piggery wastewater samples and evaluated based on yield and overall DNA quality. The three best-performing methods, using commercially available kits (QIAGEN QIAamp® PowerFecal® Pro, QIAGEN DNeasy® PowerLyzer® PowerSoil® and Macherey-Nagel NucleoSpin® Soil), were then used to extract DNA from piggery wastewater samples spiked with a mock community composed of known pig pathogens. The extracted DNA samples were then sequenced on the ONT platform, and the effectiveness of the methods was evaluated using kraken2 taxonomic classifier and an in-house database. Results demonstrated that the optimized QIAGEN PowerFecal® Pro protocol was the most suitable and reliable extraction method. Overall, this study highlights the importance of determining the optimal DNA extraction method in effective disease surveillance using a complex environmental sample and takes an important step in making metagenomic disease surveillance a practical reality.},
}
@article {pmid41133998,
year = {2025},
author = {Bağci, C and Negri, T and Atienza, EB and Gross, C and Ossowski, S and Ziemert, N},
title = {Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf135},
pmid = {41133998},
issn = {2047-217X},
abstract = {BACKGROUND: Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional complexity remain speculative despite decades of study, in part because conventional sequencing campaigns lack the depth and contiguity required to recover low-abundance and repetitive genomes. Here, we revisit this question using one of the deepest metagenomic sequencing efforts to date, applying 148 billion base pairs of Nanopore long-read and 122 billion base pairs of Illumina short-read data to a single forest soil sample.<br><br>RESULTS: Our hybrid assembly reconstructed 837 metagenome-assembled genomes, including 466 that meet high- and medium-quality standards, nearly all lacking close relatives among cultivated taxa. Rarefaction and k-mer analyses reveal that, even at this depth, we capture only a fraction of the extant diversity: non-parametric models project that more than ten trillion base pairs of sequencing data would be required to approach saturation. These findings offer a quantitative, technology-enabled update to long-standing diversity estimates and demonstrate that conventional metagenomic sequencing efforts likely miss the majority of microbial and biosynthetic potential in soil. We further identify more than 11&#xa0;000 biosynthetic gene clusters, over 99% of which have no match in current databases, underscoring the breadth of unexplored metabolic capacity.<br><br>CONCLUSIONS: Taken together, our results emphasise both the power and the present limitations of metagenomics in resolving natural microbial complexity, and they provide a new baseline for evaluating future advances in microbial genome recovery, taxonomic classification, and natural product discovery.},
}
@article {pmid41133101,
year = {2025},
author = {Li, Q and Zhou, D and Cao, L and Li, Y and Li, J and Ye, J and Chen, H and Zhao, J and Cao, S and Peng, Z},
title = {Profiling the composition of resistome and bacteriome in the upper respiratory tract of domestic cats with respiratory signs in China.},
journal = {Microbiome research reports},
volume = {4},
number = {3},
pages = {27},
pmid = {41133101},
issn = {2771-5965},
abstract = {Aim: Domestic cats, among the most popular pets globally, may harbor antimicrobial resistance genes (ARGs) and zoonotic pathogens that impact human health. This study aims to investigate the resistome and bacteriome composition in the upper respiratory tract of domestic cats with respiratory signs in China. Methods: We performed metagenomic sequencing on 1,454 oropharyngeal-nasal swabs from cats with respiratory signs across diverse living conditions in 22 Chinese provinces. Resistome and bacteriome profiles were analyzed using these sequencing data. Results: We characterized the resistome and bacteriome in the upper respiratory tract of cats, identifying a wide range of ARGs - including those conferring resistance to last-resort antibiotics {e.g., carbapenems (bla NDM, bla OXA-244, bla VIM-13, bla VIM-33), colistin (mcr), and high-level tigecycline [MIC ≥ 4 µg/mL; tet(X3), tet(X4), tet(X5), tet(X6)]}
. Additionally, we detected numerous bacterial species of public health concerns, including the six leading antimicrobial resistance-associated pathogens (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa) and other high-burden pathogens linked to global morbidity, mortality, and therapeutic challenges. Conclusion: The findings highlight the potential zoonotic risks posed by cats. Including monitoring of this companion species within the One Health approach to address public health concerns is necessary.},
}
@article {pmid41132634,
year = {2025},
author = {Liu, Y and Xia, F and Cai, W and Zhang, Y and Zhu, J and Shen, Z and Li, J and Yang, Q and Qu, Q and Chen, J},
title = {Blinatumomab Along With Combined Antifungal Agents for Refractory Adult Acute Lymphoblastic Leukemia With Invasive Aspergillosis: A Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {10},
pages = {e71342},
pmid = {41132634},
issn = {2050-0904},
abstract = {There is an increased risk of invasive aspergillosis (IA) during the induction of acute lymphoblastic leukemia (ALL) because of the use of cytoreductive chemotherapy and high-dose steroids. This case demonstrates the utility of metagenomic next-generation sequencing and repeat sampling in clarifying complex infections and highlights blinatumomab as an effective antileukemic option when conventional chemotherapy is limited by active infection. Together, these strategies enabled the successful management of refractory ALL in a patient with pulmonary IA and fungal DNAemia.},
}
@article {pmid41132583,
year = {2025},
author = {Zou, Z and Lei, D and Wang, X and Yin, Y and Li, H and Di, X and Li, X},
title = {Crocin Ameliorates Cognitive Impairment and Pathological Changes in Alzheimer's Disease Model Mice by Regulating Gut Microbiota.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {10},
pages = {e71117},
pmid = {41132583},
issn = {2048-7177},
abstract = {Alzheimer's disease (AD), a primary cause of dementia, places a significant strain on both patients and society due to the absence of effective treatments. Recent research suggests that the gut microbiota may play a role in the development of AD. Crocin, a compound derived from traditional medicine, has demonstrated potential in alleviating neurological disorders and influencing gut microbiota, yet its specific mechanisms in AD remain unclear. In this study, we administered Crocin or saline to 5xFAD mice and wild-type controls. We discovered that Crocin treatment led to notable improvements in cognitive function, as measured by the Morris water maze test, reduced beta-amyloid (Aβ) accumulation, and decreased neuroinflammation, as indicated by reduced microglial and astrocyte activation. Metagenomic sequencing revealed a significant increase in the gut microbiota diversity, specifically the abundance of Firmicutes, Verrucomicrobiota, and Akkermansia. Additionally, Crocin enhanced intestinal barrier function by upregulating tight junction proteins and Secretory immunoglobulin A, while improving the structure of the jejunal mucosa. These results suggest that Crocin may alleviate cognitive deficits and neuropathological changes in 5xFAD mice, possibly through modulation of the gut microbiota and strengthening the gut barrier, presenting it as a promising therapeutic approach for AD.},
}
@article {pmid41132557,
year = {2025},
author = {Chen, J and Luo, Y and Hao, Y and Wang, Q and Wang, Q},
title = {Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1676238},
pmid = {41132557},
issn = {2296-861X},
abstract = {INTRODUCTION: Approximately 49.3% of individuals living at high altitudes suffer from dyslipidemia. Emerging evidence indicates that gut microbiota can regulate lipid metabolism and cholesterol homeostasis, but the composition and function of gut microbiota in dyslipidemic patients from Tibetan pastoral regions remain unclear.<br><br>METHODS: To address this, we enrolled a cohort consisting of 22 dyslipidemic patients and 33 healthy controls (HCs) from the Gannan Tibetan pastoral region (average altitude: 3,600&#x202f;m). Phenotypic data, blood, and fecal samples were collected from all the participants for a metagenome-wide association study based on shotgun metagenomic sequencing.<br><br>RESULTS: Compared with HCs, dyslipidemic patients showed a significant reduction in gut microbial diversity. Specifically, the abundance of beneficial species-including Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium bifidum, and Parabacteroides distasonis-was significantly decreased, while opportunistic pathogens such as Veillonella parvula, V. tobetsuensis, Streptococcus oralis, and Streptococcus mitis were notably enriched. Functional prediction revealed that pathways involved in glycolysis, starch degradation, and biosynthesis of L-methionine, L-arginine, L-lysine, L-citrulline, and L-threonine were significantly downregulated in dyslipidemic patients, whereas pathways for the biosynthesis of lipopolysaccharides, fatty acids, polyamines, and (Kdo)&#x2082;-lipid A were enriched. Correlation analysis showed that the enriched taxa in dyslipidemic patients were significantly positively associated with total cholesterol (TC), total triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C). In contrast, the enriched functional pathways were significantly negatively correlated with TC but positively correlated with high-density lipoprotein cholesterol (HDL-C).<br><br>DISCUSSION: These findings clarify the alterations in gut microbiota composition and function in plateau-dwelling dyslipidemic populations and their associations with blood lipid levels, suggesting potential microbial biomarkers for hyperlipidemia in plateau environments.},
}
@article {pmid41132537,
year = {2025},
author = {Liu, X and Wang, L and Huang, B and Jiao, Y and Guan, Y and Nuli, R},
title = {Barnesiella intestinihominis improves gut microbiota disruption and intestinal barrier integrity in mice with impaired glucose regulation.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1635579},
pmid = {41132537},
issn = {1663-9812},
abstract = {INTRODUCTION: Impaired glucose regulation (IGR) is a prediabetic state closely associated with gut microbiota dysbiosis. Our previous metagenomic analysis identified a significant deficiency of Barnesiella intestinihominis (B. intestinihominis) in IGR patients (p < 0.01). The present study was therefore designed to investigate the therapeutic potential of B. intestinihominis supplementation in a high-fat diet (HFD)-induced IGR mouse model and to explore its potential mechanisms of action.<br><br>METHODS: A mouse model of IGR was established by HFD. The treatment group received a daily supplementation of live B. intestinihominis (1&#xd7;10[8] CFU) for 5 weeks. Gut microbiota composition was analyzed. Colonic expression levels of tight junction proteins (ZO-1 and occludin) and cytokines (IL-10, TNF-&#x3b1;, IL-6) were measured. In vitro experiments using Caco-2 human intestinal epithelial cells were conducted to assess the direct effects of B. intestinihominis. B. intestinihominis fermentation broth, heat-inactivated bacterial solution, and bacterial solution were co-cultured with Caco-2 cells. Cell viability was assessed using the CCK-8 assay, and the expression levels of tight junction proteins were evaluated. Trans-epithelial electrical resistance (TEER) and alkaline phosphatase activity were also assessed in the Caco-2 model.<br><br>RESULTS: Daily supplementation with B.intestinihominis significantly attenuated HFD-induced hyperglycemia in mice. It also modulated the gut microbiota, evidenced by an increased abundance of beneficial Ligilactobacillus and a reduction in pathogenic Lachnoclostridium. Furthermore, B. intestinihominis administration upregulated the expression of colonic tight junction proteins (ZO-1 and occludin) and the anti-inflammatory cytokine IL-10, while simultaneously inhibiting the pro-inflammatory mediators TNF-&#x3b1; and IL-6. In vitro, the fermentation broth of B.intestinihominis (10%) increased Caco-2 cell viability, and heat-inactivated bacteria (1&#xd7;10[7] CFU) enhanced ZO-1 expression. However, neither treatment significantly affected trans-epithelial electrical resistance (TEER) nor alkaline phosphatase activity in Caco-2 cells.<br><br>DISCUSSION: These findings suggest that intestinal probiotics B. intestinihominis may ameliorate IGR by modulating the gut microbiota, enhancing intestinal barrier integrity, and attenuating inflammation, thus supporting their potential as a therapeutic intervention for metabolic disorders.},
}
@article {pmid41132377,
year = {2025},
author = {Han, Z and Jia, L and Zhu, R and Fu, H and Lin, C and Huang, H and Deng, L and Zhang, J and Zhao, L},
title = {The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1665461},
pmid = {41132377},
issn = {1664-302X},
abstract = {INTRODUCTION: Coxsackievirus A12 (CVA12) is a serotype of Enterovirus A. Its evolutionary and molecular characteristics remain poorly understood.<br><br>METHODS: The metagenomic Next-Generation Sequencing (mNGS) strategy were used to investigate the viral diversity. The viral isolation, proliferation assays, phylogenetic relationships and recombination events were analyzed.<br><br>RESULTS: In this study, nine clinical specimens collected in Beijing, China, during March 2010 to October 2019 were identified as CVA12 positive, among which five were confirmed by mNGS. Then five CVA12 strains were isolated, and the proliferation assays demonstrated the preferential replication of CVA12 in rhabdomyosarcoma (RD) cells, with rapid intracellular replication before being released extracellularly, over Hep-2 cells. Transcriptomic profiling of infected RD cells revealed that the significant up-regulated genes were involved in inflammatory responses and transcriptional regulation (e.g., JUN, FOS), suggesting robust host immune activation. Phylogenetic analysis identified that four strains were clustered into genogroup E, indicating a lineage undergoing active transmission in Beijing, China, the other one into genogroups B. Recombination analysis revealed that strain s7275 exhibited recombination with CVA5 (strain 3,490, GenBank access number OK334538) at the breakpoint position 3,373-6,634, while the others showed recombination with EV-A71 (strain EV71/P1034/2013/China, GenBank access number KP289419) at breakpoint position 3,370-6,645.<br><br>DISCUSSION: These findings underscored the genetic diversity and recombination dynamics which provided insights into the evolutionary implications of CVA12, and its proliferation features in RD cells of CVA12. Further research is needed to elucidate the functional mechanisms of CVA12 infection and its role for disease.},
}
@article {pmid41132089,
year = {2025},
author = {Zhao, Y and Wang, H and Lin, W and Wang, H and Cao, LL},
title = {Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2025183},
pmid = {41132089},
issn = {1745-7270},
abstract = {Hepatocyte phospholipase D1 (PLD1) knockout alleviates metabolic dysfunction-associated steatotic liver disease (MASLD) in mice, but the underlying mechanism is largely unknown. In this study, the mice were divided into four groups: Con (wild-type mice with normal control diet), HFHC (wild-type mice with high-fat diet), Con_KO (hepatocyte PLD1-knockout mice with normal control diet), and HFHC_KO (hepatocyte PLD1-knockout mice with high-fat diet). Intestinal contents of mice are analyzed via metagenomics and metabolomics, and the liver bile acids are assessed by mass spectrometry imaging. The results show that at the phylum level the abundance of Bacillota in the intestines of MASLD model mice is significantly increased, whereas that of Bacteroidota significantly is decreased. However, after the deletion of hepatocyte PLD1, Pseudomonadota and Candidatus Bathyarchaeota are significantly decreased in the MASLD model mice. At the species level, compared with that in the Con group, the abundance of Faecalibaculum rodentium is significantly increased in the HFHC group, whereas hepatocyte PLD1 knockout causes the abundances of Desulfovibrionaceae bacterium LT0009 and Lachnospiraceae bacterium 10-1 to be significantly decreased. In terms of intestinal bile acids, the levels of two bile acids (hyodeoxycholic acid and glycolithocholic acid) differ between the HFHC_KO group and the HFHC group. Association analysis shows that Faecalibaculum co-occurs with DCA, βMCA, ΩMCA and αMCA, while probiotic Bacteroides uniformis is significantly correlated with UDCA, 12-KetoLCA, and 7-KetoLCA. Finally, mass spectrometry imaging reveals that the TCA and TDCA contents in the liver are significantly decreased after PLD1 knockout in hepatocytes. These findings demonstrate that hepatocyte PLD1 knockout alters the gut microbiota and bile acids profiles, suggesting that PLD1 deficiency may modulate MASLD progression by changing intestinal microbiota-bile acid homeostasis.},
}
@article {pmid41131686,
year = {2025},
author = {Ramchandar, N and Farnaes, L and Coufal, N},
title = {Host Transcriptomic Analysis of Operative Samples From Children With Suspected Osteoarticular Infections.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004969},
pmid = {41131686},
issn = {1532-0987},
}
@article {pmid41131658,
year = {2025},
author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y},
title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {214},
pmid = {41131658},
issn = {2049-2618},
mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; },
abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.<br><br>RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15&#xa0;days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.<br><br>CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.},
}
@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.<br><br>RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the &#x3b2; diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.<br><br>CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}
@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's &amp; Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&amp;D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.<br><br>METHODS: A cohort of treatment-na&#xef;ve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.<br><br>RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p&#x2009;=&#x2009;0.02) compared to HC, which was restored after EEN treatment at remission status (p&#x2009;<&#x2009;0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r&#x2009;=&#x2009;0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-&#x3b1;, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).<br><br>CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}
@article {pmid41131579,
year = {2025},
author = {Niemann, J and Huang, Y and Lanigan, LT and Willingham Grijalba, AL and Dunn, RR and Sikora, M and Schroeder, H},
title = {ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {365},
pmid = {41131579},
issn = {1474-760X},
support = {101045643//HORIZON EUROPE European Research Council/ ; },
mesh = {*Metagenomics/methods ; *Parasites/genetics ; *Databases, Genetic ; DNA Contamination ; Animals ; Humans ; },
abstract = {Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this study, we systematically quantify and remove contamination from 831 published endoparasite genomes to create ParaRef, a curated reference database for species-level parasite detection. We show that decontamination significantly reduces false detection rates and improves overall detection accuracy. Our study highlights the pervasive issue of contamination in public databases and offers a resource that will enhance the reliability of parasite detection using metagenomics.},
}
@article {pmid41131543,
year = {2025},
author = {Lin, P and Xu, Y and Sun, Z and Li, J and Ban, Y and Zhang, M and Wang, Y and Zhang, C},
title = {Investigating the relationship between intestinal microbiota and Th1/Th2/Th17 imbalance in subclinical hypothyroidism during the first half of pregnancy: a multi-omics approach.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {83},
pmid = {41131543},
issn = {1757-4749},
abstract = {BACKGROUND: Gestational subclinical hypothyroidism (SCH), marked by elevated Thyroid-stimulating hormone (TSH) with normal free thyroxine (FT4), links to adverse perinatal outcomes. During early pregnancy (< 20 weeks), maternal thyroid hormones are crucial for fetal neurodevelopment, with deficiencies risking irreversible deficits. SCH pregnancies show gut microbiota alterations and metabolic dysregulation. Emerging evidence suggests these changes may drive Th(helper T cells)1/Th2/Th17 immune imbalance, though mechanisms remain unclear. This study combines metagenomics and lipidomics to investigate gut microbiota-Th1/Th2/Th17 interactions in patients with SCH in the first 20 weeks during pregnancy.<br><br>METHODS: This study included 20 pregnant women with SCH (SCH group) in the first half of pregnancy (&#x2264;&#x2009;20 gestational weeks) and 20 normal pregnant women (CON group) in the same period. Collect fecal and blood samples from both groups. Metagenomic sequencing was used to determine the differences in the composition of the intestinal microbiota between the two groups, and non-targeted lipidomics was used to compare the lipid differences between the two groups. Flow cytometry was used to assess Th1, Th2 and Th17 cells in peripheral blood, and a cell microbead array was used to determine cytokine levels.<br><br>RESULTS: (1) Metagenomic sequencing showed an increased abundance of Faecalibacterium prausnitzii and a decreased abundance of Bacteroides uniformis in the SCH group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant enrichment in lipid and polysaccharide biosynthesis and mucopolysaccharide biodegradation pathways in the SCH group. (2) Lipidomics identified 692 different lipids, with Triglyceride (TG) being the most significant. KEGG pathway analysis revealed that TG was mainly concentrated in the Th1, Th2, and Th17 cell differentiation pathways. (3) Additionally, serological indicators of the two groups showed that TSH, Interleukin (IL)-2,IL-10, Tumor necrosis factor (TNF)-&#x3b1;, TG, Th1, and Th17 in the SCH group were higher than those in the CON group, while Th2 was significantly lower (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In the first half of pregnancy, patients with SCH may experience intestinal microbiota disorder, characterized by increased levels of Faecalibacterium prausnitzii and decreased levels of Bacteroides uniformis, at the same time, it was accompanied by an increase in TG synthesis and a Th1/Th2/Th17 imbalance, these factors may be involved in the occurrence of SCH during pregnancy.},
}
@article {pmid41131518,
year = {2025},
author = {Zhang, Y and Zhang, Q and Wang, L and Hu, Y},
title = {The value of second-generation gene sequencing in lung cancer immunotherapy with concurrent infections.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {1636},
pmid = {41131518},
issn = {1471-2407},
support = {023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; },
}
@article {pmid41052877,
year = {2025},
author = {Tran, LN and Castellano, D and Gutenkunst, RN},
title = {Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations.},
journal = {Molecular biology and evolution},
volume = {42},
number = {10},
pages = {},
pmid = {41052877},
issn = {1537-1719},
support = {R01GM127348/GM/NIGMS NIH HHS/United States ; R35GM149235/GM/NIGMS NIH HHS/United States ; },
mesh = {*Haplotypes ; *Supervised Machine Learning ; *Genetics, Population/methods ; *Metagenomics/methods ; Linkage Disequilibrium ; Gene Frequency ; Humans ; Neural Networks, Computer ; },
abstract = {Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful tools for population genomics inference. However, these methods often lack interpretability, making it difficult to understand which population genetics features drive their predictions-a critical limitation for method development and biological interpretation. Here, we introduce a systematic permutation approach that progressively disrupts population genetics features within input test haplotype matrices, including linkage disequilibrium, haplotype structure, and allele frequencies. By measuring performance degradation after each permutation, the importance of each feature can be assessed. We applied our approach to three published CNNs for positive selection and demographic history inference. We found that the positive selection inference CNN ImaGene critically depends on haplotype structure and linkage disequilibrium patterns, while the demographic inference CNN relies primarily on allele frequency information. Surprisingly, another positive selection inference CNN, disc-pg-gan, achieved high accuracy using only simple allele count information, suggesting its training regime may not adequately challenge the model to learn complex population genetic signatures. Our approach provides a straightforward, model-agnostic, and biologically-motivated framework for interpreting any haplotype matrix-based method, offering insights that can guide both method development and application in population genomics.},
}
@article {pmid40755398,
year = {2025},
author = {Johnson, BJ and Graham, MC and Panahi, E and Vieira, CJSP and Nath, NS and Mason, P and Gleadhill, J and Thomas, D and Onn, MB and Shivas, MA and Shearman, D and Darbro, JM and Devine, GJ},
title = {An All-in-One Metabarcoding Approach to Mosquito and Arbovirus Xenosurveillance.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70022},
doi = {10.1111/1755-0998.70022},
pmid = {40755398},
issn = {1755-0998},
support = {//Mosquito and Arbovirus Research Committee Inc./ ; },
mesh = {Animals ; *Arboviruses/genetics/isolation &amp; purification/classification ; *Culicidae/virology/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; *Mosquito Vectors/virology/classification ; High-Throughput Nucleotide Sequencing ; *Biosurveillance/methods ; *Metagenomics/methods ; Vertebrates/virology/classification ; Arbovirus Infections ; },
abstract = {Next-generation sequencing (NGS) has the potential to transform mosquito-borne disease surveillance but remains under-utilised. This study introduces a comprehensive multi-loci metabarcoding-based MX (molecular xenomonitoring) approach to mosquito and arbovirus surveillance, enabling parallel identification of mosquito vectors, circulating arboviruses, and vertebrate hosts from bulk mosquito collections. The feasibility of this approach was demonstrated through its application to a large set (n = 110) of bulk field collections. This set was complemented by a number (n = 28) of single-species mosquito pools that had previously been screened for viruses using quantitative reverse transcription PCR (RT-qPCR) and metatranscriptomics. Universal alphavirus and flavivirus primer sets were used to screen for arboviruses in the resulting metabarcoding library. Viral amplicons were then indexed and combined with mosquito-specific (ITS2), universal invertebrate (COI), and vertebrate (Cyt b) barcode amplicons prior to sequencing. This approach confirmed the presence of all previously identified mosquito species, as well as those commonly misidentified morphologically, and enabled a degree of quantification regarding their relative physical abundance in each collection. Additionally, the developed approach identified a diverse vertebrate host community (18 species), demonstrating its potential for defining host preferences and, in tandem with the viral screens and associated vector data, understanding disease transmission pathways. Importantly, metabarcoding detected a diversity of regionally prevalent arboviruses and insect-specific viruses, with all three viral diagnostics demonstrating a similar sensitivity and specificity in detecting Ross River virus and Barmah Forest virus, Australia's most common arboviruses. In summary, multi-loci metabarcoding is an affordable and efficient MX tool that enables complete mosquito-borne disease surveillance.},
}
@article {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
doi = {10.1111/1755-0998.70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}
@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}
@article {pmid41131367,
year = {2025},
author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C},
title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41131367},
issn = {2058-5276},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; },
abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.},
}
@article {pmid41131151,
year = {2025},
author = {Buffington, JD and Kuo, HC and Hu, K and Chang, YC and Javanmardi, K and Voigt, B and Li, YR and Little, ME and Devanathan, SK and Xhemalçe, B and Gray, RS and Finkelstein, IJ},
title = {Discovery and engineering of retrons for precise genome editing.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41131151},
issn = {1546-1696},
support = {F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; },
abstract = {Retrons can produce multicopy single-stranded DNA in cells through self-primed reverse transcription. However, their potential for inserting genetic cargos in eukaryotes remains largely unexplored. Here we report the discovery and engineering of highly efficient retron-based gene editors for mammalian cells and vertebrates. Through bioinformatic analysis of metagenomic data and functional screening, we identify retron reverse transcriptases that are highly active in mammalian cells. Rational design further improves the editing efficiency to levels comparable with conventional single-stranded oligodeoxynucleotide donors but from a genetically encoded cassette. Retron editors exhibit robust activity with Cas12a nuclease and Cas9 nickase, expanding the genomic target scope and bypassing the need for a DNA double-stranded break. Using a rationally engineered retron editor, we incorporate a split GFP epitope tag for live-cell imaging. Lastly, we develop an all-RNA delivery strategy to enable DNA-free gene editing in cells and vertebrate embryos. This work establishes retron editors as a versatile and efficient tool for precise gene editing.},
}
@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}
@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003456},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.<br><br>METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.<br><br>RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.<br><br>CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.<br><br>PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}
@article {pmid41130504,
year = {2025},
author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G},
title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122995},
doi = {10.1016/j.envres.2025.122995},
pmid = {41130504},
issn = {1096-0953},
abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.<br><br>METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry(Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.<br><br>RESULTS: The detection rate of microplastics in the stool samples was 98.5%, with a median mass concentration of 54.7 &#x3bc;g/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.<br><br>CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.},
}
@article {pmid41130083,
year = {2025},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}
@article {pmid41130000,
year = {2025},
author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z},
title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140201},
doi = {10.1016/j.jhazmat.2025.140201},
pmid = {41130000},
issn = {1873-3336},
abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.},
}
@article {pmid41129998,
year = {2025},
author = {Hu, K and Wang, Z and Xu, Q and Chu, Y and Qian, Y and Zhang, X and Li, W and Han, Y and Wang, B and Zhang, H},
title = {Metagenomic insights into the effects of ecological water replenishment on resistome and pathogens in urban wetland.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140117},
doi = {10.1016/j.jhazmat.2025.140117},
pmid = {41129998},
issn = {1873-3336},
abstract = {Urban wetland restoration increasingly relies on water replenishment, yet its impacts on resistome dissemination remain critically understudied. Here, we performed a comprehensive metagenomic survey of water and sediment from the Xixi National Wetland Park to investigate how water diversion from the surrounding Qiantang River affects the distribution and composition of antibiotic-resistant genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and pathogens. Among the detected ARGs, multidrug, macrolide-lincosamide-streptogramin, and bacitracin resistance genes were predominant. MGEs such as tnpA, IS91, and istA, and VFs involved in adherence and immune modulation were also abundant. Pathogens including Fusobacterium varium and Leptospira noguchii were frequently observed. RDA and MRM analysis revealed certain antibiotics emerged as influent factors of resistome composition. Notably, the vast majority of resistome types were shared between the wetland park and the external riverine environment, with a decline in resistome richness as distance from the water diversion source increased. This phenomenon indicates that river-to-wetland water diversion acts as a conduit, facilitating the broad dissemination of resistome components and pathogens into the wetland, while the wetland's self-purification capacity also plays a role. Nevertheless, a small subset of ARGs and MGEs was significantly enriched within the wetland interior. Collectively, these results highlight the ecological risks of water replenishment in urban wetlands and underscores the need for mitigation strategies, such as source-water pretreatment and wetland sediment remediation.},
}
@article {pmid41129997,
year = {2025},
author = {Lu, W and Sun, S and Wang, Q and Wang, Z and Lu, YZ and Guo, J and Zhao, HP and Lai, CY},
title = {Acesulfame degradation within a methane-fed biofilm: a novel and efficient biodegradation route.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140152},
doi = {10.1016/j.jhazmat.2025.140152},
pmid = {41129997},
issn = {1873-3336},
abstract = {Acesulfame (ACE), a persistent organic pollutant, is frequently detected across diverse aquatic environments, yet its environmental remediation remains challenging due to the inherently slow biodegradation. Here, we unveil a highly efficient ACE removal strategy using a methane-fed biofilm, achieving a degradation rate of 59.6 mg ACE/g VSS/h. Comprehensive analyses of transformation products (TPs) and toxicity profiles revealed that the biofilm mediated important and effective biodegradation pathways, promoting deep ACE degradation. Microbial community analysis, methane interruption experiments and pure culture studies implicated aerobic methanotrophs Methylococcus sp. and Methylomonas sp. as key players in ACE degradation. Metagenomic and metatranscriptomic analyses demonstrated that these methanotrophs exhibited high expression levels of particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) genes within the biofilm community. Enzyme inhibition assays, combined with TP profiling, suggested that pMMO and CYP450 initiated the degradation of ACE. Scavenging experiments further suggested that hydroxyl radicals (•OH) generated through the catalytic activity of pMMO and CYP450 are crucial mediators in the ACE hydroxylation pathway. These findings provide the first evidence of ACE degradation in a methane-fed biofilm system, offering a promising and sustainable approach for the removal of recalcitrant organic contaminants from wastewater.},
}
@article {pmid41128819,
year = {2025},
author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y},
title = {Olsenella scatoligenes-derived Skatole Promotes Smooth Muscle Cell Proliferation and Migration to Aggravate Atherosclerosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf238},
pmid = {41128819},
issn = {1751-7370},
abstract = {Coronary artery disease remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of coronary artery disease through unclear mechanisms. Here, we demonstrate that the abundance and inter-species interactions of Olsenella scatoligenes are 4.7-fold and 1.6-fold higher in patients with coronary artery disease, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of Olsenella scatoligenes. Consistently, supplementation with Olsenella scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, Olsenella scatoligenes -derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor, and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates approximately 40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking Olsenella scatoligenes to aggravated atherosclerosis through activation of aryl hydrocarbon receptor -calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of coronary artery disease.},
}
@article {pmid41128801,
year = {2025},
author = {Blomström, AL and Hansen, S and Riihimäki, M},
title = {Identification and whole-genome characterization of a novel equine papillomavirus.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41128801},
issn = {1572-994X},
support = {H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; },
abstract = {Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.},
}
@article {pmid41128541,
year = {2025},
author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S},
title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095625},
doi = {10.1128/msystems.00956-25},
pmid = {41128541},
issn = {2379-5077},
abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.<br><br>IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.},
}
@article {pmid41128412,
year = {2025},
author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H},
title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c10625},
pmid = {41128412},
issn = {1936-086X},
abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.},
}
@article {pmid41127841,
year = {2025},
author = {Turner, Z and Drabovich, AP},
title = {Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.},
journal = {Environment &amp; health (Washington, D.C.)},
volume = {3},
number = {10},
pages = {1139-1153},
pmid = {41127841},
issn = {2833-8278},
abstract = {Detection and monitoring of pathogens is a central aspect of maintaining public health. Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially, leading to unforeseen outbreaks, epidemics, and pandemics. The emerging multiomics and meta-omics techniques and workflows, such as proteogenomics and meta-genomics, offer the potential for the detection of harmful pathogens, as well as opportunities for the discovery of previously unknown bacterial, parasitic, or viral pathogens. Multiomics and meta-omics workflows provide molecular information for tracking pathogens and understanding the effectiveness of spread mitigation strategies. In addition to environmental monitoring, multiomics and meta-omics approaches have the potential for clinical applications and in-depth characterization of novel pathogens. In this review, we discuss recent applications of multiomics and meta-omics techniques, their advantages over traditional methods, and their potential implementations in biomedical research, environmental studies, and healthcare. We critically assess the benefits and challenges of multiomics and meta-omics studies and discuss their future perspectives.},
}
@article {pmid41127630,
year = {2025},
author = {Kamau, M and Ergunay, K and Bourke, BP and Mutura, J and Lebunge, R and Ochieng, G and Gathii, K and Waitumbi, J and Mutai, B and Hassell, J and von Fricken, ME and Zimmerman, D and Murray, S and Jiang, L and Liao, HM and Grieco, JP and McDermott, EG and Achee, NL and Linton, YM},
title = {Potential spillover investigated by metagenome sequencing in Laikipia, Kenya reveals tick-borne pathogens and a novel bunyavirus.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101226},
pmid = {41127630},
issn = {2352-7714},
abstract = {Tick-borne infections continue to present a global public health threat, and require a One Health approach for successful mitigation. We conducted cross-sectional tick screening utilizing an agnostic metagenomic screening strategy based on nanopore sequencing (NS), in an area spanning a range of habitats with intensified human-livestock-wildlife interactions in central Kenya. We further used targeted amplification by polymerase chain reaction (PCR) and sequence independent single primer amplification (SISPA) for confirmation and genome characterization, as necessary. We initially screened 44 ticks across pooled and individual samples belonging to seven species. Tick-associated bacteria-including spotted fever Rickettsia (13.3 %) and Coxiella-like endosymbionts, Francisella turcica and Francisella opportunistica, and tick-associated Borrelia-were detected in 86.6 % of samples. Viruses were detected in 93.3 % of samples, where Jingmen tick virus (JMTV) was observed as the most prevalent virus, detectable in 80 % of samples. A follow-up specific PCR confirmed JMTV virus detection in 75 %, associated with viral read abundance in NS. A complete JMTV genome was assembled from an Amblyomma sparsum tick, that displayed conserved motifs of putative structural and replication proteins. Maximum likelihood analyses placed the virus genome within a distinct clade in the proposed East African-Asian JMTV lineage. We further investigated a virus contig generated during the initial screening, with limited identities to Volzhskoe tick virus (VSTV). Subsequent NS and targeted PCR screening in an additional collection of 650 ticks from 11 species revealed a JMTV prevalence of 12.3 % in Amblyomma, Hyalomma and Rhipicephalus species. Follow-up NS and SISPA generated viral genomic segments, encoding a putative replicase and glycoprotein precursor. Pairwise comparisons and phylogeny indicated a novel virus-herein named as the Mpala tick virus-which is related to but distinct from VSTV and placed among unclassified members of Bunyaviricetes. In conclusion, our approach provides an effective strategy to detect a wide range of tick-borne bacteria and viruses, facilitating identification of opportunistic or endosymbiotic bacteria as well as novel viruses.},
}
@article {pmid41126918,
year = {2025},
author = {Li, W and Zhou, D and Ji, Y and Tian, H and Meng, N and Li, J and Guo, N and He, X and Dao, M and Jin, X},
title = {Exploring the molecular intersection for hypertension, hyperlipidemia and their comorbid conditions through multi-omics approaches.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1593688},
pmid = {41126918},
issn = {2297-055X},
abstract = {BACKGROUND: Hypertension and hyperlipidemia are interconnected conditions that heighten cardiovascular risk, yet their intricate multi-scale molecular signatures remain inadequately mapped. This study aimed to conduct an integrated multi-omics investigation to unravel the key pathways and biomarkers underlying hypertension, hyperlipidemia, and both conditions.<br><br>METHODS: Metabolomic analysis was performed on serum samples and metagenomic analysis on fecal samples collected from individuals with hypertension (n&#x2009;=&#x2009;16), hyperlipidemia (n&#x2009;=&#x2009;19), or both conditions concurrently (n&#x2009;=&#x2009;20). In addition, 20 healthy individuals were recruited as controls.<br><br>RESULTS: Metabolomics uncovered altered levels of sphingolipids, phosphatidylcholines, glycylprolines, and nucleic acid metabolites, which may be associated with changes in vascular tone, lipid and protein homeostasis, and thyroid signaling. Metagenomics showed depletion in the abundance of the Fibrobacteres phylum. Altered abundances of Escherichia coli and Bacteroides vulgatus were also observed, which were correlated with deviations in lipid and carbohydrate metabolism. Sphingomyelin d18:1/16:0 and sphingomyelin d18:1/24:1(15Z) were the key metabolites that were identified as potential diagnostic biomarkers across conditions. Microbial taxa such as Enterococcus cecorum, Lachnospiraceae bacterium, Prevotella histicola, and Flavobacterium discriminated these diseases. Pathway analysis revealed glycoxylate, amino acid, purine, and sphingolipid metabolism alterations intersecting hypertension and hyperlipidemia.<br><br>CONCLUSIONS: This multi-omics landscape of comorbid disease pathways and biomarkers lays the foundation for precision diagnosis and treatment of prevalent cardiovascular conditions.},
}
@article {pmid41126179,
year = {2025},
author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG},
title = {A reference metagenome sequence of the lichen Cladonia rangiformis.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {319},
pmid = {41126179},
issn = {1741-7007},
support = {310030_212428//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; },
abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.<br><br>RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises&#x2009;~&#x2009;22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.<br><br>CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.},
}
@article {pmid41125958,
year = {2025},
author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G},
title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41125958},
issn = {2058-5276},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; },
abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.},
}
@article {pmid41125530,
year = {2025},
author = {Wang, X and Zhang, P and Suo, JS and Li, QJ and Wang, LZ and Zhang, Y and Wang, ZL},
title = {Clinical and microbiological insights into endogenous endophthalmitis: A ten-year study highlighting mNGS efficacy.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2025.10.002},
pmid = {41125530},
issn = {1995-9133},
abstract = {BACKGROUND: Endophthalmitis is an ophthalmic emergency. In recent years, the incidence of endogenous endophthalmitis (EE) has increased. This study aims to elucidate the clinical characteristics and risk factors associated with the visual prognosis of EE.<br><br>METHODS: This study included 111 patients (121 eyes) diagnosed with EE who received intraocular and systemic treatment at Huashan Hospital, Fudan University, between January 2014 to December 2023. We conducted a comprehensive review of the demographic and clinical characteristics of the cohort and analyzed the risk factors linked to poor visual prognosis.<br><br>RESULTS: A total of 111 patients (121 eyes) were included in this study, of whom 101 eyes (83.5&#xa0;%) had identifiable pathogenic microorganisms, with Klebsiella pneumoniae (KP) was the most common pathogen. Compared to conventional culture methods (sensitivity 47.6&#xa0;%), metagenomic next-generation sequencing (mNGS) demonstrated significantly higher sensitivity (97.6&#xa0;%) in vitreous samples. Outcome analysis indicated that mNGS played a critical role in guiding clinical antibiotic adjustments, and patients receiving targeted therapy showed significant visual improvement (P&#xa0;=&#xa0;0.002), with stable systemic recovery. Furthermore, vitreous surgery had a positive effect on visual prognosis (P&#xa0;<&#xa0;0.001). Regression analysis revealed that poor initial visual acuity (VA) (OR: 20.622, 95&#xa0;% CI: 3.894-109.2) and KP infection (OR: 3.398, 95&#xa0;% CI: 1.096-10.538) were independent risk factors for poor final VA.<br><br>CONCLUSION: Our findings identify KP as the most common causative pathogen of EE. Infections caused by KP and poor initial VA are significant risk factors for poor visual outcomes. Looking ahead, mNGS holds promise as a crucial tool for the clinical diagnosis of EE.},
}
@article {pmid41124971,
year = {2025},
author = {Gao, Y and Liu, Z and Sun, Y and Wang, J and Wu, X and Lu, X and Zhen, G},
title = {Mitigating perfluorooctanoic acid inhibition in electrochemically-assisted spiral upflow anaerobic membrane reactor for wastewater treatment: EPS interaction-desorption dynamics and metabolic pathway reconstruction.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124761},
doi = {10.1016/j.watres.2025.124761},
pmid = {41124971},
issn = {1879-2448},
abstract = {The widespread occurrence of perfluorooctanoic acid (PFOA) in industrial wastewater poses a major challenge to anaerobic treatment systems due to its chemical stability and persistence. Here, an electrochemical spiral upflow anaerobic membrane reactor (EC-SU-AnMBR) was developed by integrating a Ru-Ir/Ti-mesh-wrapped hollow-fiber membrane anode and a spiral Ti-mesh cathode to facilitate PFOA desorption and detoxification. PFOA readily accumulated in tightly bound extracellular polymeric substances (EPS) under open-circuit mode via hydrophobic interactions and electrostatic adsorption, disrupting anaerobic granular sludge (AnGS) structure and impairing microbial functionality. Electrochemical regulation (closed-circuit) effectively alleviated PFOA inhibition, achieving COD removal of 80.7 % (vs. 66.7 %) and a 1.5-fold higher CH4 recovery (227.7 vs. 140.8 mL/g COD/d). Electric field-migration and bioanode-membrane interception/oxidation together weakened PFOA-AnGS binding capability by altering EPS structural stability and interaction-desorption dynamics, decreasing PFOA retention rate in the bioreactor from initial 60.4 % to 2.1 % (p < 0.01) and reinforcing sludge regranulation. Further analysis demonstrated that the bioelectrocatalysis upregulated the relative abundance of functional genes involved in glucose metabolism (pfk, por, and ackA) and methanogenesis (fwd, mtr, and mcr) by selectively enriching hydrolytic/acidogenic bacteria and syntrophic-methanogenic consortia (Smithellaceae, Kosmotogaceae, and Methanotrichaceae) at both bioelectrodes. This study proposes a promising EC-SU-AnMBR system for the sustainable treatment of PFOA-contaminated wastewater and elucidates the metagenome-informed metabolic adaptation mechanisms under PFOA stress.},
}
@article {pmid41124778,
year = {2025},
author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L},
title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.},
journal = {EBioMedicine},
volume = {121},
number = {},
pages = {105978},
doi = {10.1016/j.ebiom.2025.105978},
pmid = {41124778},
issn = {2352-3964},
abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.<br><br>METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.<br><br>FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P = 3 &#xd7; 10[-4]), but not &#x3b2;-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P < 2 &#xd7; 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 &#xd7; 10[-6]; P. distasonis P = 5 &#xd7; 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).<br><br>INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5&#x3b1;-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.<br><br>FUNDING: See Acknowledgements.},
}
@article {pmid41124743,
year = {2025},
author = {Chu, S and Chen, Y and Xu, Z and Zhou, J and Li, K and Zhang, Q and Qian, M and Han, J and Qu, D},
title = {Metagenomic analysis of bacterial fitness and plasmids carrying blaTEM-1 and virulence genes before and after cleaning and disinfection in pig slaughterhouses.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140168},
doi = {10.1016/j.jhazmat.2025.140168},
pmid = {41124743},
issn = {1873-3336},
abstract = {The identification of antibiotic resistance genes (ARGs), virulence genes, and pathogens in animal slaughterhouses poses a major threat to human health. However, limited data is available about the contamination and dissemination of ARGs in commercial pig slaughterhouses before and after disinfectant application. In this study, we used metagenomics and plasmid profiling to analys ethe effect of quaternary-ammonium-based cleaning and disinfection (C&amp;D) on the microbiota, antibiotic resistance genes (ARGs), and virulence genes (VFs) in a pig slaughterhouse. According to results C&amp;D effectively reduced the total microbial population and abundance of ARGs. However, the prevalence of disinfectant-resistant bacteria, particularly Escherichia coli, increased dramatically from 5.9 % to 14.9 %. Additionally, the clinically significant β-lactamase gene blaTEM-1 remained intact throughout C&amp;D process. The persistence of blaTEM-1 is primarily facilitated by low-fitness-cost IncR-type plasmids (pTZ17 and pSB24), which are characterised by their simplified structures that have no effect on bacterialgrowth or motility and exhibit stability in the absence of antibiotics. On the other hand, the high-virulence IncFIB plasmid (pYA21) harbors numerous ARGs and VFs. Despite their low survival rate after C&amp;D, the remaining bacteria may pose an even greater risk. The results suggest that current disinfection protocols may unintentionally promote the persistence and dissemination of resistance plasmids with potential fitness or economic advantages. Our findings highlight the need of integrating plasmid ecology and virulence profiling into standard surveillance practices, which will enhance disinfection strategies and help to mitigate the spread of antimicrobial resistance.},
}
@article {pmid41124226,
year = {2025},
author = {Barcytė, D and Žihala, D and Eliáš, M},
title = {Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles.},
journal = {PLoS genetics},
volume = {21},
number = {10},
pages = {e1011901},
doi = {10.1371/journal.pgen.1011901},
pmid = {41124226},
issn = {1553-7404},
abstract = {Mitochondria and plastids of various lineages exhibit genetic code alterations. However, the knowledge of the diversity and occurrence, mechanistic underpinnings, and evolutionary origins of codon reassignments in organelles remains incomplete. To address this gap, we focused on organelles of the neglected green algal class Pedinophyceae, as well as pedinophyte-derived secondary plastids of green-coloured dinoflagellates (peDinoflagellates). We isolated and characterized a novel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp. nov., and phenotypically documented the previously sequenced but morphologically uncharacterized strain YPF-701, herein described as Akinorimonas japonica gen. et sp. nov. Based on phylogenetic analyses, both new taxa were classified into the expanded family Resultomonadaceae. We sequenced the organellar genomes of O. okinawensis, and utilizing existing raw (meta)genomic data we assembled organellar genome sequences from other previously unexplored pedinophyte lineages. Bioinformatic analyses of the expanded set of pedinophyte organellar genomes painted a complex picture of their genetic code landscape. Concerning mitochondria, the stop-to-Trp reassignment of the UGA codon turned out to have evolved multiple times in pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shown to be apomorphic for the whole order Marsupiomonadales. The latter has additionally converted UUA and UUG into termination codons, relying on specific mutations in the mtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methionine rather than the standard isoleucine, and an analogous reassignment seems to be evolving also in plastids of two separate pedinophyte lineages. Finally, apart from the previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids have switched the meaning of the AGA/AGG codons from arginine to another amino acid (most likely alanine), and have modified their pRF2 protein to mediate translation termination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.},
}
@article {pmid41123794,
year = {2025},
author = {Xiong, L and Liu, X and Zhang, L and Chen, W and Mo, Q and Sun, C},
title = {Q fever sternum osteomyelitis in a patient with history of cardiovascular surgery: A case report from China.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41123794},
issn = {1435-4373},
abstract = {This article reports a rare case of sternal osteomyelitis caused by Coxiella burnetii. The patient, a 59-year-old male with a history of aortic dissection and hypertension, had undergone ascending aorta replacement and aortic valvuloplasty. He was admitted in May 2022 due to a chest mass that had been enlarging since its discovery in October 2021. Despite antibiotic treatment, the symptoms did not improve, and he experienced recurrent low-grade fevers. Upon admission, CT imaging revealed multiple mediastinal lymph node enlargements and a cystic shadow anterior to the sternum handle. The infection was confirmed as Coxiella burnetii through surgical debridement and metagenomic next-generation sequencing (mNGS). The treatment was subsequently changed to doxycycline and hydroxychloroquine. Positron emission computed tomography with 18 F-fluorodeoxyglucose ([18 F] FDG PET/CT) imaging showed that the infection was localized to the sternum, excluding vascular and implant infections. The patient completed an 18-month course of antibiotics, leading to controlled infection and normalized renal function. This case highlights the complexities of diagnosing and managing Q fever osteomyelitis in patients post-cardiovascular surgery, demonstrating the crucial roles of mNGS and [18 F] FDG PET/CT in rapid diagnosis and effective treatment. These findings provide valuable insights and guidance for managing similar cases in the future.},
}
@article {pmid41123363,
year = {2025},
author = {Yue, Z and Zhang, J and Xu, W and Peng, L and Liu, T and Sheng, S and Tao, Y and Zeng, L and Zhao, Z and Alberoni, D and Baffoni, L and Zhang, Q and Liu, B and Li, Q and Zhang, J and Zou, Y},
title = {CNPS.cycle: streamlining shotgun metagenomic data analysis for biogeochemical cycles.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0102125},
doi = {10.1128/msystems.01021-25},
pmid = {41123363},
issn = {2379-5077},
abstract = {UNLABELLED: Shotgun metagenomic data analysis for investigating biogeochemical cycles in the environment remains challenging, primarily due to the steep learning curve, intensive time investment, and high computational demands, all of which pose significant barriers for many researchers. We present a new R package called "CNPS.cycle," designed to streamline the interpretation of shotgun metagenomic data related to biogeochemical processes, complete with visually informative outputs. This comprehensive package comprises four distinct analysis modules, focused on carbon, nitrogen, phosphorus, and sulfur cycling. Users can easily utilize the package by uploading annotation result files derived from shotgun metagenomic data, specifically those based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database. The package then automates essential steps, including data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; β-diversity analysis; and, finally, data visualization. The outcome is a comprehensive analysis revealing differentially abundant genes and functionally significant microbial entities associated with the carbon, nitrogen, phosphorus, and sulfur cycles, presented in the form of tables and high-quality images. This tool will provide profound insights into the relationship between soil microorganisms and elemental chemical cycles, thereby advancing our comprehension of soil ecosystems. For accessibility, the CNPS.cycle package is available on GitHub (https://github.com/yuezhengfu/CNPS.cycle), where detailed instructions on its usage can be found in the project's GitHub page (https://github.com/yuezhengfu/CNPS.cycle/wiki).<br><br>IMPORTANCE: The "CNPS.cycle" R package offers significant environmental implications by simplifying the analysis of shotgun metagenomic data related to biogeochemical cycles. Its automated workflow identifies key genes and microbes involved in carbon, nitrogen, phosphorus, and sulfur cycling, enhancing our understanding of microbial contributions to ecosystem functions. This tool enables researchers to explore microbial-mediated nutrient cycling more efficiently, supporting informed decisions in environmental management and climate change mitigation. By providing accessible, high-quality outputs, "CNPS.cycle" facilitates data-driven insights into the interplay between microbes and global biogeochemical processes.},
}
@article {pmid41123352,
year = {2025},
author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL},
title = {Metagenomic study of food waste anaerobic digestion.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208725},
doi = {10.1128/spectrum.02087-25},
pmid = {41123352},
issn = {2165-0497},
abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.},
}
@article {pmid41122951,
year = {2025},
author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH},
title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70062},
doi = {10.1111/1755-0998.70062},
pmid = {41122951},
issn = {1755-0998},
support = {//U.S. National Science Foundation/ ; },
abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.},
}
@article {pmid41122237,
year = {2025},
author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT},
title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20232},
pmid = {41122237},
issn = {2167-8359},
mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; },
abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.},
}
@article {pmid41121668,
year = {2025},
author = {Enagbonma, BJ and Modise, DM and Babalola, OO},
title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70085},
doi = {10.1002/mbo3.70085},
pmid = {41121668},
issn = {2045-8827},
support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; },
mesh = {*Sorghum/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fabaceae/growth &amp; development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth &amp; development ; *Edible Grain/growth &amp; development/microbiology ; Agriculture/methods ; },
abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.},
}
@article {pmid41121143,
year = {2025},
author = {Zhou, H and Li, X and Mao, Y and Chen, Q and Zhu, D and Liu, C and Yao, Y and Yao, Y and Yu, Y and Feng, Y},
title = {Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1149},
pmid = {41121143},
issn = {1479-5876},
support = {82072241//National Natural Science Foundation of China/ ; 82272338//National Natural Science Foundation of China/ ; 2022YFC2504502//Key R&amp;D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//Research and Development Program of Zhejiang Province/ ; 2024C03187//Research and Development Program of Zhejiang Province/ ; },
mesh = {Humans ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Acinetobacter baumannii/genetics/pathogenicity ; *Pneumonia/microbiology ; Klebsiella pneumoniae/genetics/pathogenicity ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/pathogenicity ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has emerged as an indispensable diagnostic tool for infectious diseases. The disparity in virulence and antimicrobial resistance among strains of the same species requires mNGS to reach strain-level resolution.<br><br>METHODS: To compare the subtyping performance between mNGS and culture, thirty bronchoalveolar lavage fluid (BALF) or blood specimens positive by culture were sequenced using the Illumina NextSeq platform, while whole genome sequencing (WGS) was conducted on the corresponding cultured colonies. Additionally, thirty BALF specimens underwent both mNGS and Oxford&#xa0;nanopore technology (ONT)-based metagenomic third-generation sequencing (mTGS) to compare the subtyping efficacy of the two platforms. To characterize the strain-level composition of pneumonia pathogen Acinetobacter baumannii and Klebsiella pneumoniae, 185 BALF specimens from three hospitals were analyzed by mNGS.<br><br>RESULTS: WGS of the cultured colonies yielded identical subtyping results to mNGS at the level of clonal complex (CC). Although mNGS and mTGS predicted largely consistent primary CCs, mTGS demonstrated less accuracy and precision in CC identification. Co-infections at the CC level were detected in 5.40% of&#xa0;A. baumannii-positive and 19.55% of&#xa0;K. pneumoniae-positive BALF specimens. CC composition differed markedly according to bacterial load and between primary and secondary CCs in co-infection specimens. Antimicrobial resistance profiles remained constant for patients with single-infection but varied for those with co-infection. Spatial and temporal consistency of CC composition was observed within individual patients.<br><br>CONCLUSIONS: The heterogeneity in virulence and antimicrobial resistance among CCs, together with the prevalence of strain-level co-infections, highlights the need to extend pathogen identification to the strain level. Under current technical conditions, mNGS is a more suitable subtyping tool compared to culture and mTGS.},
}
@article {pmid41121093,
year = {2025},
author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S},
title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {447},
pmid = {41121093},
issn = {1478-811X},
support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND &amp; AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.<br><br>METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.<br><br>RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.<br><br>CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.},
}
@article {pmid41120531,
year = {2025},
author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P},
title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36670},
pmid = {41120531},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; },
abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.},
}
@article {pmid41120014,
year = {2025},
author = {Zhang, L and Zhang, Y and Li, YY and Dou, Q and Peng, Y},
title = {Sequential oxygen intervention drives novel AOB-DGAOs interaction network enabling advanced nitrogen removal in simultaneous partial nitrification and endogenous denitrification (SPNED) process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133529},
doi = {10.1016/j.biortech.2025.133529},
pmid = {41120014},
issn = {1873-2976},
abstract = {The simultaneous partial nitrification and endogenous denitrification (SPNED) process, driven by ammonia-oxidizing bacteria (AOB) and denitrifying glycogen-accumulating organisms (DGAOs), shows significant potential for low-carbon wastewater treatment. However, rapid startup and efficiency are challenged by persistent nitrite-oxidizing bacteria (NOB) proliferation under low NH4[+]-N conditions and dissolved oxygen depletion of intracellular polyhydroxyalkanoates (PHA) in DGAOs. Here, a sequential oxygen intervention strategy is innovatively proposed: DGAOs population dominance was first established through anaerobic/anoxic mode, followed by a mid-position aerobic phase to construct a DGAOs-dominated AOB-DGAOs interaction network. SPNED startup was achieved within 46 days with > 99 % nitrogen removal efficiency. Co-occurrence networks and metagenomics revealed functional bacterial cooperation enabling carbon-efficient nitrogen removal. Results demonstrated that enriched DGAOs (abundance increased from 9.22 % to 28.25 %) preferentially consumed NO2[-]-N over oxygen under microaerobic conditions, starving NOB and creating a low-competition niche for AOB. Consequently, AOB abundance surged 22.69-fold within 16 days. Correspondingly, AOB-generated low-electron-demand NO2[-]-N reduced endogenous electron (NADH from PHA degradation) requirements for DGAOs denitrification. Furthermore, Candidatus Contendobacter (NO2[-]-N → NO) and Candidatus Competibacter (NO → N2) within DGAOs potentially executed stepwise denitrification, avoiding NADH loss through intra-community substrate competition. Coupled with subsequent oxygen intervention, activation of β-oxidation (151.4 % up-regulation in key enzyme) and TCA cycle (96.0 % increase in α-ketoglutarate dehydrogenase) in DGAOs boosted intracellular NADH levels 1.76-fold. This NADH-rich environment enhanced DGAOs functionality and sustained enrichment, stabilizing the AOB-DGAOs network for advanced nitrogen removal. This study proposes a previously underappreciated NOB-inhibition function of DGAOs, offering a novel strategy for efficient endogenous carbon utilization, advanced nitrogen removal, and operational stability.},
}
@article {pmid41118772,
year = {2025},
author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.09.014},
pmid = {41118772},
issn = {1934-6069},
abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.},
}
@article {pmid41118252,
year = {2025},
author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z},
title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02690},
pmid = {41118252},
issn = {1588-2640},
abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.},
}
@article {pmid41117817,
year = {2025},
author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M},
title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {325},
pmid = {41117817},
issn = {1432-072X},
mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; },
abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.},
}
@article {pmid41117699,
year = {2025},
author = {Xie, H and Zhang, X and Liu, X},
title = {The Co-Metabolic Bioremediation of Benzo[a]pyrene Contaminated Soil by Achromobacter xylosoxidans B-2 and Its Effect on Indigenous Microbial Community.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.24576},
pmid = {41117699},
issn = {1522-7278},
support = {2023YFC3709000//National Key Research and Development Program of China/ ; 2018YFC1800600//National Key Research and Development Program of China/ ; 21677093//National Natural Science Foundation of China/ ; 21806100//National Natural Science Foundation of China/ ; },
abstract = {Benzo[a]pyrene (BaP) is a persistent polycyclic aromatic hydrocarbon (PAH) that poses significant environmental and health risks. Co-metabolic bioremediation, which uses additional carbon sources to enhance microbial degradation, offers a promising approach for BaP removal. This study investigated the effects of different co-metabolic carbon sources on the growth of Achromobacter xylosoxidans B-2 and its efficiency in degrading BaP in both mineral salt medium (MSM) and BaP-contaminated soil. The addition of supplementary carbon sources, particularly starch and salicylic acid, significantly enhanced strain B-2 growth and BaP removal in MSM (p < 0.05), with the highest degradation rate reaching 46.35% in the starch-supplemented group. In soil, salicylic acid and starch also markedly improved BaP degradation, achieving 47.99% and 23.53% removal (both p < 0.01) after 30 days, respectively, compared to only 9.78% in the BaP-only group. Metagenomic analysis revealed that co-substrate amendments significantly altered soil microbiota, enriching PAH-degrading genera such as Achromobacter, especially the introduced A. xylosoxidans. This enrichment was accompanied by reduced overall microbial diversity, indicating strong selective pressure from the amendments. Functional gene profiling based on metagenomic data indicated an increased abundance of key PAH-degrading enzymes, including dioxygenases and dehydrogenases, in response to co-substrate addition. Redundancy analysis further indicated that environmental factors such as pH, organic matter, and phosphorus were significantly correlated with microbial community composition and BaP degradation efficiency. These findings demonstrate that co-metabolism not only enhances BaP removal but also drives functional and ecological changes in soil microbiota, providing mechanistic insight and practical guidance for improved bioremediation strategies.},
}
@article {pmid41117680,
year = {2025},
author = {Karakayalı, EM and Tuğlu, M&#x130;},
title = {The contribution of probiotics to combined cellular therapy in skin wound healing in diabetic rats.},
journal = {Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma &amp; emergency surgery : TJTES},
volume = {31},
number = {10},
pages = {925-936},
doi = {10.14744/tjtes.2025.37711},
pmid = {41117680},
issn = {1307-7945},
mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Wound Healing/drug effects ; Rats ; *Diabetes Mellitus, Experimental/complications ; Male ; Skin/injuries ; *Cell- and Tissue-Based Therapy/methods ; },
abstract = {BACKGROUND: Diabetes-related wound care is still a major issue due to chronic and non-healing ulcers that are prone to infection and ultimately amputation. In recent years, cellular therapy (CT) products such as mesenchymal stem cells (MSC), platelet-rich plasma (PRP), and stromal vascular fraction (SVF) have been widely used. A combined cellular therapy (CCT) has not yet been tested as a triple combination, although its use alone and in dual combinations has been investigated. Probiotics (PB) accelerate healing by altering the intestinal microbiota. This study aims to examine the role of PB in enhancing the effects of CCT on diabetic wound healing.<br><br>METHODS: A 1&#xd7;1 cm2 full-thickness cutaneous wound was created after administering 40 mg/kg streptozotocin intraperitoneally (STZ i.p.) to induce a diabetic (DB) animal model. Animals were divided into four groups: DB, DB+PB, DB+CCT, and DB+CCT+PB, each with six adult Albino rats. The wound edges were treated with a total of 300 &#xb5;L of solution, consisting of 30 &#xb5;L each of 100 &#xb5;L 1&#xd7;106 MSC, 100 &#xb5;L SVF, and 100 &#xb5;L PRP as CCT. PB was administered orally at a dose of approximately 200 mg daily. Histochemical analyses were performed using hematoxylin and eosin (HE) and Masson's trichrome (MT). Immunohistochemical analyses were conducted for endothelial nitric oxide synthase (eNOS), Caspase-3, interleukin-10 (IL-10), vascular endothelial growth factor (VEGF), and Collagen I. The intestinal microbiome was examined through metagenomic analyses of taxonomic structure.<br><br>RESULTS: Combined cellular therapy provided more effective and faster healing in DB animals. It was discovered that PB further accelerated this process, leading to greater improvement. CCT was observed to reverse high eNOS, Caspase-3, and IL-10 expression, as well as low VEGF and Collagen I levels. Moreover, PB therapy significantly enhanced the positive effects of CCT. CCT in combination with PB significantly improved wound healing by preventing oxidative stress, apoptosis, and inflammation, while promoting vascularization and collagen organization.<br><br>CONCLUSION: Probiotic support was considered important for diabetic wound healing and was suggested to improve patients' quality of life.},
}
@article {pmid41117333,
year = {2025},
author = {Naureckas Li, C and Jordan, N and Haymond, S and Koscinski, D and Jhaveri, R},
title = {Direct cost savings associated with reduction in plasma metagenomic sequencing.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10329},
pmid = {41117333},
issn = {1559-6834},
abstract = {Following recognition that our hospital had higher use of plasma metagenomic next-generation sequencing than our peers, we implemented a process for approval by infectious diseases before test collection. This intervention is calculated to result in a direct cost savings of $79,505-$84,057/year, driven mainly by reduced laboratory costs.},
}
@article {pmid41115930,
year = {2025},
author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK},
title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {199},
pmid = {41115930},
issn = {2055-5008},
support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs &amp; derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Fusobacterium nucleatum/isolation &amp; purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation &amp; purification ; Porphyromonas gingivalis/isolation &amp; purification ; },
abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.},
}
@article {pmid41115834,
year = {2025},
author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK},
title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70216},
doi = {10.1111/1758-2229.70216},
pmid = {41115834},
issn = {1758-2229},
support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation &amp; purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.},
}
@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}
@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}
@article {pmid41114582,
year = {2025},
author = {Zhang, Z and Wang, Z and Teng, P and Yu, T and Zhang, Y},
title = {Oxygen-tolerant nitrogen fixation in a marine alga-colonizing Planctomycetota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131625},
doi = {10.1128/aem.01316-25},
pmid = {41114582},
issn = {1098-5336},
abstract = {UNLABELLED: The microbiomes colonizing macroalgal surfaces orchestrate nutrient fluxes and symbiotic interactions within the algal environment. Among these communities, Planctomycetota are often dominant taxa. Although nitrogenase (nif) gene clusters have been identified in Planctomycetota isolates and metagenome-assembled genomes, functional validation of nitrogen fixation in pure culture has remained elusive. Moreover, the mechanisms enabling these bacteria to overcome oxygen sensitivity and fix nitrogen in algal-associated oxic niches remain unexplored. Here, we isolated Crateriforma sp. HD03, a Planctomycetota strain from the surface of Saccharina japonica (kelp), and provided the first experimental evidence of nitrogen-fixing activity in pure-cultured Planctomycetota. Strain HD03 harbors a complete nifHDKBEN gene cluster and exhibits a remarkable nitrogen fixation rate of 14.2 ± 1.5 nmol C2H4/(10[7] cells)/h under aerobic conditions. Genomic and physiological analysis reveals a suite of adaptations that likely mitigate oxygen stress, including genes associated with biofilm formation, hopanoid lipid synthesis, FeSII protein, hydrogenase, and bacterial microcompartments. Notably, while strain HD03 demonstrates oxygen-tolerant nitrogen fixation in pure culture, co-culture experiments with kelp under a photoperiod revealed that nifH (nitrogenase reductase gene) expression peaks during the low-oxygen dark phase, indicating that HD03 utilizes diurnal rhythms to temporally separate nitrogen fixation from photosynthetic oxygen production. A genomic survey of 142 Planctomycetota strains from NCBI GenBank database and HD03 identified two distinct clades harboring complete nifHDK gene clusters, suggesting a nitrogen-fixing potential across the phylum. By bridging the gap between genomic potential and functional validation, this study establishes Planctomycetota as important but underappreciated contributors to marine nitrogen input.<br><br>IMPORTANCE: Planctomycetota are abundant colonizers of macroalgal surfaces, yet their role in nitrogen fixation has remained unresolved despite genomic evidence of nitrogenase (nif) genes. Until now, no functional validation of nitrogen fixation in pure-cultured Planctomycetota has been reported. Here, we isolated Crateriforma sp. HD03 from kelp and for the first time demonstrated its ability to fix nitrogen in pure culture, confirming this key metabolic potential in marine Planctomycetota. Strain HD03 overcomes oxygen stress through a combination of biofilm formation and diurnal regulation of nifH expression, allowing nitrogen fixation under aerobic conditions to cope with the algal environment's oxic nature. Furthermore, genomic surveys revealed nitrogen fixation gene clusters across multiple Planctomycetota clades, suggesting widespread nitrogen-fixing capability in this phylum. Collectively, these findings identify Planctomycetota as important nitrogen providers in the ocean.},
}
@article {pmid41114530,
year = {2025},
author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N},
title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c07003},
pmid = {41114530},
issn = {1520-5118},
abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.},
}
@article {pmid41114048,
year = {2025},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.},
journal = {OBM transplantation},
volume = {9},
number = {3},
pages = {},
pmid = {41114048},
issn = {2577-5820},
abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.},
}
@article {pmid41114028,
year = {2025},
author = {Huang, H and Tong, Y and Hu, X and Liao, FK and Chen, R},
title = {The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1686503},
pmid = {41114028},
issn = {2296-858X},
abstract = {Metagenomic next-generation sequencing (mNGS) demonstrates high sensitivity, rapid diagnostic capabilities, and the potential to identify complex pathogens in periprosthetic joint infection (PJI) following arthroplasty, particularly when conventional culture methods are limited. mNGS enables the detection of polymicrobial infections and rare/fastidious pathogens, along with the ability to predict antimicrobial resistance (AMR) genes; however, the concordance between genotypic predictions and phenotypic resistance profiles requires further validation. In clinical practice, mNGS overcomes biofilm-related diagnostic barriers, facilitating early targeted antibiotic therapy and potentially reducing unnecessary revision surgeries, thereby lowering overall healthcare costs and improving patient outcomes. Nevertheless, its widespread adoption is hindered by high costs, lack of standardization, and risks of false-positive/false-negative results. Future research priorities include optimizing sample processing protocols, host DNA depletion, establishing diagnostic thresholds, and validating mNGS through integration with conventional methods. This review synthesizes recent advances in the diagnostic accuracy and clinical utility of mNGS for PJI, aiming to provide evidence-based insights for therapeutic decision-making and enhance the prevention and management of PJI.},
}
@article {pmid41114012,
year = {2025},
author = {Wang, H and Li, J and Huang, W},
title = {Case Report: Fever of unknown origin with hemophagocytic lymphohistiocytosis and intestinal hemorrhage-a successfully treated case of severe visceral leishmaniasis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1663551},
pmid = {41114012},
issn = {2296-858X},
abstract = {In recent years, some cases of severe visceral leishmaniasis (VL) in immunocompetent adults have gradually been reported. Hemophagocytic lymphohistiocytosis (HLH) and intestinal hemorrhage are two rare complications in patients with VL. Without treatment, the mortality rate of such patients is extremely high. We report a case of a 31-year-old immunocompetent male who initially presented with fever of unknown origin (FUO), later developed HLH and experienced multiple episodes of life-threatening intestinal hemorrhage. The diagnosis of visceral leishmaniasis was confirmed through metagenomic next-generation sequencing (mNGS). The patient was successfully treated with amphotericin B deoxycholate (AmB-D) and supportive care. During the two-year follow-up period, no new complications were found. This case highlights the value of mNGS in the diagnosis of complex infectious diseases and emphasizes the clinical significance of the multidisciplinary collaborative model for patients with VL and complex complications. It can provide a reference for the early diagnosis and comprehensive treatment of severe VL.},
}
@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}
@article {pmid41113669,
year = {2025},
author = {Onohuean, H and Naik Bukke, SP and Thalluri, C and Abass, KS and Choonara, YE},
title = {Exosome engineering for targeted therapy of brain-infecting pathogens: molecular tools, delivery platforms, and translational advances.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1655471},
pmid = {41113669},
issn = {2673-3129},
abstract = {Central nervous system (CNS) infections caused by pathogens such as HIV, Herpes simplex virus, Cryptococcus neoformans, and Toxoplasma gondii remain among the most difficult to treat due to the physiological barrier posed by the blood-brain barrier (BBB), pathogen latency, and systemic toxicity associated with conventional therapies. Exosome-based delivery systems are becoming a game-changing platform that can solve these therapeutic problems using their natural biocompatibility, minimal immunogenicity, and capacity to cross the BBB. This review current developments in exosome engineering that aim to make brain-targeted therapy for neuroinfectious illnesses more selective and effective. Much focus is on new molecular methods like pathogen-specific ligand display, aptamer conjugation, lipid modification, and click-chemistry-based surface functionalisation. These methods make it possible to target diseased areas of the brain precisely. Exosomes can also carry therapeutic payloads, such as anti-viral and antifungal drugs, gene editing tools like CRISPR/Cas9 and siRNA, and more. This makes them helpful in changing pathogens' persistence and the host's immunological responses. The paper tackle problems with translation, such as biodistribution, immunogenicity, GMP production, and regulatory issues. Future possibilities like synthetic exosomes, combinatory medicines, and delivery design that uses AI. The combination of nanotechnology, molecular biology, and infectious disease therapies shows that exosome engineering offers a new way to meet the clinical needs that are not satisfied in treating CNS infections.},
}
@article {pmid41113648,
year = {2025},
author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X},
title = {Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652229},
pmid = {41113648},
issn = {1664-302X},
abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.<br><br>RESULTS: Utilizing approximately 705.81&#x202f;GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.<br><br>CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.},
}
@article {pmid41113647,
year = {2025},
author = {Meng, Y and Xu, Y and Hu, D and Pan, Q and Weng, L and Huang, W and Zhao, J and Lan, W and Shi, Q and Yu, Y and Jiang, Y},
title = {Evaluating the effects of hospital wastewater treatment on bacterial composition and antimicrobial resistome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620677},
pmid = {41113647},
issn = {1664-302X},
abstract = {Hospital wastewater treatment systems (HWTS) are crucial in reducing the spread of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacterial pathogens in hospital wastewater. This study aims to evaluate the impact of HWTS on the changes of bacterial composition and the relative abundance of ARGs. We collected wastewater samples from influent and effluent in a university hospital, and performed metagenomic sequencing. The results showed that HWTS altered the bacterial composition, with a decrease in the proportion of Gammaproteobacteria. However, phylogenetic analysis of metagenome-assembled genomes showed that Mycobacterium and Zoogloea from influent and effluent had a close relationship. A total of 140 non-redundant ARGs were identified based on open reading fragments analysis, with beta-lactam and aminoglycoside resistance genes being the most prevalent. The relative abundance of ARGs generally decreased after wastewater treatment (p < 0.0001), with 70.0% of genes that conferring resistance to "last-resort" antibiotics being undetectable in the effluent. However, the relative abundance of quaternary ammonium compounds resistance genes increased in the effluent. We identified that 66.4% of ARGs were located on plasmids, and 17.9% of ARGs were adjacent to mobile gene elements (MGEs), suggesting their potential for mobility. Subsequent analysis showed that ARGs originating from plasmids and adjacent to MGEs were negatively associated with their relative abundance reduction. In conclusion, this study provides a comprehensive evaluation of the impact of HWTS on composition of bacteria and the relative abundance of ARGs, highlighting the importance of effective wastewater treatment in combating the spread of antimicrobial resistance.},
}
@article {pmid41113646,
year = {2025},
author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M},
title = {Gut viral metagenomics identifies viral signatures and their role in depression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573851},
pmid = {41113646},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.<br><br>METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.<br><br>RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.<br><br>CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.},
}
@article {pmid41113645,
year = {2025},
author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D},
title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641185},
pmid = {41113645},
issn = {1664-302X},
abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.<br><br>METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.<br><br>RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.<br><br>CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.<br><br>TRIAL REGISTRATION: NCT05921409.},
}
@article {pmid41113638,
year = {2025},
author = {Verma, D and Zhang, Z and Liu, J},
title = {Editorial: Tobacco disease and biological control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1694523},
pmid = {41113638},
issn = {1664-302X},
}
@article {pmid41113400,
year = {2025},
author = {Ning, H and Feng, R and Wu, H and Sun, C},
title = {[Innovative Practices of Precision Nutrition in Obesity Intervention: From Theory to Application].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {4},
pages = {893-899},
pmid = {41113400},
issn = {1672-173X},
mesh = {Humans ; *Obesity/prevention &amp; control ; *Precision Medicine/methods ; Metabolomics ; Genomics ; Diet ; },
abstract = {Obesity has emerged as a critical global public health challenge, with an urgent need for effective prevention and control strategies. Traditional nutritional intervention approaches often overlook individual variability and dietary complexity, which limits their effectiveness in achieving precision-based prevention and control. In this context, nutritional intervention strategies are gradually shifting from population-based models to individualized precision nutrition models, which integrate and analyze multidimensional data to open new pathways for obesity prevention and control. The theoretical framework of precision nutrition is based on the recognition that individual heterogeneity in biological mechanisms underlies individual variations in nutritional needs. The research approaches in precision nutrition include genomics, epigenetics, metagenomics, metabolomics, and integrated multi-omics analyses. In terms of application, precision nutrition combines advanced external dietary exposure assessment tools-such as Internet-based dietary assessment systems and AI-driven image recognition-with omics-derived internal biomarkers to enable accurate quantification of dietary intake. Principles such as holistic dietary integrity, full coverage of dietary restrictions, optimized cooking methods, and chrononutrition are emphasized in intervention strategies. Future efforts in precision nutrition should focus on overcoming technical challenges, including thorough integration of multi-omics data and the development of intelligent decision-making systems. The goal is to move beyond generalized, "one-size-fits-all" model toward tailored, precision-based intervention. Precision nutrition will provide essential scientific and technological support for the Healthy China 2030 initiative and help usher in a new era of scientific and individualized obesity prevention and control.},
}
@article {pmid41112778,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20170},
pmid = {41112778},
issn = {2167-8359},
mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation &amp; purification/classification ; Metagenomics ; },
abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.},
}
@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation &amp; purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.<br><br>METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.<br><br>RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.<br><br>CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}
@article {pmid41112491,
year = {2025},
author = {Kumari V S, S and Potdar, V and Shinde, M and Parashar, D and Alagarasu, K and Cherian, S and Lavania, M},
title = {Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569523},
pmid = {41112491},
issn = {2000-2297},
abstract = {BACKGROUND: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear.<br><br>OBJECTIVE: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity.<br><br>DESIGN: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity.<br><br>RESULTS: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections.<br><br>CONCLUSION: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.},
}
@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.<br><br>METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.<br><br>RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.<br><br>CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}
@article {pmid41112053,
year = {2025},
author = {Li, P and Xie, L and Zheng, H and Feng, Y and Mai, F and Tang, W and Wang, J and Lan, Z and Lv, S and Jayawardana, T and Koentgen, S and Xu, S and Wan, Z and Chen, Y and Xu, H and Shen, S and Zhang, F and Yang, Y and Hold, G and He, F and El-Omar, EM and Yu, G and Chen, X},
title = {Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70065},
pmid = {41112053},
issn = {2770-596X},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine and reproductive disorder affecting women of reproductive age. While the gut microbiota has been implicated in PCOS pathophysiology, the role of microbial-derived metabolites as mediators of host-microbe interactions remains poorly defined. Here, we integrated untargeted gut metabolomics with metagenomic profiling in patients with PCOS and identified a marked depletion of 3,4-dihydroxyphenylacetic acid (DHPAA), a flavonoid-derived microbial catabolite. Oral administration of DHPAA ameliorated PCOS-like phenotypes in two mouse models by suppressing bone morphogenetic protein signaling and reducing anti-Müllerian hormone (AMH) levels. We found that DHPAA production depends on gut microbial degradation of dietary flavonoids. We further identified a bacterial species, Streptococcus thermophilus, consistently depleted in PCOS across two human cohorts and a mouse model, restored DHPAA levels and improved reproductive outcomes in mice. Conversely, a β-galactosidase-deficient mutant of S. thermophilus failed to confer these benefits, highlighting β-galactosidase as a critical enzyme in DHPAA biosynthesis. Our findings establish DHPAA as a key microbial metabolite linking diet, microbiota, and reproductive health, and propose its potential as a novel therapeutic candidate for PCOS.},
}
@article {pmid41112047,
year = {2025},
author = {Xu, M and Guan, S and Zhong, C and Ma, M and Tao, L and Huang, G},
title = {Characterizing the microbiome of "sterile" organs in experimental mice and evidence of translocation of bacteria from the gut to other internal organs.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70081},
pmid = {41112047},
issn = {2770-596X},
abstract = {Using culturomics and metagenomics, we demonstrate the existence of non-pathogenic microbiota in the internal organs of healthy experimental mice, challenging the traditional dogma of organ sterility. Based on the analysis of 104 commercially sourced mice (C57BL/6J, BALB/c, ICR), the study reveals that over 20% of the analyzed mice harbored a high microbial burden in the internal organs and identified a total of 463 microbial species. Several species, including Ligilactobacillus murinus, Alcaligenes faecalis, Micrococcus luteus, Pseudochrobactrum asaccharolyticum, Escherichia coli, and Microbacterium sp., were frequently identified and were abundant in the mouse tissues. Further investigation implies that microorganisms in the "sterile" tissues could be associated with the gut microbiota. Given the wide use of experimental mice in medical and biological research, these findings of resident microorganisms in the animal's internal organs raise concerns about potential variability in experimental outcomes.},
}
@article {pmid41112045,
year = {2025},
author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H},
title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70058},
pmid = {41112045},
issn = {2770-596X},
abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.},
}
@article {pmid41112040,
year = {2025},
author = {Johansen, PL and Chatzigiannidou, I and Berzina, L and Kristiansen, K and Brix, S},
title = {Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70075},
pmid = {41112040},
issn = {2770-596X},
abstract = {By combining ultra-deep short-read shotgun metagenomic sequencing with 5-sample co-assembly across 600 agricultural soil samples, we significantly enhanced the representation and recovery of microbial communities in both clay and sandy soils. Despite an average of 107 Gb clean reads per sample, projections indicated that 1-4 Tb per sample would be required to capture 95% of the microbial community. Co-assembly of five biological replicates markedly improved metagenomic recovery, yielding up to 3.7× more metagenome-assembled genomes, up to 95% more unique genes, and broader recovery of prokaryotic phyla compared to single-sample assemblies.},
}
@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}
@article {pmid41110713,
year = {2025},
author = {Wang, T and Zhang, Q and Li, J and Dan, Q and Peng, Y},
title = {Unlocking the potential of anaerobic ammonia oxidation: Enhancing nitrogen removal in municipal wastewater through strategic nitrate introduction and microbial synergy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133523},
doi = {10.1016/j.biortech.2025.133523},
pmid = {41110713},
issn = {1873-2976},
abstract = {Coordinating the utilization of raw carbon sources with anammox nitrogen removal is pivotal in mainstream wastewater treatment. A novel strategy was developed to enhance nitrogen removal and anammox performance by introducing nitrate into the anoxic stage of an anaerobic/aerobic/anoxic anammox process treating municipal wastewater. This strategy achieved a nitrogen removal efficiency of 97.6 ± 0.9 %, reducing effluent total inorganic nitrogen to 1.8 ± 0.9 mg/L at a high N loading rate (87.7 ± 1.4 g N/m[3]/d) and a low C/N (2.8). After nitrate introduction, anammox contribution increased to 58.9 % and the relative abundance of the anammox genus Candidatus Brocadia increased by 250 %. Metagenomic analysis revealed upregulation of key genes ackA and acs, supporting endogenous carbon storage and utilization by denitrifying glycogen-accumulating organisms (DGAOs). This cooperation between anammox bacteria and DGAOs provided potential for integrating anammox into the mainstream and nitrate wastewater treatment, paving the way for sustainable nutrient management.},
}
@article {pmid41110566,
year = {2025},
author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y},
title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148390},
doi = {10.1016/j.ijbiomac.2025.148390},
pmid = {41110566},
issn = {1879-0003},
abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.},
}
@article {pmid41110291,
year = {2025},
author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M},
title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109874},
doi = {10.1016/j.envint.2025.109874},
pmid = {41110291},
issn = {1873-6750},
abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.},
}
@article {pmid41109936,
year = {2025},
author = {Ali, A and Khattak, AI and Chawla, D and Hasan, F and Khan, H and Ali, MA and Moeez, A and Tanveer, S and Ubaidullah, and Afridi, MJ and Ikram, J and Hayat, S and Shah, FZ and Nadeem, A and Nadeem, MA and Mushtaq, A and Haroon, W and Bharadwaj, HR and Dahiya, DS and Mansoor, E},
title = {Diagnostic Performance of Metagenomic Next-Generation Sequencing (mNGS) and Culture in Infected Pancreatic Necrosis: A Systematic Review and Meta-Analysis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41109936},
issn = {1573-2568},
abstract = {BACKGROUND: Infected pancreatic necrosis (IPN) is a severe complication of acute pancreatitis, requiring prompt diagnosis. Conventional microbial culture, the current gold standard, has limitations in sensitivity and turnaround time. Metagenomic next-generation sequencing (mNGS) offers rapid, comprehensive pathogen detection, but its diagnostic performance for IPN remains unclear.<br><br>METHODS: We conducted a systematic review and meta-analysis following PRISMA-DTA guidelines, prospectively registered in PROSPERO (CRD420251008574). PubMed, Embase, and Web of Science databases were searched from inception to March 2025. Seven studies (313 patients) evaluating mNGS for IPN diagnosis were included, with four providing direct comparisons to culture. Pooled sensitivity, specificity, and area under the curve (AUC) were calculated using a random-effects model. Heterogeneity was assessed using I[2] statistics.<br><br>RESULTS: In double-arm analysis, mNGS showed significantly higher sensitivity (0.87, 95% CI: 0.72-0.95) than culture (0.36, 95% CI: 0.23-0.51), with comparable specificity (0.83 for both). The AUC for mNGS (0.92, 95% CI: 0.79-0.94) surpassed that of culture (0.52, 95% CI: 0.27-0.86). Single-arm analysis confirmed mNGS as a reliable standalone test (sensitivity: 0.86; specificity: 0.85; AUC: 0.89). A threshold effect (r&#x2009;= -&#xa0;0.991) indicated variability in diagnostic criteria across studies.<br><br>CONCLUSIONS: mNGS outperforms culture in diagnosing IPN, offering higher sensitivity and faster results. Its ability to detect diverse pathogens, including fastidious and polymicrobial infections, makes it a valuable tool for early intervention. However, challenges like cost, standardization, and interpretation persist. Future studies should focus on prospective validation and cost-effectiveness to integrate mNGS into routine clinical practice.},
}
@article {pmid41109511,
year = {2025},
author = {Wang, W and Wang, H and Zhang, Q and Li, L and Lian, X and Yin, C and Lin, Y and Li, Z and Wang, Y and Han, Z and Shen, F and Chen, X and Sun, R and Wang, T},
title = {Diagnosis of spinal infections caused by fastidious bacteria: a multicenter, retrospective observational study.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2025.10.019},
pmid = {41109511},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Identifying pathogens in pyogenic spinal infections is essential for guiding clinical treatment. However, the fastidious characteristics of certain bacteria often make traditional microbial culture methods ineffective, resulting in diagnostic delays and postponed intervention. In recent years, metagenomic next-generation sequencing (mNGS) has shown strong potential in analyzing complex microbial communities, offering a more advanced strategy for pathogen detection.<br><br>PURPOSE: Evaluating mNGS versus microbial culture for diagnosing fastidious bacteria in pyogenic spinal infections.<br><br>STUDY DESIGN: A multicenter, retrospective observational study.<br><br>PATIENT SAMPLE: We retrospectively reviewed clinical data from 553 patients diagnosed with spinal infections across four medical centers between December 2019 and December 2024.<br><br>OUTCOME MEASURES: Identification of fastidious bacteria in patients.<br><br>METHODS: All patients underwent imaging and standard laboratory testing. Specimens from infected sites obtained through puncture or surgery were analyzed using both microbial culture and mNGS. According to predefined diagnostic, inclusion, and exclusion criteria for fastidious bacteria, 49 patients (8.86%, 49/553) were identified with pyogenic spinal infections caused by fastidious organisms. We compared the diagnostic outcomes of mNGS with those of culture-based methods for detecting fastidious bacterial pathogens in spinal infections.<br><br>RESULTS: Among the 49 patients, mNGS yielded a positive detection rate of 87.76% (43/49), which was significantly higher than that of conventional culture methods at 16.33% (8/49) (&#x3c7;&#xb2;=12.683, p < 0.001). Among the 41 culture-negative cases, mNGS successfully identified fastidious bacteria in 37, corresponding to an effective supplementary detection rate of 90.24% (37/41). While culture identified 5 species of fastidious bacteria, mNGS detected 15, giving an effective pathogen supplementation rate of 66.7% (10/15). These 15 bacteria fell into two groups: the first included those that cannot be cultured using routine clinical media (26/43, 60.47%), and the second included those that may sporadically grow in standard cultures but tend to show low positivity (17/43, 39.53%). Out of the total 553 cases, 382 were culture-negative. Among these, 37 (37/382, 9.69%) were identified as fastidious bacteria via mNGS. mNGS yielded results within 48 hours, significantly faster than the 3-7 days typically required by culture methods.<br><br>CONCLUSIONS: In cases of pyogenic spinal infections caused by fastidious bacteria, mNGS demonstrated a higher detection rate, wider pathogen range, and significantly shorter turnaround compared to traditional microbial culture. The culture-independent approach of mNGS presents a distinct advantage in identifying fastidious pathogens.},
}
@article {pmid41109083,
year = {2025},
author = {Wu, W and Song, J and Wu, Q and Wu, X and Sun, N and Xia, X},
title = {Development and evaluation of CD45-conjugated magnetic particles-based host cell depletion for enhanced metagenomic next-generation sequencing in bloodstream infection.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1267},
number = {},
pages = {124823},
doi = {10.1016/j.jchromb.2025.124823},
pmid = {41109083},
issn = {1873-376X},
abstract = {Metagenomic next-generation sequencing (mNGS) enables unbiased detection of human pathogens without prior assumptions. However, the direct detection of bloodstream infection pathogens is limited by host DNA interference, leading to the clinical adoption of microbial cell-free DNA mNGS (plasma cfDNA mNGS). This study developed a host cell depletion method based on immunomagnetic separation using CD45-conjugated magnetic particles (CD45-MPs, termed the IP method) to reduce host DNA interference and enhance mNGS performance for bloodstream pathogen detection. In simulated samples, known concentrations of pathogens (intact Escherichia coli and Candida albicans cells, fragmented Staphylococcus aureus genomic DNA) were spiked into whole blood samples, serially diluted 10-fold, and divided into whole blood, plasma, and IP-treated groups. These groups were analyzed using hematological analysis, microscopic smear, DNA concentration measurement, relative quantification of GAPDH using qPCR, and mNGS. Results showed that CD45-conjugated magnetic particles effectively removed host cells from whole blood (reducing cell count by 99.9%). The results of nucleic acid measurement and qPCR indicated that the supernatant from IP-treated samples contained significantly lower host DNA compared to whole blood and plasma groups. mNGS detection of simulated samples demonstrated that the IP method enabled detection of pathogens at concentrations as low as 100 CFU/mL for E. coli and S. aureus, and 50 CFU/mL for C. albicans. In clinical testing of 77 samples from patients with suspected bloodstream infections, mNGS combined with the IP method showed significantly higher positivity rates than plasma cfDNA mNGS. In conclusion, CD45-conjugated magnetic particles effectively deplete human cells and enhance the clinical performance of mNGS on the detection of bloodstream infections.},
}
@article {pmid41108980,
year = {2025},
author = {Liu, C and Li, C and Guo, X and Wang, L and Wang, N},
title = {Swine farming emissions drive deterministic assembly of antibiotic resistance genes in receiving River: A new ecological perspective.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124803},
doi = {10.1016/j.watres.2025.124803},
pmid = {41108980},
issn = {1879-2448},
abstract = {Livestock farming constitutes a critical reservoir of antibiotic resistance genes (ARGs). Following the fertilization of manure, ARGs enter agricultural soils and subsequently migrate into riverine ecosystem via paddy water (PW), posing potential environmental and public health risks. Understanding the ecological processes behind the assembly of ARG profiles is crucial for predicting the dynamics of ARGs and guiding effective mitigation strategies, while research gaps persist regarding how exogenous inputs affect ARG assembly in receiving environments. This study integrated source fingerprinting via metagenomic sequencing with analytical frameworks from community ecology processes to determine the specific influence of livestock farming emissions on ARG assembly in receiving river. The research targeted intensive swine farming regions in the lower Yangtze River Basin in China, and systematically collected manure-impacted PW as pollution source, alongside receiving river water (RW) and sediment (RS) matrices. In the ecosystem, 946 ARGs belonging to 24 types were identified. Despite the elevated abundance of ARGs in RW relative to RS, the composition in RS closely resembled that in PW and was enriched in high-risk genes (e.g., acrE and acrF), resulting in a higher risk score for RS compared to RW (p < 0.01). Network topology analysis revealed characteristics indicative of exogenous-driven ARG transmission, including high modularity and intra-type clustering of ARGs within modules. Variance partitioning analysis (VPA) collectively revealed that ARGs in RW exhibited a greater potential for horizontal transfer, whereas host communities exerted a predominant influence on ARG distribution in RS. Neutral model yielded fits of R[2] = 0.197 and 0.175 for RW and RS, respectively. Meanwhile, a null model-based stochasticity ratio ranged 30.3 %∼42.7 %, jointly demonstrating that deterministic processes, particularly heterogeneous selection, dominated ARG assembly in the river ecosystem, with a more pronounced effect in sediments. Crucially, removal of PW-specific ARGs led to a marked increase in the contribution of neutral processes, confirming livestock emissions as the core driver shifting assembly towards determinism. Fast expectation-maximization microbial source tracking (FEAST) quantified the contribution of swine farming to ARGs in RW and RS at 12.35 % and 31.09 %, respectively. This study provided novel insights into the deterministic role of exogenous inputs in governing ARG assembly within receiving environments, thus offering theoretical support for developing targeted strategies to control ARG dissemination.},
}
@article {pmid41108960,
year = {2025},
author = {Han, C and Zhang, H and Guan, W and Li, L and Zhao, Y and Gao, C and Zhao, Z and Xing, Q and Yuan, A and Guo, D and Gao, Y and Qiao, J and Peng, Y and Zhong, C and He, J and Li, Z and Xiong, X},
title = {From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119205},
doi = {10.1016/j.ecoenv.2025.119205},
pmid = {41108960},
issn = {1090-2414},
abstract = {The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding.},
}
@article {pmid41108937,
year = {2025},
author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL},
title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105956},
doi = {10.1016/j.psj.2025.105956},
pmid = {41108937},
issn = {1525-3171},
abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.},
}
@article {pmid41108646,
year = {2025},
author = {Jeon, JY and Allen, NM and Black, AN and DeWoody, JA},
title = {Short-Read Pangenomes and Their Potential Utility in Population and Conservation Genomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70060},
doi = {10.1111/1755-0998.70060},
pmid = {41108646},
issn = {1755-0998},
abstract = {As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches developed for humans and model organisms are financially impractical for conservation genomic studies of threatened or endangered species due to the high costs associated with deep sequencing multiple individuals using long-read platforms. Here, by integrating metagenomic and iterative map-then-assemble approaches, we (1) propose novel workflows to construct graph pangenomes from multiple low-coverage short-read datasets; (2) benchmark these short-read pangenomes (both linear and graph) against a previously published long-read graph pangenome of the barn swallow; and (3) evaluate the utility of our workflows in population and conservation genomics. Our results indicate that economical short-read graph pangenomes can recover the vast majority of the variants identified through expensive long-read graph approaches, and that these variants accurately detect important biological signals (e.g., spatial structure and independent taxonomic delineations). These results mean that researchers can utilize their limited, conservation-oriented funding to more fully characterize all the variants in a particular gene pool for population-level analyses.},
}
@article {pmid41108124,
year = {2025},
author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ},
title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251370995},
doi = {10.1177/00220345251370995},
pmid = {41108124},
issn = {1544-0591},
abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.},
}
@article {pmid41107843,
year = {2025},
author = {Meki, IK and Ahn, KB and Dundon, WG and Settypalli, TBK and Leth, C and Steinrigl, A and Revilla-Fernández, S and Schmoll, F and Ceglie, L and Berete, K and Metlin, A and Dhingra, M and Nowotny, N and Cattoli, G and Lamien, CE},
title = {Novel multiplex family-wide PCR and Nanopore sequencing of amplicons (FP-NSA) approach for surveillance of influenza- and coronaviruses in humans and animals.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {123},
pmid = {41107843},
issn = {1756-994X},
mesh = {Humans ; Animals ; *Nanopore Sequencing/methods ; *Coronavirus/genetics/isolation &amp; purification/classification ; *Multiplex Polymerase Chain Reaction/methods ; *Influenza, Human/virology/diagnosis/epidemiology ; SARS-CoV-2 ; *Coronavirus Infections/virology/diagnosis ; *Orthomyxoviridae/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for initial virus identification. This study introduces a multiplex family-wide PCR coupled with Nanopore sequencing of amplicons (FP-NSA) for surveillance of novel and known zoonotic respiratory viruses, including influenza A and D viruses (IAV and IDV), alpha (α-), beta (β-), and gamma (γ-) coronaviruses (CoVs).<br><br>METHODS: This assay utilized primers in conserved regions of each virus group for multiplex reverse transcription (RT)-PCR coupled with the portable MinION device for rapid Nanopore sequencing. The FP-NSA was optimized using seven IAV subtypes, IDVs, and &#x3b1;- and &#x3b2;-CoVs. The analytical sensitivity of the FP-NSA was assessed using positive controls of known concentrations from each targeted viral family and validated using clinical samples and cell culture isolates from various host species and geographical origins. Potential novel viruses detected in the clinical samples, based on the FP-NSA, were further analyzed using metagenomics sequencing with the Sequence-Independent Single Primer Amplification (SISPA) approach.<br><br>RESULTS: The optimized FP-NSA assay efficiently detected all the targeted viruses singly as well as in co-infection scenarios of multiple respiratory viruses. Evaluation of the assay on 78 selected clinical and cell culture samples (from 184 initially screened) successfully detected IAVs; &#x3b1;-CoVs: porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) NL63, and HCoV-229E; &#x3b2;-CoVs: HCoV-OC43, severe acute respiratory syndrome (SARS)-CoV-(1), SARS-CoV-2, and MERS-CoV; and &#x3b3;-CoV infectious bronchitis virus (&#x3b3;-CoV_IBV) infections. Additionally, the FP-NSA assay discovered a novel &#x3b3;-CoV_IBV from Guinea that is phylogenetically distant from known genotypes using a SISPA metagenomics approach.<br><br>CONCLUSIONS: The assay's short PCR amplicons enable screening of samples within 4&#xa0;h, from PCR to sequencing and bioinformatics analysis, providing an adequate number of pathogens' reads. The portable MinION device makes the assay suitable for pathogen surveillance in disease hotspots and resource-limited regions such as low- and middle-income countries. Thus, the FP-NSA assay is a valuable tool for detecting potential novel and known zoonotic respiratory viruses in the targeted families across various host species.},
}
@article {pmid41106786,
year = {2025},
author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z},
title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.},
journal = {Fitoterapia},
volume = {187},
number = {},
pages = {106935},
doi = {10.1016/j.fitote.2025.106935},
pmid = {41106786},
issn = {1873-6971},
abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.},
}
@article {pmid41106415,
year = {2025},
author = {Grimm, SL and Kaufman, JT and Rice, DP and Whittaker, C and Bradshaw, WJ and McLaren, MR},
title = {Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101187},
doi = {10.1016/j.lanmic.2025.101187},
pmid = {41106415},
issn = {2666-5247},
abstract = {BACKGROUND: Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses.<br><br>METHODS: In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel.<br><br>FINDINGS: After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3&#xb7;8&#x2009;&#xd7;&#x2009;10[-10] to 2&#xb7;4&#x2009;&#xd7;&#x2009;10[-7] across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7&#xb7;87 million to $287&#x2009;000) and 29-fold (from $1&#xb7;98 million to $69&#x2009;100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0&#xb7;01% cumulative incidence.<br><br>INTERPRETATION: The large variation in viral relative abundance after controlling for epidemiological factors indicates that other sources of inter-study variation, such as differences in sewershed hydrology and laboratory protocols, have a substantial impact on the sensitivity and cost of W-MGS. Well chosen hybridisation capture panels can greatly increase sensitivity and reduce cost for viruses in the panel, but might reduce sensitivity to unknown or unexpected pathogens.<br><br>FUNDING: The Wellcome Trust, Open Philanthropy, and Musk Foundation.},
}
@article {pmid41106267,
year = {2025},
author = {Cai, F and Wang, Y and Xie, M and Li, G and Wang, S and Daygon, VD and Tian, D and Ni, G and Liu, X and Zhang, R and Lei, L and Yuan, Z and Guo, J and Zhang, X and Hu, S},
title = {Pyrogenic carbon-stimulated nitrate-dependent anaerobic methane oxidation: insights into redox activity and conductivity in anaerobic methanotrophic archaea metabolism and microbial dynamics.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124798},
doi = {10.1016/j.watres.2025.124798},
pmid = {41106267},
issn = {1879-2448},
abstract = {Pyrogenic carbon (PC) plays a critical role in regulating greenhouse gas emissions by influencing methanogenesis and methane oxidation in aquatic environments. However, its impact on nitrate-dependent anaerobic oxidation of methane (AOM), associated methane emissions, and the underlying mechanisms remain poorly understood. Here, we demonstrated that in nitrate-dependent AOM consortia amended with HNO3-treated biochar and graphite (representing redox-active and conductive forms of PC, respectively), AOM rates were significantly elevated by 2.7- and 4.4-fold, respectively, compared to unamended biotic controls. This enhancement was accompanied by a pronounced proliferation of anaerobic methanotrophic archaea, specifically "Candidatus Methanoperedens nitroreducens", along with elevated metabolic activity driven by enhanced electron transport and energy conservation, as indicated by significantly increased electron transfer system activity, total adenine nucleotide levels, and concentrations of key redox carrier F420. Metagenomic analysis revealed that PC addition reshaped microbial interactions. Notably, graphite facilitated the potential establishment of direct interspecies electron transfer between "Ca. M. nitroreducens" and coexisting denitrifying populations (Bacteroidota sp. and Ignavibacteriaceae sp.), while also fostering the formation of new interspecies networks that enabled division of labor within the denitrification pathway. These findings not only advance the mechanistic understanding of PC-facilitated methane mitigation in aquatic ecosystems but also suggest strategies for engineering AOM-based systems to optimize methane removal and nitrogen cycling in environmental applications.},
}
@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}
@article {pmid41104935,
year = {2025},
author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF},
title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150825},
doi = {10.1128/aem.01508-25},
pmid = {41104935},
issn = {1098-5336},
abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.},
}
@article {pmid41104113,
year = {2025},
author = {Kulaš, A and Lemonnier, C and Alric, B and Kahlert, M and Trobajo, R and Udovič, MG and Rimet, F},
title = {Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf171},
pmid = {41104113},
issn = {2730-6151},
abstract = {Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.},
}
@article {pmid41104112,
year = {2025},
author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK},
title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf169},
pmid = {41104112},
issn = {2730-6151},
abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.},
}
@article {pmid41103765,
year = {2025},
author = {Li, M and Bi, J and Wang, X and Li, H},
title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652652},
pmid = {41103765},
issn = {1664-302X},
abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.},
}
@article {pmid41103762,
year = {2025},
author = {Sheng, X and Zhu, J and Li, W and Wan, J and Wu, K and Yang, P and Duan, R and Yang, Z and Bai, J and Zheng, Y},
title = {Antimony-resistant PGPR mitigates Sb toxicity and accumulation in peppers by restructuring rhizosphere microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658223},
pmid = {41103762},
issn = {1664-302X},
abstract = {Plant growth-promoting rhizobacteria (PGPR) provide a sustainable biofertilizer strategy for remediating heavy metal-contaminated soils by enhancing plant stress resistance through rhizosphere microbiota interactions. However, the mechanisms by which PGPR modulate rhizosphere communities and plant growth under antimony (Sb) stress remain poorly understood. This study investigated the effects of inoculating Sb-tolerant Cupriavidus sp. S-8-2 in pepper (Capsicum annuum L.) cultivated under varying levels of Sb contamination (0, 500, 1,000 mg/kg), employing a combination of metagenomic profiling and physicochemical analyses. Pot experiments demonstrated that inoculation significantly enhanced plant growth and nutrient acquisition while alleviating oxidative stress in Sb-stressed plants. Crucially, it reduced Sb translocation, resulting in a 54.75% decrease in shoot Sb content, along with a 33.33% increase in leaf biomass and a 38.98% increase in root biomass under 1,000 mg/kg Sb treatment. In parallel, rhizosphere properties such as total nitrogen (TN), total phosphorus (TP), and soil organic matter (SOM) were improved, as evidenced by an 81.35% increase in acid phosphatase activity under the same Sb concentration. Microbiota analysis revealed that inoculation enriched stress-responsive bacterial phyla, such as Proteobacteria and Actinobacteria, as well as key functional genera associated with Sb tolerance (e.g., Ramlibacter) and nutrient cycling (e.g., Nitrospira), despite a decrease in alpha-diversity. Co-occurrence networks analysis indicated that inoculation significantly enhance node connectivity and mean degree in rhizosphere bacterial networks, reflecting an increase in structural complexity, especially under severe Sb stress (1,000 mg/kg). These findings demonstrate that Cupriavidus sp. S-8-2 enhances plant resistance to Sb by restructuring the rhizobacterial community and improving soil health, with reducing Sb accumulation in edible parts, thereby highlighting its potential as a biofertilizer for safe crop production in Sb-contaminated soils. For the first time, our study explored the potential of Sb-tolerant PGPR to alleviate Sb stress in pepper plants cultivated in Sb-polluted soils.},
}
@article {pmid41103722,
year = {2025},
author = {Menozzi, E and Geiger, M and Meslier, V and Fierli, F and Gilles, M and Chau, KY and David, A and Shahar Golan, R and Famechon, A and Koletsi, S and Morabito, C and Quinquis, B and Pons, N and Ehrlich, SD and Macnaughtan, J and Almeida, M and Schapira, AH},
title = {Exploring the relationship between GBA1 host genotype and gut microbiome in the GBA1 [L444P/WT] mouse model: implications for Parkinson's disease pathogenesis.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1546203},
pmid = {41103722},
issn = {1662-4548},
abstract = {BACKGROUND: Heterozygous variants in GBA1 are the commonest genetic risk factor for Parkinson's disease (PD), but penetrance is incomplete. GBA1 dysfunction can cause gastrointestinal disturbances and microbiome changes in preclinical models. Mounting evidence suggests that the microbiota-gut-brain axis is potentially implicated in PD pathogenesis. Whether the gut microbiome composition is influenced by host GBA1 genetics in heterozygosis has never been explored.<br><br>OBJECTIVES: This study aimed to evaluate whether heterozygosity for the GBA1 pathogenic L444P variant can cause perturbations in gut microbiome composition.<br><br>METHODS: Faecal samples collected from GBA1 [L444P/WT] and GBA1 [WT/WT] mice at 3 and 6&#x202f;months of age were analysed through shotgun metagenomic sequencing.<br><br>RESULTS: No differences in &#x3b1;- and &#x3b2;-diversities were detected between genotyped groups, at either time point. Overall, we found a little variation in the gut microbiome composition and functional potential between GBA1 [L444P/WT] and GBA1 [WT/WT] mice over time.<br><br>CONCLUSION: Host GBA1 genotype does not impact gut microbiome structure and composition in the presented GBA1 [L444P/WT] mouse model. Studies investigating the effect of a second hit on gut physiology and microbiome composition could explain the partial penetrance of GBA1 variants in PD.},
}
@article {pmid41103389,
year = {2025},
author = {Shi, G and Yan, P and Shen, S and Tang, P and Chen, P and Sun, L and Xing, S and Fang, C and Li, C and Lin, L and Zhang, C},
title = {The insight into instability mechanism of Jiangxiangxing Baijiu fermentation and the key functional regulation of Schizosaccharomyces pombe.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103085},
pmid = {41103389},
issn = {2590-1575},
abstract = {Jiangxiangxing Baijiu (JXXB) suffers from quality instability due to its complex spontaneous fermentation. This study compared fermented grains from excellent (Group-E) and normal (Group-N) workshops, identifying 28 volatiles as distinguished substances for quality. The core functional species were revealed by integrated meta-genomic and meta-transcriptomic sequencing analysis. Moreover, Schizosaccharomyces pombe and Acetilactobacillus jinshanensis were demonstrated as key functional contributors, while only Schi. pombe was highlighted active participation in both heap fermentation and pit fermentation. Notably, the proportions and doses of the functional yeasts, particularly Schi. pombe, were higher in Group-E, resulting in the higher quality. Furthermore, the industrial-scale bioaugmentation with Schi. pombe enhanced substrate utilization, elevated the production of flavor substances by 13.61 %, and improved the yield and excellent-quality proportion of base Baijiu by 32.18 % and 37.16 %, respectively. This study provided insights into the quality instability mechanism of JXXB, and fostered a foundation for ensuring consistent quality in solid-state fermentation.},
}
@article {pmid41102833,
year = {2025},
author = {Rodriguez, K and Ricci, F and Ni, G and Iram, N and Palfreyman, R and Gonzalez-Garcia, RA and Heffernan, J and Greening, C and Adame, MF and Marcellin, E},
title = {Abundant and active acetogens enhance the carbon dioxide sink of Blue Carbon ecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {207},
pmid = {41102833},
issn = {2049-2618},
support = {CE 200100029//Australian Research Council Centre of Excellence in Synthetic Biology/ ; },
mesh = {*Carbon Dioxide/metabolism ; Wetlands ; Soil Microbiology ; Carbon Cycle ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; Hydrogen/metabolism ; *Carbon Sequestration ; Bioreactors/microbiology ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; Photosynthesis ; Carbon/metabolism ; Ecosystem ; },
abstract = {BACKGROUND: Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO2) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal for chemosynthetic microbes such as acetogens.<br><br>RESULTS: In this study, we show that acetogens are abundant and active mediators of carbon sequestration in tidal wetland soils. We combined metagenomic analysis of CO2 fixation genes and reconstruction of microbial genomes with enrichment and analysis of gas-fermenting acetogens in bioreactors. Genome-resolved metagenomics revealed that diverse microbes can mediate carbon fixation, primarily through the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl pathway (WLP). These include various bacteria and archaea capable of reductive acetogenesis. Based on these findings, we established bacterial enrichment cultures from tidal wetland soils using hydrogen (H2) and CO2 as the sole energy and carbon sources. Bioreactor analysis revealed that these enrichments are dominated by clostridial acetogens that grow rapidly by converting CO2 into acetate and other products.<br><br>CONCLUSIONS: Collectively, these results reveal Blue Carbon ecosystems harbor microbial communities that can exclusively subsist by using CO2 as their sole electron acceptor and carbon source. This provides evidence for a novel carbon sink pathway within these ecosystems beyond the well-known mechanisms of photosynthetic carbon fixation and soil sequestration. Additionally, the discovery and enrichment of these chemosynthetic communities provide opportunities for developing further mechanisms of CO2 removal through industrial gas fermentation. Video Abstract.},
}
@article {pmid41102734,
year = {2025},
author = {Lv, Y and Zhang, L and Zhang, Y},
title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {208},
pmid = {41102734},
issn = {2049-2618},
support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; },
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; },
abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.<br><br>RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48&#x2009;&#xd7;&#x2009;(nxrA) and 1.28&#x2009;&#xd7;&#x2009;(aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.<br><br>CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.},
}
@article {pmid41102233,
year = {2025},
author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF},
title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36158},
pmid = {41102233},
issn = {2045-2322},
support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; },
abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.},
}
@article {pmid41102171,
year = {2025},
author = {Leu, AO and Woodcroft, BJ and McIlroy, SJ and Tyson, GW},
title = {Potential for aerobic hydrocarbon oxidation in archaea.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9188},
pmid = {41102171},
issn = {2041-1723},
mesh = {Oxidation-Reduction ; *Hydrocarbons/metabolism ; *Archaea/metabolism/genetics/classification ; Aerobiosis ; Phylogeny ; Genome, Archaeal ; Metagenome ; Gene Transfer, Horizontal ; Mixed Function Oxygenases/genetics/metabolism ; },
abstract = {Over the last decade, there have been significant advances in our understanding of anaerobic hydrocarbon oxidation in archaea. However, the ability to oxidise hydrocarbons aerobically has been described in bacteria but not yet in archaea. Here, we provide evidence supporting potential aerobic hydrocarbon oxidation ability in archaea belonging to a novel order within the class Syntropharchaeia, which we propose to name Candidatus 'Aerarchaeales'. This order is represented by six metagenome-assembled genomes (MAGs) spanning three genera that are found in terrestrial and marine ecosystems. In particular, MAGs belonging to a newly defined genus, Ca. 'Aerovita', encode a copper monooxygenase complex with homology to bacterial hydrocarbon monooxygenases. The presence of genes encoding other oxygen-dependent enzymes, such as haem-copper oxygen reductase, indicates that Ca. 'Aerovita' may be capable of aerobic respiration. Our findings suggest that horizontal gene transfer between archaeal and bacterial domains facilitated the evolution of aerobic hydrocarbon-oxidizing archaea.},
}
@article {pmid41101270,
year = {2025},
author = {Wang, H and Wu, Y and Zhang, Q and Li, X and Weng, H and Zhang, L and Peng, Y},
title = {Dynamic redox regimes drive metabolic versatility of a Candidatus Brocadia in municipal wastewater treatment.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124781},
doi = {10.1016/j.watres.2025.124781},
pmid = {41101270},
issn = {1879-2448},
abstract = {Deciphering the adaptive mechanisms of anaerobic ammonium-oxidizing (anammox) bacteria to redox dynamics is pivotal for overcoming critical bottlenecks in achieving carbon-neutral wastewater treatment. This study uncovers the survival strategy and response mechanisms of a Candidatus Brocadia strain (B. SW5) thriving in municipal wastewater treatment system with continuous anaerobic-aerobic-anoxic cycling. Isotopic labeling and metagenomic analyses confirmed that the B. SW5 adapts to fluctuating environmental stresses. Comparative genomic and transcriptomic analyses demonstrated that B. SW5 exhibits more comprehensive metabolic pathways than conspecific strains in single environments. Beyond fatty acid metabolism/transport, B. SW5 alleviates organics inhibition by upregulating enzymes for aromatic compound and antibiotic efflux/catabolism in anaerobic stage. In addition to the classical superoxide dismutase-catalase antioxidant system, B. SW5 employs a complete aerobic respiratory chain containing cbb3-type cytochrome c oxidase to directly scavenge intracellular oxygen during aerobic stage. Furthermore, B. SW5 encodes and expresses multiple functionally redundant nitrate reductase genes. These phylogenetically distinct duplicate genes enable survival in substrate-deprived anoxic conditions by constructing complete assimilatory/dissimitative nitrate reduction pathways. These findings elucidate the molecular mechanisms underlying B. SW5 adaptability to redox-fluctuating systems through metabolic versatility, providing a theoretical foundation and novel paradigm for developing energy-efficient wastewater treatment technologies.},
}
@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}
@article {pmid41100443,
year = {2025},
author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D},
title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003436},
doi = {10.1371/journal.pbio.3003436},
pmid = {41100443},
issn = {1545-7885},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; },
abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.},
}
@article {pmid41099560,
year = {2025},
author = {Patel, RR and Triplett, LR and Taerum, SJ and Nason, SL and Wilson, CO and Steven, B},
title = {Diverse soil protists show auxin regulated growth in partnership with auxin-producing bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf234},
pmid = {41099560},
issn = {1751-7370},
abstract = {Predatory protists are single-cell eukaryotic organisms capable of hunting and ingesting bacteria and other microorganisms, which are thought to enrich populations of beneficial bacteria in the rhizosphere, potentially influencing plant health. However, the mechanisms underpinning protist interactions with plant growth promoting bacteria are not well understood. We examined the conservation of plant beneficial traits in bacteria associated with ten protists of diverse lineages that were isolated from the maize rhizosphere. Metagenomics, whole-genome sequence analysis, and functional assays of 61 groups of protist-associated bacteria identified tryptophan-dependent biosynthesis of the auxin hormone indole-3-acetic acid (IAA) as the most prevalent predicted trait. Mass spectrometry confirmed that all the protist cultures accumulated IAA after tryptophan supplementation, and that IAA production was bacterial-dependent. Hypothesizing that IAA affects protist function, we observed that exogenous IAA significantly increased the culture density and cell size of all ten protists. Examination of four partial protist genome assemblies identified 13 candidate auxin metabolic gene homologs conserved across plants and protists, and transcriptomic analysis of a Colpoda sp. protist revealed differential expression of thousands of genes in the presence of IAA, further supporting auxin regulation of protist function. These findings demonstrate that soil microeukaryotes can widely host auxin-producing bacteria and that much broader range of eukaryotic lineages perceive and respond to auxin signals than previously recognized. This significantly expands the known breadth of auxin perception as an interkingdom signal, with important implications for soil nutrient cycling and rhizosphere ecology.},
}
@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.<br><br>IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}
@article {pmid41099512,
year = {2025},
author = {Elkassas, SM and Fortunato, CS and Grim, SL and Butterfield, DA and Holden, JF and Vallino, JJ and Algar, CK and Zeigler Allen, L and Larson, BT and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, B and Huber, JA},
title = {Metabolic and population profiles of active subseafloor autotrophs in young oceanic crust at deep-sea hydrothermal vents.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0186825},
doi = {10.1128/aem.01868-25},
pmid = {41099512},
issn = {1098-5336},
abstract = {UNLABELLED: At deep-sea hydrothermal vents, magmatically driven rock-water reactions in the crust generate gases and other reduced compounds that subseafloor microorganisms use for chemolithoautotrophy. In this study, microbial autotrophs from three diffuse flow hydrothermal vents at Axial Seamount in 2013 and 2014 were isotopically labeled using RNA stable isotope probing, targeting subseafloor autotrophic mesophiles (30°C), thermophiles (55°C), and hyperthermophiles (80°C). We constructed taxonomic and functional profiles of active chemolithoautotrophs, examined population distributions across sites, and linked primary producers to their specific metabolic strategies within the subseafloor community. Dominant autotrophs exhibited hydrogen-dependent dissimilatory metabolisms, such as sulfur and nitrate reduction and methanogenesis, as well as microaerophilic sulfide oxidation even at 80°C, consistent with fluid chemistries at each site. While hydrogenotrophic methanogenic archaea (Methanothermococcus) were restricted in their distribution and activity, hydrogenotrophic sulfur and nitrate reducers from the Aquificota (Thermovibrio) and Campylobacterota (Nautiliaceae, Hydrogenimonas, and Desulfurobacteriaceae) were consistently active and present at all sites and years at both the population and community levels. Hydrogenase transcripts were significantly differentially expressed, and diverse hydrogenases were found in metagenome-assembled genomes of Aquificota members, highlighting the importance and versatility of their hydrogen utilization strategies, which likely contribute to their cosmopolitan distribution across geochemically disparate subseafloor sites. Together, this study provides new insights into the functional dynamics and distribution of key subseafloor autotrophic microbial communities in young oceanic crust at deep-sea hydrothermal vents.<br><br>IMPORTANCE: Deep-sea hydrothermal vents are hotspots for life in the dark ocean, where rich animal ecosystems are supported by microbial primary producers utilizing the abundant chemical energy supplied by high-temperature water-rock reactions. Despite increasing knowledge about the geochemistry and microbiology of deep-sea hydrothermal vents, there is still a gap in our understanding of the key microbial players who fix much of the carbon at these sites, especially in the productive subseafloor. In this study, stable isotope probing was used to label active microbial autotrophs in diffuse flow venting fluids from three sites over 2 years and was combined with metatranscriptomic sequencing to identify their specific metabolic strategies. This research highlights the microbial community composition, function, gene regulation, and population dynamics that enable hydrothermal ecosystems to persist.},
}
@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/msystems.01208-25},
pmid = {41099510},
issn = {2379-5077},
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.<br><br>IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Cura&#xe7;ao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}
@article {pmid41099501,
year = {2025},
author = {Feeser, K and Longley, R and Gallegos-Graves, LV and Albright, M and Shakya, M},
title = {Recovering new viruses from New Mexico soils.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0090825},
doi = {10.1128/mra.00908-25},
pmid = {41099501},
issn = {2576-098X},
abstract = {Here, we utilized metagenomic and size-filtered virome sequencing to recover 4,157 medium, high, or complete quality viral genomes from soils taken from three high elevation sites in New Mexico, USA. Among recovered viral genomes, 90% were from size-filtered samples, indicating the importance of this enrichment in assessments of complex viromes.},
}
@article {pmid41098988,
year = {2025},
author = {Bautista, J and Fuentes-Yépez, MP and Adatty-Molina, J and López-Cortés, A},
title = {Microbial signatures in metastatic cancer.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1654792},
pmid = {41098988},
issn = {2296-858X},
abstract = {Metastasis remains the leading cause of cancer-related death, yet the biological determinants that enable tumor cells to disseminate and colonize distant organs are incompletely understood. Emerging evidence identifies the microbiome, not merely as a bystander, but as an active architect of the metastatic cascade. Microbial communities residing in the gut, mucosal barriers, and within tumors shape metastatic progression by modulating immune surveillance, stromal remodeling, oncogenic signaling, and therapy response. Intratumoral and even intracellular microbes regulate epithelial-mesenchymal transition, angiogenesis, and immune escape, while gut-derived metabolites condition pre-metastatic niches and alter systemic immunity. Technological advances in spatial transcriptomics, single-cell multi-omics, and metagenomics have revealed a spatially organized, functionally integrated microbial ecosystem within tumors, challenging long-held assumptions of sterility in cancer biology. This review synthesizes five converging dimensions of this paradigm: microbial interactions in the metastatic tumor microenvironment; microbiome-mediated immunoediting and metastatic escape; the role of intratumoral and intracellular bacteria in dissemination; spatial-multi-omic approaches to map microbial niches; and microbial biomarkers predictive of metastasis and therapy outcomes. Collectively, these findings recast the microbiome as a critical and targetable determinant of metastasis. Deciphering the tumor-microbe-host triad holds transformative potential for biomarker development, therapeutic innovation, and precision oncology.},
}
@article {pmid41098928,
year = {2025},
author = {Kimbell, LK and Ali, N and Adelgren, M and Kohls, S and Folvarska, V and Marshall, CW and Newton, RJ and Wang, Y and McNamara, P},
title = {Antibiotic Resistome Changes Associated with Different Types of Corrosion Inhibitors When Chlorine is Used as a Disinfectant.},
journal = {ACS ES&amp;T engineering},
volume = {5},
number = {10},
pages = {2474-2485},
pmid = {41098928},
issn = {2690-0645},
abstract = {Drinking water distribution systems contain chlorine and metals that can promote antibiotic resistance. Corrosion inhibitors are required to prevent the leaching of metals into drinking water. While utilities have a choice of which corrosion inhibitor they employ, the impact of corrosion inhibitor type when combined with chlorine on antibiotic resistance is unknown. The objective of this research was to understand the impacts of zinc orthophosphate, sodium orthophosphate, and sodium silicate, three commonly used corrosion inhibitors, on antibiotic resistance when mixed with chlorine. Culture-based plating was paired with metagenomics analysis on lab-scale microcosms. The addition of all three corrosion inhibitors resulted in a significantly higher absolute abundance of antibiotic resistant bacteria with resistance to rifampicin, sulfamethoxazole, and vancomycin, while the addition of phosphate-based inhibitors (sodium orthophosphate and zinc orthophosphate) at 1 mg/L also resulted in significantly higher absolute abundance of ampicillin-resistant bacteria. Exposure to all three types of corrosion inhibitors and free chlorine led to significantly higher abundances of ARGs conferring resistance to the target antibiotics used in the phenotypic assessment. Observed changes in the resistomes compared to the controls were influenced by an enrichment in ARGs responsible for multidrug resistance and resistance to peptide antibiotics. In general, most of the ARGs were associated with chromosomes, but a significant increase in the number of ARGs colocated with plasmid and integron sequences was observed. In contrast, the abundance of viral-associated ARGs decreased in the treatments compared to the controls. These results highlight the importance of corrosion inhibitor selection and the potential impacts on antibiotic resistance in potable water systems.},
}
@article {pmid41098901,
year = {2025},
author = {Gong, W and Ma, X and Wang, G and Guo, Y and Zhuo, Z and Han, C and Wu, Y},
title = {Analysis of co-infection in severe and critical patients with influenza A (H1N1) pneumonia using metagenomic next-generation sequencing on bronchoalveolar lavage samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1669328},
pmid = {41098901},
issn = {2235-2988},
mesh = {Humans ; *Coinfection/microbiology/epidemiology/virology ; Male ; Female ; *Influenza, Human/virology/complications/epidemiology ; Middle Aged ; *Influenza A Virus, H1N1 Subtype/genetics/isolation &amp; purification ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Adult ; Metagenomics/methods ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Critical Illness ; *Pneumonia, Viral/virology ; Prevalence ; },
abstract = {OBJECTIVES: The study aimed to clarify the co-infection patterns in adult patients with severe influenza A (H1N1) pneumonia using Metagenomic Next-Generation Sequencing (mNGS) and to examine their impact on clinical outcomes, particularly focusing on the differences between severe and critical patient groups.<br><br>METHODS: This retrospective analysis evaluated bronchoalveolar lavage fluid (BALF) from 53 adult patients diagnosed with severe influenza A (H1N1) pneumonia. Patients were categorized into severe and critical groups depending on the need for invasive ventilation. mNGS was utilized to detect and analyze co-infections, which included fungal, bacterial and viral pathogens. Statistical analysis was conducted to assess the prevalence of these co-infections and their association with clinical outcomes, such as 28-day mortality.<br><br>RESULTS: In the cohort, 48 patients (90.6%) experienced co-infections. In the severe group, fungal infections were noted in 14 patients (66.7%), bacterial in 4 patients (19.0%), and viral in 11 patients (52.4%). Among the critical group, 22 patients (68.8%) had fungal, 23 patients (71.9%) had bacterial, and 10 patients (31.3%) had viral co-infections. There was a significantly higher incidence of co-infections in critical patients (P =&#xa0;0.0002), with notable differences in Acinetobacter baumannii prevalence between the groups (P =&#xa0;0.0339). Aspergillus emerged as the predominant fungal genus across the study. Septic shock (odds ratio [OR] 33.63[4.29-538.3]; P =&#xa0;0.003) and fungal co-infection (OR 24.42[1.98-810.6]; P =&#xa0;0.029) were identified as independent risk factors for 28-day mortality.<br><br>CONCLUSION: The study revealed a high rate of co-infections in both severe and critical patients suffering from influenza A (H1N1) pneumonia, with a higher frequency of bacterial infections in critical patients. Importantly, septic shock and fungal co-infections were independently associated with increased 28-day mortality, highlighting the need for monitoring and management of co-infections in these patients.},
}
@article {pmid41098899,
year = {2025},
author = {Li, W and Di, X and Lv, X and Zhang, L and Yu, J},
title = {Characteristics of adults with influenza A virus pneumonia and co-infections identified by mNGS in Jilin, China during 2024-2025.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1662422},
pmid = {41098899},
issn = {2235-2988},
mesh = {Humans ; *Coinfection/epidemiology/virology/microbiology/diagnosis ; Male ; China/epidemiology ; Female ; *Influenza, Human/epidemiology/virology/diagnosis ; Middle Aged ; Retrospective Studies ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; *Influenza A virus/genetics/isolation &amp; purification/classification ; *Pneumonia, Viral/epidemiology/virology/diagnosis ; Metagenomics/methods ; Severity of Illness Index ; Influenza A Virus, H3N2 Subtype/genetics/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/virology ; Influenza A Virus, H1N1 Subtype/genetics/isolation &amp; purification ; },
abstract = {INTRODUCTION: Influenza A virus (IAV) was included in the World Health Organization priority pathogen list for 2024 owing to its pandemic potential. We aimed to investigate the characteristics of IAV pneumonia and co-infection identified using metagenomic next-generation sequencing (mNGS) in hospitalized patients in Jilin, China, during 2024-2025.<br><br>METHODS: This retrospective study included patients hospitalized for IAV pneumonia. All patients underwent mNGS testing using sputum or bronchoalveolar lavage fluid. Patients were categorized into mild-to-moderate (MM) and severe-to-critical (SC) groups, depending on their disease severity. We analyzed demographic data, clinical manifestations, laboratory findings, and imaging results, and compared the two groups.<br><br>RESULTS: Of the 73 patients included, 45 were in the MM group and 28 were in the SC group. Compared with nucleic acid tests of throat swabs, mNGS has higher sensitivity for detecting IAV (60% vs 100%). H1N1 and H3N2 were the predominant IAV subtypes. Underlying conditions, especially asthma and chronic obstructive pulmonary disease, were associated with an increased risk of severe illness. The D-dimer levels were higher, and lymphocyte counts were lower in patients in the SC group than in those in the MM group. Of the 73 patients, 63 (86.3%) had secondary infections, with bacterial infections being more prevalent (mild/moderate: 26 [58%] and severe/critical: 24 [86%]) than fungal infections (23 [51%] and 23 [82%], respectively).<br><br>CONCLUSIONS: mNGS is a sensitive method for detecting IAV co-infections, effectively identifying co-infection with pathogenic bacterial strains. Hospitalized patients with IAV pneumonia, especially those with H3N2 infection and chronic airway disease, showed a high prevalence of severe and critical illness [total: 8 [11%], severe/critical: 7 [25%]). Fungal infections were frequent regardless of the presence of underlying comorbidities, and patients with SC disease were more likely to develop gram-negative bacterial and fungal infections. These findings may assist clinicians in the early identification of critically ill patients and the provision of appropriate empirical treatment.},
}
@article {pmid41098770,
year = {2025},
author = {Zhou, F and Wu, Y and Ren, B and Liu, Y and Luo, K and Li, Q and Huang, F and Peng, X and Li, Y and Su, Z and Li, J},
title = {Meta-omics reveals subgingival plaque reconstruction dynamics.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569528},
pmid = {41098770},
issn = {2000-2297},
abstract = {BACKGROUND: The homeostasis of the subgingival microbiome is crucial for periodontal health, although the dynamics governing its community variation remain insufficiently studied. This study aims to investigate the dynamics of subgingival microbiota reassembly after disruption, focusing on core taxa, functions, and driving forces.<br><br>METHODS: 339 subgingival plaques in periodontally healthy states were collected before and after ultrasonic cleaning across 12 timepoints for 1 year. All samples underwent full-length 16S rRNA sequencing; 30 were selected for metagenomic sequencing.<br><br>RESULTS: Our findings revealed that disturbed subgingival microbiota underwent short-term disruptions but subsequently reverted to baseline, maintaining stability within a year. Homogeneous selection dominated assembly, driving convergent structure under consistent pressure. Such a recovery process was accompanied by key taxa increased sequentially: Pseudomonas fluorescens early, Haemophilus parainfluenzae mid-stage, and Capnocytophaga spp. late. Functionally, reconstruction began with energy metabolism, expanded via biofilm formation and LPS biosynthesis mid-stage, and involved late apoptosis and complex amino acid metabolism. Microbial interactions, including positive regulation from Veillonella HMT 780 to Fusobacterium HMT 248, internally drove community assembly.<br><br>CONCLUSION: Our study clarifies species and functional dynamics during subgingival microbiota reconstruction and maps time-directed networks among stage-specific bacteria, offering a theoretical basis for targeted microbiome regulation.},
}
@article {pmid41098739,
year = {2025},
author = {Fan, Y and Tan, Z and Wang, Z and Pan, H and Zhou, J and Yang, J and Zhang, G},
title = {Evaluation of non-invasive diagnostic tests for Mycoplasma pneumoniae pneumonia.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1656192},
pmid = {41098739},
issn = {1664-3224},
mesh = {Humans ; *Pneumonia, Mycoplasma/diagnosis/microbiology/immunology/blood ; Male ; Female ; *Mycoplasma pneumoniae/immunology/genetics ; Middle Aged ; Immunoglobulin M/blood ; Retrospective Studies ; Adult ; Aged ; Sensitivity and Specificity ; Antibodies, Bacterial/blood ; Community-Acquired Infections/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *Diagnostic Tests, Routine/methods ; High-Throughput Nucleotide Sequencing ; Young Adult ; },
abstract = {BACKGROUND: Accurate and timely identification of Mycoplasma pneumoniae pneumonia (MPP) remains a clinical challenge. Although nasopharyngeal swab nucleic acid testing (NAAT) and serum IgM antibody assays are widely used, their diagnostic performance varies across studies. This study aimed to retrospectively evaluate the sensitivity and specificity of the two non-invasive methods (NAAT and serum IgM antibody assays) for MPP in real-world clinical settings.<br><br>METHODS: We conducted a retrospective study of adult patients hospitalized for community-acquired pneumonia (CAP) from January 2024 to October 2024. All enrolled patients underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) and had received at least one of two non-invasive tests (NAAT or serum IgM antibody assays). The sensitivity and specificity of NAAT and serum IgM antibody assays were calculated against the final diagnosis. A non-inferiority test was used to determine whether the sensitivity of NAAT or serum IgM antibody assays was not inferior to that of mNGS.<br><br>RESULTS: Among 594 patients included in the analysis, 60 were diagnosed with MPP based on a composite reference standard that included laboratory testing results and adjudication by two senior clinicians in accordance with clinical and radiological findings. The sensitivity and specificity of NAAT were 74.1% and 99.3%, respectively, while those of serum IgM antibody assays were 23.6% and 98.0%. McNemar's test revealed a statistically significant difference in sensitivity between mNGS and the two non-invasive tests (NAAT and serum IgM antibody assays) (P<0.05). The non-inferiority analysis revealed that both NAAT (sensitivity difference: -24.2%, 95% CI: -36.1 to -12.1%; P<0.01) and serum IgM antibody assays (-76.5%, 95% CI: -96.6 to -56.3%; P<0.01) failed to meet the 10% non-inferiority margin compared to mNGS.<br><br>CONCLUSION: In clinical practice, a positive result from either NAAT or serum IgM antibody assays can serve as reliable adjunct evidence for diagnosing MPP. However, in cases with a high clinical suspicion of MPP, negative results from both methods are not sufficient to rule out the diagnosis. For MPP, mNGS remains the most effective diagnostic method compared to non-invasive testing alternatives.},
}
@article {pmid41098538,
year = {2025},
author = {He, X and Zhao, Q and Zhang, J and Shi, J and Wan, N and Tang, B and Tian, B and Li, P},
title = {Potential and application of Fusobacterium nucleatum in the diagnosis and treatment of colorectal cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652702},
pmid = {41098538},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC), as a globally prevalent malignant tumor, relies on in-depth analysis of tumor microenvironment regulation mechanisms for precision diagnosis and treatment. Fusobacterium nucleatum (F. nucleatum), a key carcinogenic bacterium, has been revealed in recent studies to play multidimensional roles in CRC initiation, progression, and metastasis. This review systematically summarizes the progress of Fn applications in CRC full-cycle management: (1) In the diagnostic field, Fn detection technology based on fecal samples has developed into a new non-invasive screening strategy. Cohort studies show its diagnostic performance (AUC 0.82-0.89), with significant correlations to tumor stage (III/IV stage OR = 2.87), lymph node metastasis (HR = 1.94), and reduced 5-year survival rate (35% vs. 62%); (2) For therapeutic monitoring, dynamic Fn load changes can predict chemotherapy (OR = 0.63) and immunotherapy responses (PFS extended by 2.1 months); (3) In prognostic evaluation, metagenomic analysis shows that high Fn abundance is closely related to TNM staging (C-index 0.81 vs. 0.69) and recurrence risk (AUC = 0.88). Notably, a nomogram model integrating Fn biomarkers can improve the predictive accuracy of the traditional TNM staging system by 17.3%. Although existing evidence supports the clinical translational value of Fn, its standardized detection protocols, threshold setting, and targeted intervention strategies (such as antibiotic therapy and phage therapy) still require validation through multi-center prospective studies. This review provides evidence-based medical evidence for the application of Fn in CRC precision medicine by integrating multi-omics data.},
}
@article {pmid41098531,
year = {2025},
author = {Juárez-Aragón, MC and Pantoja-Irys, JR and de la Rosa-Manzano, E and Garrido-Olvera, L and Mujica-Sánchez, H and Trejo-De León, CR and Vázquez-Lobo, A},
title = {Microbiome diversity across physicochemical gradient in low-medium enthalpy springs at the Sierra Madre Oriental eastern flank, northeastern Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663000},
pmid = {41098531},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial communities are fundamental to the functionality of thermal springs where they engage in essential processes such as the oxidation of sulfur, reduction of nitrates, carbon fixation, production of unique metabolites, and stabilization of microbial trophic networks. Northeastern Mexico presents a diverse array of thermal springs located within tropical karst systems situated among folded mountains and ancient inactive karstic regions. The geological complexity of these environments indicates a substantial potential for microbiome diversity; however, the composition and functional dynamics of microbial communities in these springs have not been thoroughly investigated.<br><br>METHODS: This study involved the collection of water samples from six hot springs, to characterize the planktonic microbiome using advanced metagenomic sequencing techniques. Additionally, we examined the relationship between microbial composition and physicochemical parameters.<br><br>RESULTS: Our analysis identified a total of 425 microbial species, which included 409 bacterial species, 13 eukaryotic organisms, and 3 archaeal taxa. The Ojo Caliente and Mainero Azufroso springs displayed the highest microbial diversity, whereas the Balneario El Ba&#xf1;ito and Taninul springs exhibited the lowest. The Phyum Pseudomonadota was the predominant across the majority of springs, while Campylobacterota and Chlorobiota were specifically identified in the less diverse Balneario El Ba&#xf1;ito and Taninul springs, respectively. A total of 30 indicator species were identified, predominantly in El Ba&#xf1;ito and Potrero Prieto springs, emphasizing the distinctiveness of their microbial environments. Moreover, we found that electrical conductivity and bicarbonate concentration had a significant impact on the structure of this microbial communities.<br><br>DISCUSSION: This study highlights the ecological importance of these unique ecosystems in northeastern Mexico, with the Mainero Azufroso and Ojo Caliente springs identified as reservoirs of high microbial diversity.},
}
@article {pmid41098344,
year = {2025},
author = {Li, H and Wei, J and Zhou, S and Zhan, Z and Tang, J and Wang, W and Tang, H},
title = {Metagenomic Next-Generation Sequencing Unmasks Atypical Rabies - Guangxi Zhuang Autonomous Region, China, 2024.},
journal = {China CDC weekly},
volume = {7},
number = {39},
pages = {1251-1257},
pmid = {41098344},
issn = {2096-7071},
abstract = {Human rabies remains nearly universally fatal despite medical advances. Diagnosis is frequently delayed when patients present with atypical symptoms, and the failure to receive postexposure prophylaxis (PEP) continues to be a major contributor to mortality worldwide.<br><br>WHAT IS ADDED BY THIS REPORT?: This represents the first confirmed human rabies case in Guangxi caused by the JSTZ190314 strain, successfully identified through metagenomic next-generation sequencing (mNGS). The patient initially presented with urinary symptoms that led to a misdiagnosis before characteristic neurological manifestations developed, ultimately progressing to brain death 28 days after neurological onset (34 days from initial urinary symptoms).<br><br>This case demonstrates the critical importance of mNGS in diagnosing atypical rabies presentations and emphasizes the urgent need for enhanced early clinical recognition, standardized PEP administration protocols, and strengthened regional viral surveillance systems.},
}
@article {pmid41098206,
year = {2025},
author = {Chen, Y and Li, M and Gan, X and Wang, Y and Tang, X and Zhou, Y and Niu, T},
title = {Metagenomic Next-Generation Sequencing Unveils Prognostic Microbial Synergism and Guides Precision Therapy in Candidemia: A Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5263-5275},
pmid = {41098206},
issn = {1178-6973},
abstract = {PURPOSE: Candidemia remains a life-threatening infection, compounded by diagnostic delays and limited prognostic tools. While metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection, its prognostic utility and therapeutic impact in candidemia remain unestablished.<br><br>PATIENTS AND METHODS: This retrospective cohort study analyzed 97 candidemia patients with positive blood mNGS at West China Hospital (2020-2024). Multivariable logistic regression and survival analyses identified mortality predictors, while therapeutic impacts were assessed through antifungal regimen modifications.<br><br>RESULTS: The 28-day mortality was 44.3% (43/97). Blood mNGS outperformed cultures in species identification (5 vs 4 species) and co-infection detection. Bacterial co-detections (HR=2.00, 95% CI:1.15-3.48; p<0.05) doubled mortality risk. SOFA score was the strongest mortality predictor (adjusted OR=1.29 per point; p<0.001). mNGS-guided antifungal initiation reduced mortality by 52.4% in treatment-na&#xef;ve patients (22.6% vs 75.0%; p<0.05), though regimen adjustments in pretreated cases showed no benefit (p>0.05). Notably, Candida species exhibited equivalent virulence (log-rank p>0.05), and mNGS read counts lacked prognostic value (p>0.05).<br><br>CONCLUSION: mNGS transforms candidemia management by enabling early risk stratification (via SOFA scores and co-infection profiles) and precision therapy initiation. Its capacity to unmask high-risk bacterial synergists and guide time-sensitive interventions supports integration into diagnostic algorithms, particularly for culture-negative cases. Further validation of standardized mNGS protocols is warranted to maximize clinical impact.},
}
@article {pmid41097911,
year = {2025},
author = {Verhoeven, JTP and Malwe, AS and Roussel, N and Nielsen, IB and Mak, SST and Nielsen, TK and Barnes, CJ},
title = {Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.},
journal = {The New phytologist},
volume = {248},
number = {4},
pages = {1620-1624},
doi = {10.1111/nph.70450},
pmid = {41097911},
issn = {1469-8137},
support = {60770//Villum Fonden/ ; AUFF-E-2024-9-14//Aarhus Universitets Forskningsfond/ ; },
}
@article {pmid41097662,
year = {2025},
author = {He, J and Shu, X and Pan, H and Wang, M and Song, Y and Zhou, F and Lian, L and Chen, L and Ma, G and Zhao, Y and Li, R and Liu, L},
title = {Ginseng Polysaccharides Inhibit Aspergillus sydowii-Driven Lung Adenocarcinoma via Modulating Gut Microbiota-Bile Acid Metabolism Axis.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193134},
pmid = {41097662},
issn = {2072-6694},
support = {(82204677, 82474267//National Natural Science Foundation of China/ ; 2024ZD0521405//National Science and Technology Major Project of China/ ; GZNL2023A02009//Major Project of Guangzhou National Laboratory/ ; 20241112//Traditional Chinese Medicine Bureau of Guangdong Province Project/ ; QZ2023ZZ11//State Key Laboratory of Traditional Chinese Medicine Syndrome/ ; HQL2024PZ005//Chinese Medicine Guangdong Laboratory/ ; 2025M773868//China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related mortality globally, with lung adenocarcinoma (LUAD) as the most common subtype. Dysbiotic intratumoral mycobiomes drive LUAD pathogenesis, and Aspergillus sydowii (A. sydowii) acts as a key oncogenic fungal species. Ginseng polysaccharides (GPs), bioactive phytochemicals with immunomodulatory and oncostatic properties, counteract fungal infections and restore immunosurveillance in LUAD.<br><br>METHODS: Subcutaneous and orthotopic LUAD murine models were established by implanting Lewis lung carcinoma (LLC) cells. Subcutaneous tumors were infected intratumorally and orthotopic models via nasal inoculation. GPs (200 mg/kg/day) were orally administered to evaluate tumor growth. Metagenomic and targeted bile acid metabolomic profiling of fecal and tumor tissues was performed, with Spearman correlations analyzed using R packages.<br><br>RESULTS: GPs significantly inhibited A. sydowii-induced tumor growth in both models. In subcutaneous tumors; GPs reduced volume (p < 0.05) and weight vs. infected controls. In orthotopic models, GPs decreased pathological nodules and lung weight, with micro-CT/H&amp;E confirming attenuated hyperplasia. Metagenomics showed GPs restored gut homeostasis by enriching Lactobacillus/Muribaculum intestinale and suppressing pro-inflammatory Alistipes. Targeted metabolomics revealed reduced &#x3b2;-Hyodeoxycholic Acid (3&#x3b2;-HDCA), Chenodeoxycholic acid 24-acyl-b-D-glucuronide (CDCA-24G) and 3&#x3b2;-hydroxychol-5-en-24-oic acid (5-isoLCA) after GP treatment. Network analysis confirmed significant microbe-bile acid interactions.<br><br>CONCLUSIONS: GPs exert antitumor effects against A. sydowii-induced LUAD by modulating gut microbiota and bile acid metabolism. This identifies GPs as a promising therapy for mycobiome-influenced cancers, with dual targeting of fungal infection and metabolic reprogramming.},
}
@article {pmid41097145,
year = {2025},
author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I},
title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193068},
pmid = {41097145},
issn = {2072-6643},
support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; },
abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.},
}
@article {pmid41097095,
year = {2025},
author = {Russell, T and Formiconi, E and Casey, M and McElroy, M and Mallon, PWG and Gautier, VW},
title = {Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199831},
pmid = {41097095},
issn = {1422-0067},
support = {101132970//European Commission/ ; },
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; One Health ; *Communicable Diseases, Emerging/virology/epidemiology ; *Viruses/genetics ; SARS-CoV-2/genetics ; Genome, Viral ; Zoonoses/virology ; },
abstract = {Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS, highlighting its integration within the One Health paradigm and its application to the surveillance and discovery of (re)emerging viruses at the human-animal-environment interface. We provide a detailed overview of vmNGS workflows including sample selection, nucleic acid extraction, host depletion, virus enrichment, sequencing platforms, and bioinformatic pipelines, all tailored to maximise sensitivity and specificity for diverse sample types. Through selected case studies, including SARS-CoV-2, mpox, Zika virus, and a novel henipavirus, we illustrate the impact of vmNGS in outbreak detection, genomic surveillance, molecular epidemiology, and the development of diagnostics and vaccines. The review further examines the relative strengths and limitations of vmNGS in both passive and active surveillance, addressing barriers such as cost, infrastructure requirements, and the need for interdisciplinary collaboration. By integrating molecular, ecological, and public health perspectives, vmNGS stands as a central tool for early warning, comprehensive monitoring, and informed intervention against (re)emerging viral threats, underscoring its critical role in global pandemic preparedness and zoonotic disease control.},
}
@article {pmid41095773,
year = {2025},
author = {Suárez-Cortés, M and Juan-Pérez, A and Molina-Rodríguez, A and Araújo de Castro, J and Castaño-Molina, M&#xc1; and Fernández-Ruiz, VE and Jiménez-Méndez, A and Martínez Pérez-Munar, P and Rico-Chazarra, S and Ramos-Molina, B and Sánchez-Solís, M and Blanco-Carnero, JE and Ruiz-Alcaraz, AJ and Núñez-Sánchez, M&#xc1;},
title = {Dynamics of the Epigenome, Microbiome, and Metabolome in Relation to Early Adiposity in the Maternal-Infant Axis: Protocol for a Prospective, Observational Pilot Study in the Spanish NEMO Cohort.},
journal = {Journal of clinical medicine},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/jcm14196694},
pmid = {41095773},
issn = {2077-0383},
support = {22080/JLI/22//Fundaci&#xf3;n S&#xe9;neca - Agencia de Ciencia y Tecnolog&#xed;a de la Regi&#xf3;n de Murcia/ ; CP23/00051//Instituto de Salud Carlos III/ ; },
abstract = {Background: Childhood obesity has reached epidemic levels in developed countries and is an emerging concern in developing regions. Children with excess weight are more likely to maintain this condition over time into adulthood and face a higher risk of developing metabolic disorders such as type 2 diabetes, hypertension, metabolic dysfunction-associated liver disease, and dyslipidemia. Early identification of obesity risk is, therefore, a key public health challenge. Methods: This is an observational, prospective, single-center cohort pilot study in 66 mother-infant dyads recruited at the Gynecology and Obstetrics Service of the Virgen de la Arrixaca University Hospital (Murcia, Spain). The primary objective is to identify early-life, non-invasive biomarkers associated with increased adiposity by integrating multi-omics approaches and analyzing maternal-infant interactions. Pregnant women will be enrolled during the third trimester and will undergo a baseline visit at 38 weeks of gestation for clinical and anthropometric assessment. Buccal swabs and fecal samples will be collected at baseline and in the peripartum period for epigenetic (DNA methylation), metagenomic, and metabolomic analyses. Infants will be evaluated at birth and followed at 6 months, 1 year, 2 years, and 3 years. Each visit will include detailed anthropometric measurements, along with collection of buccal swabs and fecal samples for multi-omics profiling. Conclusions: This multidisciplinary study aims to assess how maternal factors influence infant epigenetic and microbial patterns, and their relation to adiposity development. Early identification of such biomarkers may guide personalized prevention strategies and reduce the long-term burden of obesity-related comorbidities.},
}
@article {pmid41095699,
year = {2025},
author = {Ziad, GA and Jalal, D and Hashem, M and Sayed, AA and Mahfouz, S and Bayoumi, A and Lotfi, M and Hassanain, O and Tolba, M and Madney, Y and Shalaby, L and Elanany, M},
title = {Rapid Identification of Carbapenemase Genes Directly from Blood Culture Samples.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/diagnostics15192480},
pmid = {41095699},
issn = {2075-4418},
support = {#54699605//Pfizer Global Medical Grants/ ; },
abstract = {Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert[®] Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert[®] Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children's Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert[®] Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert[®] Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were blaNDM, blaOXA-48-like, and dual blaNDM/blaOXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert[®] Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert[®] Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections.},
}
@article {pmid41094699,
year = {2025},
author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M},
title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {204},
pmid = {41094699},
issn = {2049-2618},
support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; },
mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; },
abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.<br><br>RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (>&#x2009;10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.<br><br>CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.},
}
@article {pmid41094674,
year = {2025},
author = {Yuan, M and Lv, X and Yuan, Y and Kang, M and He, F},
title = {Disseminated Listeria monocytogenes and human pegivirus-1 coinfection.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1335},
pmid = {41094674},
issn = {1471-2334},
mesh = {Humans ; Middle Aged ; *Listeria monocytogenes/isolation &amp; purification/genetics ; *Coinfection/virology/microbiology/diagnosis ; Male ; *Listeriosis/complications/drug therapy ; *Flaviviridae Infections/complications/virology/diagnosis ; *Flaviviridae/isolation &amp; purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Meningitis, Listeria/drug therapy/diagnosis/complications/microbiology ; },
abstract = {BACKGROUND: Listeria monocytogenes is one of the major bacteria responsible for meningitis. Controversy exists regarding the neuropathological effect of human pegivirus-1 (HPgV-1). Whether HPgV-1 interacts with L. monocytogenes is unknown. Herein, we describe a multiple myeloma patient with disseminated L. monocytogenes and HPgV-1 coinfection.<br><br>CASE PRESENTATION: The case of a 57-year-old patient with fever accompanied by headache, dizziness, nausea, vomiting of stomach contents, and urinary and faecal incontinence is presented. Through metagenomic next-generation sequencing and the detection of L. monocytogenes and HPgV-1 in cerebrospinal fluid, along with blood culture of L. monocytogenes and PCR of HPgV-1 in the blood, a diagnosis of HPgV-1 and L. monocytogenes meningitis, HPgV-1 viremia, and L. monocytogenes sepsis was made, enabling timely and proper treatment with meropenem. After treatment, the patient recovered and was discharged from the hospital.<br><br>CONCLUSIONS: To our knowledge, this is the first reported case of disseminated L. monocytogenes and HPgV-1 coinfection. Determining whether HPgV-1 was responsible for meningitis will require further research, including histopathological analysis.},
}
@article {pmid41094150,
year = {2025},
author = {Zhang, Y and Bhosle, A and Bae, S and Eckenrode, K and Huang, X and Tang, J and Lavrentovich, D and Awad, L and Hua, J and Wang, Y and Morgan, XC and Li, B and Krueger, A and Garrett, WS and Franzosa, EA and Huttenhower, C},
title = {Predicting functions of uncharacterized gene products from microbial communities.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41094150},
issn = {1546-1696},
support = {R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U19AI110820//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions for >443,000 protein families (~82.3% previously uncharacterized), including >27,000 protein families with weak homology to known proteins and >6,000 protein families without homology. These were drawn from 1,595 gut metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2/iHMP). Integrating additional information such as sequence similarity, genomic proximity and domain-domain interactions improves performance of the method. Our method's implementation, FUGAsseM, is generalizable and predicts protein function in both well-studied and undercharacterized communities. FUGAsseM achieves similar levels of accuracy in the context of microbial communities when compared to state-of-the-art approaches designed for application to single organisms while simultaneously providing much greater breadth of coverage. This initial study expands the functional landscape of the human gut microbiome and allows for exploration of microbial proteins in undercharacterized communities.},
}
@article {pmid41094135,
year = {2025},
author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ},
title = {Isolation, engineering and ecology of temperate phages from the human gut.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41094135},
issn = {1476-4687},
abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.},
}
@article {pmid41093983,
year = {2025},
author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR},
title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36025},
pmid = {41093983},
issn = {2045-2322},
support = {NIH R35 award GM152079/NH/NIH HHS/United States ; },
mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists &amp; inhibitors/metabolism ; Sex Characteristics ; },
abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.},
}
@article {pmid41093555,
year = {2025},
author = {Suto, Y and Horiba, K and Masuda, Y and Tanaka, K and Hashino, M and Kuroda, M and Fukuda, H},
title = {Candida tropicalis Brain Abscess Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
doi = {10.2169/internalmedicine.5937-25},
pmid = {41093555},
issn = {1349-7235},
abstract = {We report the case of a 59-year-old HIV-negative male diagnosed with a brain abscess following vasculitis-associated stroke. The causative pathogen remains unidentified using conventional methods including culture and rapid multiplex PCR. Craniotomy and biopsy were performed to establish a definitive diagnosis, and metagenomic next-generation sequencing (mNGS) of the abscess tissue identified Candida tropicalis as the causative pathogen. This case highlights the utility of mNGS in identifying pathogens in culture-negative CNS infections, even when conventional methods fail to detect the causative agent, particularly when evaluating abscess pus.},
}
@article {pmid41093108,
year = {2025},
author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V},
title = {Inverse association between serum vitamin B12 level and abundance of potential B12-producing gut microbes in Indian children.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.021},
pmid = {41093108},
issn = {1541-6100},
abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B-vitamins, which are utilized by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.<br><br>OBJECTIVE: To test whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking B12 as a case example.<br><br>METHODS: Fecal samples were collected from non-deficient (serum B12 level > 210 pg/mL, n=29) and B12 deficient (serum B12 level < 210 pg/mL, n=30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential B12 producers were compared, and their association with serum B12 level was established.<br><br>RESULTS: A comparison of within-sample diversity between the two groups didn't show any difference; however, between-sample diversity was significantly less in the B12 deficient group. Differential abundance testing also showed different microbiome structure in the B12 deficient group, where a higher abundance of B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known B12 producers was observed. Potential B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum B12 levels.<br><br>CONCLUSION: A higher abundance of potential B12 producers in the deficient group suggested an adaptive mechanism by the gut microbiome to meet the community's B12 requirements, by selectively promoting the growth of B12 producers, but causality remains to be proved.},
}
@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}
@article {pmid41093027,
year = {2025},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}
@article {pmid41092906,
year = {2025},
author = {Wu, L and Li, Y and Wang, W and Deng, L and Ge, H and Cui, M and Bi, N},
title = {Gut microbiota predictive of the efficacy of consolidation immunotherapy and chemoradiotherapy toxicity in lung cancer.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100877},
doi = {10.1016/j.medj.2025.100877},
pmid = {41092906},
issn = {2666-6340},
abstract = {BACKGROUND: Gut microbiota (GM) predict responses to immune checkpoint inhibitors (ICIs) in patients with advanced lung cancer. However, its role in patients with locally advanced lung cancer undergoing chemoradiotherapy (CRT) combined with consolidation ICIs remains unclear.<br><br>METHODS: A total of 177 fecal samples were collected pre- and post-CRT. Using 16S ribosomal RNA (16S rRNA) sequencing and metagenomic data from an internal cohort and published studies, the kinetics of microbiota were analyzed using the Wilcoxon signed-rank test, while prognostic factors for progression-free survival (PFS) were identified using Cox regression modeling and machine learning algorithms.<br><br>FINDINGS: The GM configuration was unaffected by traditional CRT. However, in cases of CRT with consolidation ICIs, patients with long-PFS showed a higher alpha diversity at baseline, followed by a reduction during treatment, contrasting with the stable diversity observed in the short-PFS group. Enrichment of the symbiotic microbe Akkermansia muciniphila (Akk) after CRT was observed, with its increased abundance correlating with extended distant metastasis-free survival in patients undergoing CRT with consolidation ICIs. Notably, the trend in Akk variation was a prognostic indicator of survival outcomes in patients undergoing CRT combined with ICIs. GM was also involved in the development of treatment-related pneumonia and was a promising predictive marker for severe pneumonia.<br><br>CONCLUSIONS: CRT with consolidation ICIs has more pronounced effects on the GM than CRT alone in patients with locally advanced lung cancer. The dynamic variation in Akk has predictive potential for patient survival in this context.<br><br>FUNDING: This study was supported by the National Science and Technology Major Project.},
}
@article {pmid41092847,
year = {2025},
author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W},
title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.},
journal = {Research in veterinary science},
volume = {197},
number = {},
pages = {105922},
doi = {10.1016/j.rvsc.2025.105922},
pmid = {41092847},
issn = {1532-2661},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.<br><br>RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.<br><br>CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.},
}
@article {pmid41092755,
year = {2025},
author = {Hu, X and Gu, H and Wang, Y and Xu, Y and Li, Y and Yu, Z and Liu, J and Jin, J and Liu, X and Wang, G},
title = {Biodegradable microplastics show greater potential than conventional types in facilitating antibiotic resistance gene enrichment and transfer through viral communities.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109855},
doi = {10.1016/j.envint.2025.109855},
pmid = {41092755},
issn = {1873-6750},
abstract = {Whether and how conventional (CP) and biodegradable microplastics (BP) affect viral communities and virus-carried antibiotic resistance genes (ARGs) in agricultural soils remains largely unknown. Here, we established a soil microcosm incubation with addition of 1 % (w/w) microplastics (MPs) in maize-cultivated soil that had been treated with different fertilizers for over 10 years, and the dynamic variations of viral communities and ARG profiles were investigated using a combination of metagenomic and metatranscriptomic methods. Our results revealed that BP, but not CP, significantly decreased viral α-diversity, changed viral community structure, community resistance and taxonomic turnover in all fertilized treatments. Caudoviricetes was the most dominate viral class and BP significantly increased the abundances of viral families (i.e. Phycodnaviridae) in all fertilized treatments, while CP altered the viral family abundance mainly observed in manure-amended soils. Also, BP was associated with increased ARG α-diversity, altered ARG community structure and community resistance, especially at the transcriptional level. Particularly, BP significantly enriched high-risk ARGs and mobile genetic elements (MGEs) in soils regardless of fertilization regimes. Correlation analysis revealed the important role of lytic viruses in shaping the abundance of high-risk ARGs and MGEs. Furthermore, BP induced more variations in reconstructed metagenome-assembled genome (MAGs), and significantly enriched high-risk ARGs carried by phage genomes. Co-occurrence patterns revealed three Actinobacteriota MAGs as primary viral hosts sharing high-risk ARGs with phages and containing multiple MGEs. Notably, we identified four viral genomes carrying ARG transcripts identical to their hosts. Both CP and BP differentially stimulated ARG expression in these virus-host systems, withmarkedlystronger effects observed in manure-amended soils. In conclusion, this study revealed a high risk of ARG dissemination induced by biodegradable MP residues regardless of fertilization regimes, while conventional MPs strengthen the ARG health risks mainly in manure-amended soils.},
}
@article {pmid41092742,
year = {2025},
author = {Norgan, AP and Sadiq, Q and Fedyshyn, B and Wolf, MJ and Enninga, EAL},
title = {Pan-viral metagenomic sequencing demonstrates that cryptic viral infection is rarely observed in villitis of unknown etiology.},
journal = {Placenta},
volume = {171},
number = {},
pages = {205-209},
doi = {10.1016/j.placenta.2025.10.009},
pmid = {41092742},
issn = {1532-3102},
abstract = {INTRODUCTION: Aberrant maternal immune responses are implicated in villitis of unknown etiology (VUE), but the underlying cause of this loss of tolerance, including cryptic causative or precipitating infections, has been difficult to define. Herein, we performed pan-viral metagenomic sequencing of placentas with VUE to investigate the possibility of cryptic viral infection as a contributing factor in this inflammatory pathology.<br><br>METHODS: Placentas evaluated at a single tertiary medical center between 2010 and 2024 were included in this study. Overall, the cohort included infectious villitis due to cytomegalovirus (CMV; n&#xa0;=&#xa0;4), VUE (n&#xa0;=&#xa0;25), and a reference group composed of pathologically unremarkable placentas (n&#xa0;=&#xa0;17). Total nucleic acid was extracted from formalin-fixed paraffin embedded (FFPE) placental tissues and subjected to pan-viral metagenomic sequencing (PVMS) to identify viral-associated reads.<br><br>RESULTS: PVMS detected reads mapping to CMV in 4 (of 4) of CMV cases. For VUE cases, 22 (of 25) had no identifiable viral reads, while 1 case demonstrated CMV reads and two had papillomavirus reads. The control samples demonstrated no identifiable reads in 13 (of 17) samples, while 3 cases had reads mapping to human papillomavirus 16 and one case had reads mapping to human Herpesvirus 6.<br><br>DISCUSSION: Utilizing PVMS, we did not identify cryptic viral sequences in 88&#xa0;% of morphologic VUE cases. In one clinical VUE case, CMV sequences were identified, suggesting a misclassification of infectious villitis. Both papillomavirus and herpesvirus sequences have previously been identified in the placenta, with unknown clinical significance. Overall, these findings exclude active viral infection as a potential etiology of VUE.},
}
@article {pmid41092730,
year = {2025},
author = {Wang, Y and Wen, S and Yu, Q and Huang, H and Tang, Y and Miao, C and Xia, Y and Guan, F},
title = {Microbiologically influenced corrosion of oil-water pipeline steel from local field failure case to specific Shewanella &amp; Desulfovibrio corrosion highlights the significance of hydrocarbon-degrading bacteria.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {168},
number = {},
pages = {109129},
doi = {10.1016/j.bioelechem.2025.109129},
pmid = {41092730},
issn = {1878-562X},
abstract = {Unconventional natural gas pipeline corrosion is associated with microbes, especially sulfate-reducing bacteria (SRB), though it is uncertain if SRB's role is overemphasized. Using metagenomics, corrosion immersion, and microbial cultivation, diverse hydrocarbon-degrading microorganisms, such as Shewanella, in corroded pipeline rust layers, oil-water mixtures, and produced water from unconventional natural gas fields are identified. These bacteria use crude oil as a carbon source, accelerating pitting corrosion of carbon steel and forming corrosion product films (Pitmax = 28.96 μm). The 16S rRNA sequencing results show that Shewanella, prevalent in various steel service environments, is a potential key microorganism in pipeline corrosion. X70 steel exhibits lower electron transfer resistance than Desulfovibrio in the Shewanella medium. Shewanella's aerobic respiration degrades crude oil and oxidizes iron, speeding up iron oxide formation and magnesium phosphate precipitation. Microbial acidification of the oil-water medium also contributes to severe pitting corrosion beneath the oil film. Crude oil accelerates microbial growth. Thus, studying carbon steel corrosion in oil-water environments must consider the impact of hydrocarbon-degrading microorganisms.},
}
@article {pmid41092706,
year = {2025},
author = {Zhang, X and Yang, B and Zhang, H and Guo, X and Zhang, Y},
title = {Nicosulfuron-driven antibiotic resistance in corn silage: Effect and its mitigation by zinc oxide nanoparticles.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140119},
doi = {10.1016/j.jhazmat.2025.140119},
pmid = {41092706},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in animal feed represent a significant threat to human health via the food chain, and pesticide application in crop production may further accelerate the ARGs dissemination. Corn silage, a primary forage for herbivorous livestock, has been shown to harbor diverse ARGs; however, the impact of pesticide-induced stress and potential mitigation strategies on ARG proliferation remains poorly understood. This study investigated the mechanistic link between nicosulfuron exposure and ARG dynamics in corn silage, as well as the mitigating effects of zinc oxide nanoparticles (ZnO NPs) on ARG under nicosulfuron exposure using metagenomic sequencing and high-throughput quantitative PCR. Nicosulfuron exposure increased (P < 0.05) ARG diversity and abundance, enriched (P < 0.05) ARG-hosting genera such as Pantoea, Escherichia, and Klebsiella, and intensified (P < 0.05) the correlation between ARGs and mobile genetic elements (MGEs). Additionally, it disrupted microbial metabolic pathways and elevated (P < 0.05) the ARG-associated risk index in corn silage. Conversely, ZnO NPs alleviated (P < 0.05) these effects by reducing the abundance of key ARGs-bacA, tetM, and ermB, enhancing microbial diversity, promoting beneficial genera such as Levilactobacillus and Companilactobacillus, and decreasing the complexity of ARG-MGE-microbe co-occurrence networks in corn silage under nicosulfuron exposure. Structural equation modeling indicated that there was a significant association between bacterial community and ARGs proliferation, and it had the strongest explanatory power for the variation in ARGs abundance, followed by MGEs. These findings underscore the ecological risks associated with nicosulfuron and demonstrate that ZnO NPs have the potential to mitigate ARGs dissemination in pesticide-contaminated silage. However, this potential does not qualify ZnO NPs as an effective strategy, and their role in promoting safer forage production still requires further evaluation.},
}
@article {pmid41092232,
year = {2025},
author = {Meneguzzi, M and Bravo, J and Gaire, TN and Ferm, PM and Torremorell, M and Boucher, C and Noyes, NR},
title = {Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf261},
pmid = {41092232},
issn = {1537-1719},
abstract = {At present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in a field or clinical sample, particularly when followed by long-read sequencing. Our work addressed this limitation by combining targeted enrichment with long-read, real-time sequencing. Using a panel of probes targeting 16,069 complete viral genomes, we validated this workflow (termed TELSVirus) on complex sample matrices collected from pigs, and compared its performance to traditional methods including rRT-PCR and shotgun metagenomics. Using serial dilutions of samples with known viral status, we observed that TELSVirus generated viral reads for dilutions up to 10-9. TELSVirus was able to detect viral targets when shotgun metagenomic long- and short-read datasets did not, and when rRT-PCR results were undetermined. Finally, we performed TELSVirus on 144 oral fluid samples collected in the field, which are highly complex and diverse samples used for viral surveillance in swine. We identified a high prevalence of relatively understudied viruses, often found co-circulating with better-characterized viruses. In many cases, TELSVirus generated ultra-deep genome coverage, allowing for further genomic epidemiological investigations, although bioinformatic methods need further development to work robustly with TELSVirus data. Our results support using TELSVirus for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.},
}
@article {pmid41091222,
year = {2025},
author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY},
title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {49},
pmid = {41091222},
issn = {1432-1831},
support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.},
}
@article {pmid41089932,
year = {2025},
author = {Zhang, W and Guo, H and Xu, W and Chen, W and Hu, Y and Wang, Z},
title = {Di-(2-ethylhexyl) phthalate-degrading functional microorganisms were identified in black soil based on high throughput analysis.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100479},
pmid = {41089932},
issn = {2666-5174},
abstract = {Di-(2-ethylhexyl) phthalate (DEHP) has become an increasingly serious pollutant in soils. Microbial degradation represents a highly promising approach for its remediation. In this study, four black soils were used to simulate the natural degradation of DEHP over a 75-day microenvironmental experiment. High-throughput analysis was conducted to investigate the distribution and abundance of functional genes in soil microorganisms, aiming to explore functional microbial information. The degradation efficiency of DEHP in black soils was 76.37 %, 74.16 %, 92.21 %, and 75.35 %. The α-diversity of microbial community was positively correlated with the degradation rate. Actinobacteria and Proteobacteria exhibited sensitivity to DEHP contamination. Xanthomonaceae, Sphingomonadaceae, Hypomicrobiaceae, and Comamonadaceae contributed to the upstream metabolism of DEHP. The abundances of Rhodococcus, Sphingomonas, Nocardioides, and Arthrobacter were positively correlated with the abundance of functional genes enriched in the black soil for benzoate degradation. Concurrently, 10 DEHP-degrading bacterial communities were identified, and the taxonomic and functional profiles of certain members within these communities were consistent with the metagenomic data. Bacterial communities JQ104, JQ52, and JQ129 degraded >98 % of DEHP (400 mg/L) in 48 h, demonstrating remarkable degradation efficiency. This study demonstrated the dynamic impact of the indigenous microbiome on DEHP contamination and verified the degradation capabilities of key functional microorganisms.},
}
@article {pmid41089718,
year = {2025},
author = {Takahashi, Y and Fujitani, H and Taniguchi, I and Gotoh, Y and Shimada, Y and Ikeda, S and Hayashi, T and Tago, K and Hayatsu, M and Tsuneda, S},
title = {Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf167},
pmid = {41089718},
issn = {2730-6151},
abstract = {Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: a complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-tolerant bacteria, rather than with previously reported Nitrospira species.},
}
@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.<br><br>METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.<br><br>RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.<br><br>DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}
@article {pmid41089363,
year = {2025},
author = {Park, T and Praisler, G and Wenner, BA},
title = {Treatment of dual-flow continuous culture fermenters with an organic essential oil product minimally influenced prokaryotic microbiome.},
journal = {Journal of animal science and technology},
volume = {67},
number = {5},
pages = {1018-1032},
pmid = {41089363},
issn = {2055-0391},
abstract = {Previous research reported an essential oil (EO) product decreasing methane (CH4) production by dual-flow continuous culture (DFCC); this product could assist organic dairy producers in decreasing emissions. Our objective was to assess the effect of this EO product on the microbial populations within DFCC. Here, we hypothesized that the EO either decreased protozoal population or induced shifts in the bacterial relative abundance to decrease CH4 production. Metagenomic DNA was extracted from previous effluent samples taken from a DFCC system (n = 2) across four experimental periods, after which samples were sequenced the 16S rRNA gene and microbial taxonomy was assigned using the SILVA v138 database. The treatments included a control (CON) diet (60:40 concentrate:orchardgrass pellet mix, 17.1% crude protein, 33.0% neutral detergent fiber, 20.1% acid detergent fiber, and 27.1% starch) fed twice daily for a total of 80 g/d dry matter, or the same CON diet with the addition of EO at 3 mg/d. Protozoa were also quantified in both fermenter contents and unpooled daily effluent samples. The statistical model included fixed effects of treatment and fermenter, and random effect of period, using either MaAsLin2 or the adonis2 function in the vegan package of R for microbial features, or SAS mixed model for protozoal counts. The results were deemed significant at Q < 0.05 and p < 0.05 for the MaAsLin2 and adonis2/SAS analyses, respectively. For the protozoal populations, the treatments had no significant effect (p > 0.10) on the total counts, differentiated groups, or cell outflow. The addition of EO increased the relative abundance of Methanobrevibacter and decreased that of uncultured Methanomethylophilaceae (Q < 0.05). In contrast, EO addition had no significant effect on archaeal α- or β-diversity (p > 0.05). Despite not having a significant effect on the β-diversity of archaeal and bacterial communities, EO decreased (p < 0.05) α-diversity indices in prokaryotic communities. Moreover, EO decreased (Q < 0.01) the relative abundance of Clostridia UCG-014, Rikenellaceae RC9 gut group, and Christenellaceae R7 group, and increased (Q < 0.01) others including Treponema, Succinivibrionaceae UCG-002, and Ruminococcus. Offsetting shifts in the relative abundance of fiber-degrading bacteria and detailed methanogen communities deserves further investigation including predicted metabolic pathways impacted by population shifts induced by this EO combination.},
}
@article {pmid41089014,
year = {2025},
author = {Li, B and Xu, F and Xia, M and Li, X and Hou, X and Lyu, X and Guo, X},
title = {[Retrospective clinical analysis of 31 cases of necrotizing fasciitis of the neck with or without descending necrotizing mediastinitis].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {39},
number = {10},
pages = {971-975},
doi = {10.13201/j.issn.2096-7993.2025.10.014},
pmid = {41089014},
issn = {2096-7993},
mesh = {Humans ; Retrospective Studies ; *Fasciitis, Necrotizing/complications/therapy ; *Mediastinitis/complications ; *Neck/pathology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Prognosis ; },
abstract = {Objective:To summarize the clinical characteristics and management experience of complications in patients with cervical necrotizing fasciitis （CNF） with or without descending necrotizing mediastinitis （DNM）, in order to provide a basis for optimizing diagnosis and treatment strategies. Methods:A retrospective analysis was conducted on the clinical data of 31 patients diagnosed with CNF and DNM at Shandong Provincial Hospital Affiliated to Shandong First Medical University between October 2019 and March 2024. A comprehensive evaluation was performed based on the patients' clinical characteristics, metagenomic next-generation sequencing （mNGS） pathogen detection results, imaging assessments, surgical interventions, management approaches for specific complications, and prognostic outcomes. Results:Among the 31 patients, 10 had severe diabetes mellitus. Etiological analysis was summarized as follows: 5 cases were odontogenic, 3 were of tonsillar origin, 3 were due to endogenous esophageal injury, 2 were due to exogenous cervical trauma, 2 originated from a congenital branchial cleft fistula, and 16 cases had an unknown etiology. Among them, 29 patients underwent surgery via an external cervical approach, 1 patient underwent surgery via an intraoral approach, and 1 patient received ultrasound-guided puncture and drainage therapy. Ultimately, 29 patients were cured and discharged （including 1 patient who experienced two instances of major neck vessel rupture and successfully underwent two interventional embolization procedures for hemostasis）; 2 patients died after failed rescue efforts due to concurrent sepsis and multiple organ dysfunction. The treatment success rate was 93%, and the mortality rate was 7%. In this cohort of CNF and DNM cases, only a minority had a clearly identified odontogenic cause; although the etiology was unknown in most cases, imaging consistently showed oropharyngeal lymph node necrosis, suggesting a possible pharyngeal origin of infection in adults. The mNGS pathogen profile was predominantly Gram-positive bacteria, accompanied by anaerobic bacilli and fungi. Conclusion:CNF and DNM are severe and rapidly progressive conditions that can lead to life-threatening complications within hours. Timely recognition can reduce unnecessary examinations and expedite treatment.},
}
@article {pmid41088813,
year = {2025},
author = {Guo, YN and De, R and Wang, FM and Han, ZZ and Liu, LY and Sun, Y and Yao, Y and Ma, XL and Liu, S and Zhu, C and Qu, D and Zhao, LQ},
title = {Molecular Characterization of New Recombinant Human Adenoviruses Detected in Children with Acute Respiratory Tract Infections in Beijing, China, 2022-2023.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {9},
pages = {1071-1081},
doi = {10.3967/bes2025.105},
pmid = {41088813},
issn = {2214-0190},
mesh = {Humans ; *Adenoviruses, Human/genetics/classification/isolation &amp; purification ; *Respiratory Tract Infections/virology/epidemiology ; Child, Preschool ; Child ; *Recombination, Genetic ; Male ; Beijing/epidemiology ; Infant ; Female ; Phylogeny ; *Adenovirus Infections, Human/virology/epidemiology ; Acute Disease ; Genome, Viral ; },
abstract = {OBJECTIVE: Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control.<br><br>METHODS: Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes.<br><br>RESULTS: Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16.<br><br>CONCLUSION: A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.},
}
@article {pmid41088467,
year = {2025},
author = {Osburn, ED and Weissman, JL and Strickland, MS and Bahram, M and Stone, BW and McBride, SG},
title = {Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {131},
pmid = {41088467},
issn = {2524-6372},
support = {2131837//National Science Foundation/ ; 2020-67034-41310//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.<br><br>RESULTS: Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~&#x2009;60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.<br><br>CONCLUSIONS: Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.},
}
@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."<br><br>METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35&#xa0;mg/kg) for modeling. ZAC rats were orally administered 5&#xa0;mg/kg Zacopride daily for 7&#xa0;days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.<br><br>RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.<br><br>CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}
@article {pmid41088296,
year = {2025},
author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J},
title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1083},
pmid = {41088296},
issn = {1479-5876},
support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; },
abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.<br><br>METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.<br><br>RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC&#x2009;=&#x2009;91.12%) and predict the treatment effect (AUC&#x2009;=&#x2009;91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.<br><br>CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .},
}
@article {pmid41088250,
year = {2025},
author = {Koehler, AV and Wang, T and Stevens, MA and Haydon, SR and Gasser, RB},
title = {Long-term molecular surveillance of Cryptosporidium and Giardia in wildlife in protected drinking water catchments.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {413},
pmid = {41088250},
issn = {1756-3305},
support = {LP160101299//Australian Research Council/ ; },
mesh = {*Cryptosporidium/genetics/isolation &amp; purification/classification ; Animals ; *Giardia/genetics/isolation &amp; purification/classification ; *Cryptosporidiosis/epidemiology/parasitology ; Feces/parasitology ; *Giardiasis/epidemiology/veterinary/parasitology ; *Animals, Wild/parasitology ; *Drinking Water/parasitology ; Victoria/epidemiology ; Genotype ; Longitudinal Studies ; Prevalence ; Epidemiological Monitoring ; },
abstract = {BACKGROUND: This study presents findings from a 15-year longitudinal surveillance program (2009-2024) monitoring Cryptosporidium and Giardia in protected drinking water catchments in Melbourne and environs in the State of Victoria, Australia. As one of the few major cities worldwide sourcing largely unfiltered water from forested catchments, Melbourne presents a unique opportunity to assess the occurrence and prevalence of protozoan parasites in a minimally disturbed ecosystem.<br><br>METHODS: A total of 14,960 animal faecal samples were analysed using polymerase chain reaction (PCR)-based sequencing, including 8695 samples collected over the past 9&#xa0;years.<br><br>RESULTS: Cryptosporidium was detected in 3.15% of samples and Giardia in 0.16%. A total of 12 recognised Cryptosporidium species and genotypes were identified, nine of which have known zoonotic potential, as well as two sub-assemblages (AI and AIII) of Giardia duodenalis, including four novel assemblage AI variants. Parasite diversity was the highest in eastern grey kangaroos, which hosted at least 18 Cryptosporidium variants. Temporal analyses revealed significant inter-annual variation, with peak prevalence during the 2023 La Ni&#xf1;a year and seasonal differences by host group. Notably, C. ubiquitum, C. muris and C. occultus were recorded for the first time in these catchments. In spite of the low prevalence of high-risk species such as C. parvum and the absence of C. hominis, the detection of emerging and previously uncharacterised genotypes emphasises the importance of sustained surveillance.<br><br>CONCLUSIONS: These findings have broad implications for managing zoonotic risk in unfiltered water systems worldwide. Advances in metagenomics and high-throughput sequencing platforms will be critical for enhancing future pathogen monitoring and catchment management strategies in the context of increasing climate and environmental pressures.},
}
@article {pmid41087996,
year = {2025},
author = {Kruasuwan, W and Pathomchareansukchai, D and Tangsawad, W and Wankaew, N and Arigul, T and Nitayanon, P and Nimsamer, P and Duangjanchot, R and Arayamethakorn, S and Chancharussin, N and Jenjaroenpun, P and Kamolvit, W and Suputtamongkol, Y and Wongsurawat, T and Tansirichaiya, S},
title = {Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1299},
pmid = {41087996},
issn = {1471-2334},
}
@article {pmid41087940,
year = {2025},
author = {Li, C and Liu, M and Ji, Y and Pang, S and Tian, J and Li, X and Zhang, M and Gu, Y and Chen, H and He, L and Wu, Y},
title = {Clinical characteristics and prognostic indicators in Listeria monocytogenes meningoencephalitis: A retrospective case series and literature review.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {420},
pmid = {41087940},
issn = {1471-2377},
support = {YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; },
mesh = {Humans ; Middle Aged ; Male ; Retrospective Studies ; Female ; Prognosis ; Adult ; *Listeria monocytogenes ; Aged ; *Meningitis, Listeria/diagnosis/cerebrospinal fluid ; *Meningoencephalitis/diagnosis/cerebrospinal fluid ; *Listeriosis/diagnosis/cerebrospinal fluid ; },
abstract = {BACKGROUND: Listeria monocytogenes meningoencephalitis (LMM) is a rare but severe central nervous system (CNS) infection. This study aimed to characterize the clinical manifestations, diagnostic findings, treatment responses, and prognostic factors associated with LMM.<br><br>METHODS: We retrospectively analyzed the clinical data of 13 patients diagnosed with LMM at Xuzhou Medical University Affiliated Hospital between 2018 and 2023. An additional five cases were identified through a literature search in the China National Knowledge Infrastructure (CNKI) and Wanfang databases from 2019 to 2022. Clinical features, cerebrospinal fluid (CSF) and blood test results, imaging findings, treatments, and outcomes were summarized.<br><br>RESULTS: Among 18 patients (11 males, 7 females; mean age 51.6&#x2009;&#xb1;&#x2009;17.2 years), all had acute onset with fever (100%), headache (83.3%), and altered consciousness (77.8%). CSF analysis showed elevated pressure in 83.3%, increased leukocytes and protein in all cases, and variable glucose levels. LM was cultured from CSF in 10 patients and detected via metagenomic next-generation sequencing (mNGS) in 12. Imaging findings included hydrocephalus in 4 cases and meningeal enhancement in 2 cases. Full recovery was observed in 2 cases, improvement in 9, palliative care in 3, and death in 4. Early seizures and hydrocephalus were linked to worse outcomes.<br><br>CONCLUSION: Listeria monocytogenes meningoencephalitis is a rapidly progressive CNS infection with variable presentations and significant risk of poor outcomes. Early recognition, appropriate antimicrobial coverage, and timely diagnostic testing are essential to improving prognosis.<br><br>TRIAL REGISTRATION: Not applicable.},
}
@article {pmid41040331,
year = {2025},
author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM},
title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41040331},
issn = {2692-8205},
abstract = {Human disruption of ecosystems poses a significant threat to global health, driving the need for low-cost, low-power, and easily deployable sensors for environmental and health monitoring. Microbial bioelectronic sensors are particularly well-suited as they generate electrical signals and can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies for bioelectronic sensors lack modularity, are limited to a few microbial chassis, and depend on specialized instruments for signal detection. Here, we present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play platform for bioelectronic sensor development. This system comprises a "sender" bacterium that produces electron mediators in response to analytes and a "receiver" bacterium that utilizes the electron mediators to generate electrical signals via extracellular electron transfer (EET). By modularly swapping the sender bacterium and its associated genetic sensing elements, we achieved bioelectronic sensing of metals, small molecules, and peptides in distinct environmental, food, and human-relevant settings. Moreover, we designed a centimetre-sized bioelectronic device that enables low-cost, portable signal readout from e[-]COSENS using a household digital multimeter. The e[-]COSENS platform greatly simplifies the bioelectronic sensor design and opens unprecedented potential for bioelectronic sensor applications.},
}
@article {pmid40889483,
year = {2025},
author = {Bertrans-Tubau, L and Martínez-Campos, S and López-Doval, JC and Abril, M and Pladelasala-Rocafiguera, G and Ponsá, S and Suñer, AC and Salvadó, V and Hidalgo, M and Doménech-Pascual, A and Romaní, AM and Pico-Tomàs, A and Balcázar, JL and Proia, L},
title = {Improving small urban wastewater treatment plants with a nature-based reactor for tertiary treatment.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126983},
doi = {10.1016/j.jenvman.2025.126983},
pmid = {40889483},
issn = {1095-8630},
mesh = {*Wastewater ; Nitrogen ; Phosphorus ; *Bioreactors ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; Sewage ; Biofilms ; },
abstract = {Urban wastewater treatment has significantly improved in recent decades, reducing the environmental impacts of their effluents and improving the chemical and ecological status of receiving water bodies. However, specific treatments, focused on nitrogen and phosphorus removal, have been implemented principally in large urban wastewater treatment plants (UWWTPs) serving over 10,000 population equivalents (P.E). In contrast, small UWWTPs (<10,000 P.E.) are generally not required to meet nutrient discharge limits despite the revised Urban Wastewater Treatment Directive. Nature-Based Solutions (NBS) offer cost-effective alternatives for small facilities as potential tertiary treatments. This research evaluated a pond-stream system, based on the biological activity of benthic (biofilms) and planktonic microbial communities (biofilm-plankton reactor, BPR), as an additional treatment step for activated sludge UWWTPs. The BPR achieved removal efficiencies for nitrogen (67.4 ± 11.1 %) and Escherichia coli (75.4 ± 37.3 %), while phosphorus, carbon, and targeted contaminants of emerging concern were highly variable and were not consistently removed. Microbial communities' structure and functions were assessed through algal biomass, stoichiometry, and extracellular enzymatic activities, providing a distinctive perspective into the BPR's microbial ecological dynamics related to removal efficiencies. Shotgun metagenomics identified a broad range of nitrogen functional genes, mainly involved in biodegradation and biosynthesis processes. This next-generation sequencing approach complemented conventional E. coli count methods, offering a deeper understanding of potential pathogen hotspots in treated effluents. Overall, the BPR system demonstrated a promising NBS for nitrogen and microbiological contaminant removal in small UWWTPs, whereas further investigation is needed to optimise the removal of other important water quality parameters.},
}
@article {pmid41087922,
year = {2025},
author = {Wang, Y and Liang, M and Hu, M and Mao, G},
title = {Disseminated Talaromyces marneffei infection in a patient with Ankylosing Spondylitis: a case report and review of the literature.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1316},
pmid = {41087922},
issn = {1471-2334},
abstract = {BACKGROUND: Ankylosing Spondylitis (AS) is a prevalent autoimmune disorder that necessitates the prolonged use of corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDs), and disease-modifying antirheumatic drugs (DMARDs). Immunosuppressive medications are now commonly incorporated into treatment plans; however, this may increase patients' risk of severe infections. Infections caused by Talaromyces marneffei (TM) are rarely seen in patients with AS, yet if left untreated, they could result in severe morbidity and even death.<br><br>CASE REPORT: This report presents a comprehensive case study of a 44-year-old Human Immunodeficiency Virus (HIV)-negative male with Ankylosing Spondylitis (AS) complicated by diabetes mellitus, who developed both soft tissue and pulmonary infections. Initial diagnosis suggested a bacterial etiology; however, clinical response to broad-spectrum antibiotics was suboptimal. Subsequent diagnostic procedures, including biopsy and culture of axillary lymph nodes and pulmonary tissue, coupled with Metagenomic Next-Generation Sequencing (mNGS), confirmed the diagnosis of disseminated TM infection. The patient achieved favorable outcomes following targeted antifungal therapy.<br><br>CONCLUSION: Patients with compromised immune function due to chronic immunosuppressive treatments require vigilant monitoring for uncommon opportunistic pathogens, particularly fungal infections. Advanced diagnostic techniques for early identification of pathogens, prompt and accurate prescription of antimicrobial agents, tailored dosing schedules, and stringent monitoring for potential complications are crucial for optimizing patient outcomes.},
}
@article {pmid41087898,
year = {2025},
author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C},
title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {660},
pmid = {41087898},
issn = {1471-2180},
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.<br><br>METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.<br><br>RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.<br><br>CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.},
}
@article {pmid41087864,
year = {2025},
author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X},
title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {663},
pmid = {41087864},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China,China/ ; },
abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.<br><br>METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.<br><br>RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.<br><br>CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).},
}
@article {pmid41087617,
year = {2025},
author = {Liu, M and Yang, L and Nan, D and Ma, L and Zhang, J and Liang, F and Yang, J and Liu, X},
title = {Hyperbaric oxygen treatment mitigates gut dysbiosis of mice with spinal cord injury.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41087617},
issn = {1432-1440},
support = {No. 82101964//National Natural Science Foundation of China/ ; No. 7202055//Natural Science Foundation of Beijing Municipality/ ; CYDXK 202208//Beijing Chao-Yang Hospital Multi-disciplinary Team Program/ ; },
abstract = {Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.},
}
@article {pmid41087549,
year = {2025},
author = {Chauhan, M and Maniya, H and Mori, P and Nagpal, R and Tirgar, P and Kumar, V},
title = {Assessment of multi-strain probiotics in regulating diet-induced obesity in Balb/c mice model.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {41087549},
issn = {1476-5497},
abstract = {BACKGROUND/OBJECTIVES: This study investigated the efficacy of a novel multi-strain probiotic (MSP), composed of Limosilactobacillus fermentum BAB 7912, Bacillus rugosus PIC5CR, and Bacillus rugosus PIB9CR, in preventing and reverting diet-induced obesity in Balb/c male mice.<br><br>SUBJECTS/METHODS: This study used 8-week-old Balb/c mice. A total of 40 mice were divided into five groups namely control negative (CN), control with obesity (CO), and three treatment groups: microbial consortium treated (MCT), Healthy control 1 (HC1), and Healthy control 2 (HC2). Obesity was induced using a high-fat diet. MSP formulation developed indigenously as part of previous study, was fed to Balb/c mice at different time intervals to study its preventive and ameliorative potential. Animals were dissected for the collection of blood as well as various organs to study the effect of MSP feeding on obesity status. Results were validated using histopathological and metagenomic data.<br><br>RESULTS: The CN and other treatment groups gained significant weight at the end of 6 weeks, while no significant weight gain was observed among HC1 group animals that were fed with HFD and MSP together. This highlights the preventive effect of continuous MSP feeding in the HC1 animal group. Initial liver histopathology in the HC1 group revealed enlarged hepatocytes and fat droplets. By week 9, the MCT group, which received MSP with a basal diet, showed liver recovery towards normal, accompanied by body weight improvement from 28.02&#x2009;&#xb1;&#x2009;0.7&#x2009;g to 26.18&#x2009;&#xb1;&#x2009;0.96&#x2009;g. Metagenomic analysis revealed that MSP treatment increased the relative abundance of health-promoting bacteria, notably Lactobacillaceae (specifically Lactobacillus).<br><br>CONCLUSIONS: Findings indicated that continuous consumption of MSP contributes significantly in prevention of obesity and associated metabolic disorders. Future studies are needed to explore the mechanisms underlying these effects and to evaluate the potential of MSP for human health.},
}
@article {pmid41087370,
year = {2025},
author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D},
title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35782},
pmid = {41087370},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; },
abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.},
}
@article {pmid41087364,
year = {2025},
author = {Boulay, A and Leprince, A and Enault, F and Rousseau, E and Galiez, C},
title = {Empathi: embedding-based phage protein annotation tool by hierarchical assignment.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9114},
pmid = {41087364},
issn = {2041-1723},
support = {325947//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Viral Proteins/genetics/metabolism/classification ; *Molecular Sequence Annotation/methods ; Machine Learning ; Genome, Viral ; Databases, Protein ; *Software ; Bacteria/virology ; *Computational Biology/methods ; },
abstract = {Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner. New categories were specifically elaborated for phage protein functions and organized such that molecular-level functions are respected in each category, making them well suited for training machine learning classifiers based on protein embeddings. Empathi outperforms homology-based methods on a dataset of cultured phage genomes, tripling the number of annotated homologous groups. On the EnVhogDB database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.},
}
@article {pmid41086989,
year = {2025},
author = {Zheng, L and Yao, L and Zhu, B and Chen, S and JinQian, and Liu, S and JinZhao, and Chen, Z and ShuaiXiang, and Xie, Z and Zhu, J and Wang, S and KaiWu, and Chen, J and Zhang, S and Lu, X},
title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120399},
doi = {10.1016/j.jad.2025.120399},
pmid = {41086989},
issn = {1573-2517},
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.},
}
@article {pmid41086964,
year = {2025},
author = {Zhang, X and Qaisar, M and Xu, F and Sun, J and Li, J and Cai, J},
title = {Bio-induced hydroxylated magnesium ammonium phosphate precipitation drives non-biological ammonium removal in sulfide-based denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133492},
doi = {10.1016/j.biortech.2025.133492},
pmid = {41086964},
issn = {1873-2976},
abstract = {The sulfide-based autotrophic denitrification (SAD) process showed remarkable efficiency in nitrate (98.18 ± 2.13 %) and sulfide (97.4 ± 2.75 %) removal, while also resulting in unintentional ammonium elimination (18.92 ± 9.79 %) through a 138-day continuous-flow experiment. Batch tests demonstrated kinetic decoupling between ammonium removal and SAD activity, with ammonium elimination exhibiting a substantial dependence on pH (p < 0.01), indicating a chemically driven process. XRD and SEM-EDS analysis suggested biologically induced precipitation of magnesium ammonium phosphate-like compounds (Mg3(NH4)2H4(PO4)4·8H2O). Metagenomic analysis further confirmed the absence of biological ammonium conversion pathways, as dominant functional genes were linked to sulfur-oxidizing denitrification (napAB and nosZ), driven by genus Sulfurovum (42.89 % relative abundance). No genes (hdh and hzsA) associated with ammonium oxidation were detected which ruled out the biological nitrogen transformation. These findings definitively confirm that magnesium ammonium phosphate precipitation was the principal mechanism for ammonium removal in SAD systems, offering essential insights for enhancing energy-efficient nitrogen removal in wastewater treatment.},
}
@article {pmid41086845,
year = {2025},
author = {White, AE and Koch, TJ and Jensen, TZT and Niemann, J and Pedersen, MW and Søtofte, MB and Binder, D and Lepère, C and Harb, C and Huber, R and Kramer, L and Mauvilly, M and Ebersbach, R and Wahl, J and Little, A and Wales, N and Regert, M and Schroeder, H},
title = {Ancient DNA and biomarkers from artefacts: insights into technology and cultural practices in Neolithic Europe.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2057},
pages = {20250092},
doi = {10.1098/rspb.2025.0092},
pmid = {41086845},
issn = {1471-2954},
support = {//HORIZON EUROPE European Research Council/ ; //Carlsbergfondet/ ; //HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
mesh = {*DNA, Ancient/analysis ; Archaeology ; Humans ; Europe ; History, Ancient ; Biomarkers/analysis ; Plant Bark/chemistry ; Animals ; },
abstract = {Birch bark tar was widely used throughout prehistoric Europe for hafting stone tools as well as various other purposes. While previous research has mainly focused on the identification and production of birch bark tar, its diverse uses remain to be fully explored. In this study, we combined ancient DNA with organic residue analysis to analyse 30 birch tar artefacts from nine Neolithic sites in and around the Alps. We identified birch tar as the main component, with some samples also containing conifer resin or tar, possibly added to modify its properties. Degradation markers indicate that tar used for ceramic repair was heated repeatedly, probably during cooking. Additionally, the presence of human and oral microbial DNA in some of the samples suggests the tar was chewed, in some cases by multiple individuals. The human DNA also enables us to determine the sex of those who chewed the tar, offering insights into gendered practices in the past, while plant and animal DNA shed light on past diets and the possible use of additives. This study underscores the value of integrating organic residue and ancient DNA analysis of archaeological artefacts to deepen our understanding of past cultural practices.},
}
@article {pmid41086610,
year = {2025},
author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J},
title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107607},
doi = {10.1016/j.marenvres.2025.107607},
pmid = {41086610},
issn = {1879-0291},
abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.},
}
@article {pmid41086517,
year = {2025},
author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q},
title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.},
journal = {Virology},
volume = {613},
number = {},
pages = {110712},
doi = {10.1016/j.virol.2025.110712},
pmid = {41086517},
issn = {1096-0341},
abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.},
}
@article {pmid41086499,
year = {2025},
author = {Li, Y and Zheng, X and He, H and Hu, R and Han, Z and Tao, J and Lin, T and Chen, W},
title = {Microalgal-bacterial granular sludge enhances oxytetracycline removal: Microbial responses, degradation pathways, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140103},
doi = {10.1016/j.jhazmat.2025.140103},
pmid = {41086499},
issn = {1873-3336},
abstract = {Oxytetracycline (OTC), an emerging "low-concentration, high-toxicity" contaminant, presents considerable hurdles to wastewater treatment processes. This study systematically evaluated for the first time the impacts of OTC on the operational performance, sludge characteristics, and microbial metabolic activity across three treatment systems: microalgal-bacterial granular sludge (MBGS), aerobic granular sludge (AGS), and activated sludge (AS). Results demonstrated that MBGS exhibited superior treatment efficiency, maintaining stable removal of 500 μg/L OTC at 88.06 ± 1.45 % (p < 0.05). MBGS adapted to OTC exposure by increasing ATP content and reducing lactate dehydrogenase release. Acclimated MBGS primarily removed OTC through biodegradation. Moreover, multiple OTC transformation products with reduced toxic potential were detected, signifying that MBGS systems achieve efficient microbial degradation. Metagenomic analyses revealed that Pseudomonadota in MBGS displayed high adaptability under OTC exposure. Additionally, OTC exposure upregulated carbohydrate and energy metabolism in MBGS, thereby enhancing overall microbial metabolic activity. Alphaproteobacteria contributed most significantly to key functional genes, underscoring their critical role in contaminant removal in the MBGS. Redundancy analysis highlights a robust association between Alphaproteobacteria and the abundance of antibiotic resistance genes. This study confirms the MBGS's resilience to OTC-contaminated wastewater, highlighting its potential for efficient antibiotic wastewater treatment.},
}
@article {pmid41086488,
year = {2025},
author = {Chen, L and Lin, Y and Jia, X and Zheng, X and Zhuo, Y and Chen, Q and Fan, H and Fang, Y and Zhang, H and Lin, C},
title = {Dual-Path valorization of organic waste via black soldier fly: Synergistic enhancement of feed efficiency, crop quality, and climate mitigation in closed-loop aquaculture.},
journal = {Waste management (New York, N.Y.)},
volume = {209},
number = {},
pages = {115186},
doi = {10.1016/j.wasman.2025.115186},
pmid = {41086488},
issn = {1879-2456},
abstract = {The rapid expansion of aquaculture generates vast quantities of hyperhydrated organic waste (e.g., eel feces), posing a severe waste management challenge due to its recalcitrance and high disposal costs. This study presents a circular bio-strategy using black soldier fly (BSF, Hermetia illucens) larvae to synergistically convert aquaculture waste and agro-industrial residue (Flammulina velutipes substrate) within a closed-loop system. The process achieved 92.6 % waste utilization efficiency, yielding two valuable co-products: First, BSF larvae accumulated nutrient-rich biomass (17.9 % crude protein, 8.03 % lauric acid). As a 1.0 % supplement in broiler diets, it significantly enhanced feed efficiency by 2.6 % and increased 42-day body weight by 7.5 % (P < 0.01), demonstrating a viable fishmeal alternative. Second, BSF frass was composted into a superior organic fertilizer, which outperformed conventional composting by reducing NH3 emissions by 34 % (P < 0.001) and increasing total nitrogen retention by 15.3 %, attributed to pH modulation and chitin-NH4[+] complexation. The frass also enhanced phosphorus (7.05 %) and potassium (2.76 %) bioavailability. Metagenomics analysis revealed that frass inoculation enriched functional microbes (Azoarcus, LDA > 2.5; Roseisolibacter) driving synchronized nitrogen fixation and phosphate solubilization. Field application of the compost boosted tomato yields by 12.1 % (P < 0.05) and improved fruit quality (vitamin C + 18.6 %, soluble sugars + 20 %). This work establishes a scalable waste-to-resource paradigm that concurrently addresses waste management, livestock feed security, and sustainable crop intensification.},
}
@article {pmid41085836,
year = {2025},
author = {Vidal-Silva, IM and Loza, A and Gutierrez-Rios, RM},
title = {Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {384},
pmid = {41085836},
issn = {1573-0972},
support = {IN202524//PAPIIT-DGAPA/ ; 319234//Ciencia B&#xe1;sica y/o Ciencia de Frontera. Modalidad: Paradigmas y Controversias de la Ciencia 2022/ ; },
}
@article {pmid41085703,
year = {2025},
author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J},
title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.},
journal = {Molecular genetics and genomics : MGG},
volume = {300},
number = {1},
pages = {97},
pmid = {41085703},
issn = {1617-4623},
support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&amp;IC/J/14/2022/160//JKST&amp;IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; },
mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; },
abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.},
}
@article {pmid41085588,
year = {2025},
author = {Purohit, HV and Chakraborty, J},
title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {383},
pmid = {41085588},
issn = {1573-0972},
}
@article {pmid41085530,
year = {2025},
author = {Fan, M and Wang, Z and Yao, M and Li, X and van der Meer, W and Tao, Y and Rose, JB and Liu, G},
title = {Unveiling Chemical-Microbial Cascade Risk Factors from Plastic Pipe Leaching in Drinking Water.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10244},
pmid = {41085530},
issn = {1520-5851},
abstract = {Plastic pipes are increasingly used in drinking water distribution systems, yet their impact on water quality remains insufficiently understood. Here, we systematically investigate the dual outcomes posed by plastic pipes─chemical leaching and cascaded microbial exposure risks─by integrating Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and metagenomic analysis. Our results reveal that plastic pipes continuously release dissolved organic matter (DOM), including organic additives such as bisphenols (BPs) and organophosphate esters (OPEs), which profoundly reshape microbial communities. Under chlorinated conditions, leached DOM alters microbial diversity, promoting chlorine-resistant bacteria and opportunistic pathogens (OPs), while under nonchlorinated conditions, it accelerates microbial growth and enriches antibiotic resistance genes (ARGs), OPs, and virulence factors (VFs). Among plastic materials, polyethylene (PE) exhibited the highest chemical risk, releasing high concentrations of TCPP (700 ng/L) and BPF (200 ng/L) along with 207-227 unique DOM molecules. In contrast, polyvinyl chloride (PVC) supported the highest OP abundance, while polypropylene random copolymer (PPR) fostered the greatest OP diversity. These findings challenge conventional drinking water safety assessments that separate chemical contamination from microbial risk, underscoring the urgent need for an integrated risk assessment framework. Furthermore, they highlight the necessity of paying greater attention to the chemical and cascading microbial issues arising from the leaching of plastic pipes into drinking water, and of conducting a more comprehensive assessment of the associated potential health risks.},
}
@article {pmid41084448,
year = {2025},
author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP},
title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {15},
pages = {4315-4324},
doi = {10.19540/j.cnki.cjcmm.20250421.401},
pmid = {41084448},
issn = {1001-5302},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration &amp; dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; },
abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.},
}
@article {pmid41083999,
year = {2025},
author = {Holst, BS and Bonnevie, A and Spens, J and Lindahl, JF and Huupponen, A and Syrjä, P and Blomström, AL},
title = {Tick-borne encephalitis virus associated with foetal death in a bitch, a case report.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {326},
pmid = {41083999},
issn = {1743-422X},
mesh = {Animals ; Dogs ; Female ; Pregnancy ; *Dog Diseases/virology/pathology/diagnosis/transmission ; *Encephalitis Viruses, Tick-Borne/isolation &amp; purification/genetics ; *Infectious Disease Transmission, Vertical/veterinary ; *Fetal Death/etiology ; *Encephalitis, Tick-Borne/veterinary/virology/transmission/pathology/diagnosis ; *Pregnancy Complications, Infectious/veterinary/virology ; Placenta/virology/pathology ; },
abstract = {BACKGROUND: For the first time, a case of vertical transmission of TBEV in a dog associated with foetal death is described.<br><br>CASE PRESENTATION: A six-year-old beagle bitch experienced foetal death from day 49 in pregnancy. A caesarean section was performed on day 56, and one live and three dead pups in different stages of resorption were delivered. Black mucoid, non-smelling foetal membranes surrounded the dead foetuses. The live-born foetus died despite efforts to save it and was sent for autopsy together with the placenta. Autopsy demonstrated lung atelectasis and no malformations. A mild acute necrotizing placentitis was diagnosed on histopathology. Selective bacteriological cultures for Brucella canis from blood, vagina and the foetus were all negative, as was PCR for canine herpes virus (CHV). Viral metagenomics analysis identified the presence of tick-borne encephalitis virus (TBEV) in the placental tissue and in situ hybridization revealed TBEV in the trophoblasts. The bitch had antibodies to TBEV. One year later, the bitch had a normal pregnancy and whelping.<br><br>CONCLUSION: With the spread of both ticks and TBEV, infection with TBEV should be given further consideration as a potential differential diagnosis in cases of foetal death in dogs.},
}
@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}
@article {pmid41082849,
year = {2025},
author = {Su, R and Zhu, L and He, X and Zhang, H and Huang, R and Zeng, J and Zhao, D},
title = {Denitrifying anaerobic methane oxidation reduces greenhouse gas emissions in floodplain sediments of the largest freshwater lake in China under flash drought.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127532},
doi = {10.1016/j.jenvman.2025.127532},
pmid = {41082849},
issn = {1095-8630},
abstract = {Climate change-induced extreme heat, flooding and drought events influence the carbon and nitrogen cycling, including the denitrifying anaerobic methane oxidation (DAMO) process which couples the nitrogen removal and methane (CH4) mitigation. To assess the impacts of 2022 record-breaking flash drought (summer FD) on the DAMO process, we collected bulk soils and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during summer FD and winter drought. The in situ CH4 fluxes and potential DAMO rates were determined using static-chamber technique and [13]C stable isotope method. The abundance, composition and metabolic pathways of DAMO archaeal and bacterial communities were investigated using quantitative PCR, high-throughput and metagenomic sequencing techniques. Higher DAMO rates (8.73 ± 3.79 and 16.03 ± 7.45 nmol [13]CO2 g[-1] d[-1] for nitrate-DAMO and nitrite-DAMO respectively) were observed during summer FD compared to winter drought, and nitrite-DAMO (52%∼74%) dominated the DAMO processes. DAMO bacterial pmoA genes (4.7 × 10[4]∼1.1 × 10[6] copies g[-1] dry soil) were more abundant than DAMO archaeal mcrA genes (1.4 × 10[3]∼1.3 × 10[4] copies g[-1] dry soil). Nitrate- and nitrite-DAMO rates were mainly driven by temperature, available nitrogen substrate and the abundance of DAMO archaea and bacteria, possibly contributing to CH4 consumption in the littoral wetlands of Poyang Lake. Several reconstructed metagenome-assembled genomes possessing genes involved in anaerobic methane oxidation and nitrate/nitrite reduction could potentially participate in cooperative DAMO process. This study elucidates the DAMO process and microbial mechanisms under flash droughts, providing a novel insight for the carbon-nitrogen coupling and mitigation of greenhouse gases in aquatic ecosystems.},
}
@article {pmid41082619,
year = {2025},
author = {Huang, PH and Liao, YC and Chen, FJ and Wu, HC and Liu, PY},
title = {Metagenomic Sequencing of Blood Culture Broth for Diagnosing Fastidious Endocarditis.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf554},
pmid = {41082619},
issn = {1537-6591},
}
@article {pmid41082531,
year = {2025},
author = {Mwasi, L and Khamadi, S and Bulimo, W and Kinyua, J and Yalwala, S and Sang, LP and Robert, H and Kellar, GG and Eads, J and Eyase, F},
title = {Identification and genetic characterization of Jingmen tick virus from ticks sampled in select regions of Kenya; 2022-2024.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0329878},
doi = {10.1371/journal.pone.0329878},
pmid = {41082531},
issn = {1932-6203},
mesh = {Animals ; Kenya/epidemiology ; Phylogeny ; *Ticks/virology ; *Flavivirus/genetics/isolation &amp; purification/classification ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Cattle ; },
abstract = {Jingmen tick virus (JMTV), an emerging segmented RNA virus classified as an ungrouped flavivirus, poses a growing public health concern globally. Known for its association with febrile illnesses and wide host range, JMTV has been detected in Rhipicephalus, Hyalomma, and Amblyomma ticks collected from cattle, goats, sheep, camels, and chickens in pastoral regions of Kenya, including Baringo, Mandera, Malindi, Lamu, Mombasa, Wajir, Isiolo, and West Pokot. Using viral metagenomics next-generation sequencing, this study analysed adult ticks (n = 1629, 72 pools). A total of 53% (38/72) pools were positive for at least one viral pathogen, with JMTV detected in 87% (33/38) of these pools across all study sites. Phylogenetic analyses revealed evidence of distinct Kenyan JMTV strains, with sequence segments from Malindi and Wajir clustering uniquely in their own clade; suggesting potential localised evolutionary pressures. Time calibrated phylogeny for the segment 1(RdRp) suggested varied ancestral origins and evolutionary relationships for the JMTV strains. MEME, BUSTED and FUBAR methods implemented in the Data-Monkey, unanimously identified codon 290 in segment 1 and 30 in segment 4 to be undergoing episodic positive selection. Recombination analysis performed using the RDP4 recombination detection tool indicated a recombination event in segment 2 of the Lamu JMTV strain that was confirmed by seven detection methods of the RDP4 tool and visualised in BootScan. These findings suggest that Kenyan JMTV strains are undergoing positive selection, potentially driven by unique ecological and host factors. Segmented genome evidence of recombination highlights the increasing virus's potential for antigenic diversity. Host diversity and virus phylogenetic patterns underscore the zoonotic potential and its capacity for regional spread, emphasizing the critical need for enhanced vector surveillance. Temporal and ecological drivers like seasonal tick activity and livestock movement warrant investigation to elucidate JMTV transmission dynamics. Prioritizing tick-borne virus surveillance in Kenya will strengthen public health strategies and mitigates emerging viral risks.},
}
@article {pmid41082485,
year = {2025},
author = {Zhou, W and Zhang, D and Alhaskawi, A and Ezzi, SHA and Kota, VG and Abdulla, MHAH and Abdulla, AHAH and Abdalbary, SA and Lu, H and Liang, J},
title = {Rare Pathogen in Diabetic Foot Gangrene: A Case of Wohlfahrtiimonas chitiniclastica Infection.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {223},
pages = {},
doi = {10.3791/68877},
pmid = {41082485},
issn = {1940-087X},
mesh = {Humans ; Male ; Aged ; *Diabetic Foot/microbiology ; *Gangrene/microbiology ; *Gram-Negative Bacterial Infections/microbiology/diagnosis ; },
abstract = {Wohlfahrtiimonas chitiniclastica is a rare Gram-negative bacterium typically associated with wound infections, particularly in immunocompromised patients or individuals exposed to unsanitary conditions. Although clinical cases are infrequent, the infection can lead to severe complications such as bacteremia, septic shock, and even death if unrecognized or inadequately treated. We present the case of a 76-year-old diabetic male who developed chronic, non-healing foot ulcers complicated by gangrene and maggot infestation. Diagnostic challenges were addressed using metagenomic next-generation sequencing, which identified W. chitiniclastica alongside Proteus mirabilis and Corynebacterium striatum. Management included aggressive surgical debridement to remove necrotic tissue, local application of gentamicin-impregnated bone cement, systemic antibiotic therapy with ertapenem, and wound reconstruction using a dorsally based fascial flap. This combined approach resulted in significant clinical improvement, progressive wound healing, and marked reductions in infection markers. The case highlights the decisive role of advanced sequencing technologies in identifying rare pathogens within polymicrobial infections, where conventional methods such as MALDI-TOF mass spectrometry may fail. It also emphasizes the importance of integrating precision diagnostics with surgical intervention, targeted antimicrobial therapy, and rigorous postoperative care to achieve successful outcomes. By documenting this unusual presentation, we aim to expand clinical awareness of W. chitiniclastica infections and provide a practical framework for managing similarly complex diabetic foot infections.},
}
@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}
@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173025},
doi = {10.1128/spectrum.01730-25},
pmid = {41081627},
issn = {2165-0497},
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}
@article {pmid41081605,
year = {2025},
author = {Lee, S and Kim, J and Mirdita, M and Gilchrist, CLM and Steinegger, M},
title = {Easy and interactive taxonomic profiling with Metabuli App.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf557},
pmid = {41081605},
issn = {1367-4811},
abstract = {SUMMARY: Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often requires command-line proficiency and high-performance computing resources. To lower these barriers, we developed Metabuli App, an all-in-one desktop application that efficiently runs taxonomic profiling locally on a consumer-grade computer. It features user-friendly graphical interfaces for custom database curation, raw read quality control (QC), taxonomic profiling, and interactive result visualization.<br><br>GPLv3-licensed source code and prebuilt apps for Windows, macOS, and Linux are available at https://github.com/steineggerlab/Metabuli-App and are archived at https://doi.org/10.5281/zenodo.15876171. Analysis scripts are available at https://github.com/jaebeom-kim/metabuli-app-analysis. The Sankey-based taxonomy visualization component is available at https://github.com/steineggerlab/taxoview for easy integration into other web projects.},
}
@article {pmid41081506,
year = {2025},
author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W},
title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0034825},
doi = {10.1128/msphere.00348-25},
pmid = {41081506},
issn = {2379-5042},
abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems.IMPORTANCECurrently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.},
}
@article {pmid41081392,
year = {2025},
author = {Rasmussen, AN and Langenfeld, K and Tolar, BB and Perzan, Z and Maher, K and Cardarelli, EL and Bargar, JR and Boye, K and Francis, CA},
title = {Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0082925},
doi = {10.1128/msystems.00829-25},
pmid = {41081392},
issn = {2379-5077},
abstract = {UNLABELLED: Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter (utp, urt, dur3). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase (cynS), nitrilase (nit1), omega-amidase (nit2), nitrile hydratase (nthA), and genes related to purine degradation, including biuret hydrolase (biuH), oxamic transcarbamylase (allFGH), and catabolic carbamate kinase (allK). AOA often encoded an uncharacterized amidohydrolase collocated with biuH, rather than allophanate hydrolase (atzF). A small number of AOA encoded atzF, functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes (trtA, biuH, and atzH), and in comammox, these genes were also collocated with allFGHK. The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.<br><br>IMPORTANCE: Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen-from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)-is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying microorganisms, expanding their potential metabolic substrates.},
}
@article {pmid41080808,
year = {2025},
author = {Zhang, Z and Huang, W},
title = {Exoskeleton Robot Gait Training and Its Impact on the Gut Microbiota-Brain Axis in Incomplete Spinal Cord Injury Patients: A Narrative Review of Rehabilitation Mechanisms.},
journal = {Journal of multidisciplinary healthcare},
volume = {18},
number = {},
pages = {6411-6430},
pmid = {41080808},
issn = {1178-2390},
abstract = {Exoskeleton robot-assisted gait training represents a significant advancement in neurorehabilitation for patients with incomplete spinal cord injury (iSCI). While its efficacy in improving motor function is increasingly documented, emerging evidence suggests these interventions may exert therapeutic effects through previously unrecognized physiological pathways involving the gut microbiota-brain axis. This review synthesizes current evidence regarding the bidirectional relationship between exoskeleton-based locomotor training and alterations in gut microbiome composition and function in the context of iSCI. Following spinal cord injury, significant dysbiosis occurs, characterized by reduced microbial diversity and altered taxonomic representation, which correlates with neuroinflammation, autonomic dysfunction, and impaired recovery. Exoskeleton-mediated gait rehabilitation appears to partially restore microbial homeostasis through multiple mechanisms, including autonomic nervous system regulation, altered intestinal transit time, modified intestinal barrier integrity, and immunomodulation. These microbiome modifications potentially facilitate neuroplasticity and functional recovery through microbiota-derived metabolites that traverse the blood-brain barrier or communicate via vagal afferents. The integration of metagenomic analysis with functional neuroimaging and detailed autonomic assessment in prospective studies represents a critical research direction. This emerging perspective extends beyond biomechanical rehabilitation, suggesting a comprehensive neurobiological effect that includes modulation of the microbiota-gut-brain axis, with significant implications for optimizing therapeutic strategies for individuals with incomplete spinal cord injury.},
}
@article {pmid41080802,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Metagenomic insights into viral dynamics and funcation in Baijiu.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101189},
pmid = {41080802},
issn = {2665-9271},
abstract = {Baijiu fermentation represents a sophisticated microbial-driven biochemical process mediated by complex microbial consortium. Despite extensive characterization of bacterial and fungal roles in fermentation systems, the virus remains a critical knowledge gap. In this study,we employed metagenomics to profile the dynamics of viral community in fermented grains across five stages (day 0, 5, 10, 20 and 30) of a Baijiu fermentation. The metagenomics revealed 101 viral families, dominated by Metaviridae, Parvoviridae, Aliceevansviridae, Herelleviridae, Geminiviridae, Iridoviridae, and Genomoviridae, and lactic acid bacteria was identified as primary phage hosts. The results revealed that ssRNA viruses and ssDNA viruses were more abundant during 0-5 days, dsDNA viruses became dominant during 10-30 days. Multivariate analysis indicated that the viral community dynamics during the fermentation were primarily governed by microbes in succession, environmental factors (temperature,pH, moisture and glucose) and metabolites (lactic acid, acetate and ethanol) in the biosystem. Notably, predicting phages exhibited strong positive correlations with their respective hosts (P < 0.01, r > 0.6). We have identified viral auxiliary metabolic genes (AMGs) related to amino acid metabolism and vitamin biosynthesis. At 30 days of fermentation, the number and abundance of AMGs significantly increased. Our findings provide novel insights into the viral ecology in complex Baijiu fermentation ecosystem, shedding light on the intricate interactions within fermentation microbial communities.},
}
@article {pmid41080577,
year = {2025},
author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z},
title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636876},
pmid = {41080577},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.},
}
@article {pmid41080528,
year = {2025},
author = {Wu, XT and Qiu, M and He, YQ and Wu, K and Zhao, JY and Wang, J and Ren, HY and Su, JY and Bao, P},
title = {Disproportionation of elemental sulfur by Exiguobacterium from marine sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf168},
pmid = {41080528},
issn = {2730-6151},
abstract = {Elemental sulfur disproportionation is an ancient microbial metabolic process, and the phylogenetic distribution of elemental sulfur disproportionators may be broader than previously thought. We enriched a bacterial community capable of this process, with Exiguobacterium making up 99.45% of the total population. The results indicate that Exiguobacterium facilitates the formation of thiosulfate and sulfide through elemental sulfur disproportionation. This study represents the first report documenting elemental sulfur disproportionation by Bacilli. Metagenomic analysis shows that rhodanese-like sulfur transferase genes are significantly more abundant in the experimental group than in the control group, suggesting that they are implicated in elemental sulfur disproportionation in Exiguobacterium. These findings support the idea that Bacilli and/or Firmicutes are the oldest extant bacterial phyla. Our research fills a critical gap in understanding sulfur biogeochemical cycles. Given the widespread occurrence of Exiguobacterium across various environments, direct microbial transformations between elemental sulfur and thiosulfate are likely prevalent throughout ecological systems.},
}
@article {pmid41080188,
year = {2025},
author = {Geniselli da Silva, V and Smith, NW and Mullaney, JA and Roy, NC and Wall, C and McNabb, WC},
title = {Mathematical models of the colonic microbiota: an evaluation of accuracy using in vitro fecal fermentation data.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1623418},
pmid = {41080188},
issn = {2296-861X},
abstract = {Traditional approaches for studying diet-colonic microbiota interactions are time-consuming, resource-intensive, and often hindered by technical and ethical concerns. Metagenome-scale community metabolic models show promise as complementary tools to overcome these limitations. However, their experimental validation is challenging, and their accuracy in predicting colonic microbial function under realistic dietary conditions remains unclear. This study assessed the accuracy of the Microbial Community model (MICOM) in predicting major short-chain fatty acid (SCFA) production by the colonic microbiota of weaning infants, using fecal samples as a proxy. Model predictions were compared with experimental SCFA production using in vitro fecal fermentation data at the genus level. The model exhibited overall poor accuracy, with only a weak, significant correlation between measured and predicted acetate production (r = 0.17, p = 0.03). However, agreement between predicted and measured SCFA production improved for samples primarily composed of plant-based foods: acetate exhibited a moderate positive correlation (r = 0.31, p = 0.005), and butyrate a trend toward a weak positive correlation (r = 0.21, p = 0.06). These findings suggest that the model is better suited for predicting the influence of complex carbohydrates on the colonic microbiota than for other dietary compounds. Our study demonstrates that, given current limitations, modeling approaches for diet-colonic microbiota interactions should complement rather than replace traditional experimental methods. Further refinement of computational models for microbial communities is essential to advance research on dietary compound-colonic microbiota interactions in weaning infants.},
}
@article {pmid41080146,
year = {2025},
author = {He, X and Yang, F and Qu, G and Zhang, H and Yi, M and Wang, X and Sun, S},
title = {Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103062},
pmid = {41080146},
issn = {2590-1575},
abstract = {Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: -69.8 %; IgG: -54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization.},
}
@article {pmid41079703,
year = {2025},
author = {Akinnola, OO and Samuel, AE and Omonhinmin, CA},
title = {Dataset on characterisation of microbiome of prostate tissue and expressed prostatic secretions.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112098},
pmid = {41079703},
issn = {2352-3409},
abstract = {Prostate cancer (PCa) is the second most prevalent cancer in men, particularly affecting those of Black African descent. Nigeria currently has the fourth highest risk for PCa mortality in the world. The microbiome of the prostate has emerged as a critical factor in understanding the aetiology and progression of prostate diseases, such as prostate cancer (PCa), benign prostatic hyperplasia (BPH) , benign stromal hyperplasia (BSH) and prostatitis (PRO). This study to comparatively characterise the microbiome present in prostate tissue and expressed prostatic secretion (EPS) from 30 study subjects diagnosed with PCa, BPH, BSH and PRO and sampled from the urology clinic of Lagos State University Teaching Hospital Ikeja. Bacterial species community composition and diversity were analysed based on 16S rRNA metagenome nucleotide data to ensure the accuracy, reproducibility, and broader applicability of microbiological and genomic research. Data information allows for precise identification of organisms at the species or strain level, essential for verifying experimental results and comparisons of the isolated organism's genome with related strains, providing insights into genetic diversity, virulence factors, and metabolic pathways of the sample population microbiome.},
}
@article {pmid41079637,
year = {2025},
author = {Tóth, AG and Nagy, S&#xc1; and Lakatos, I and Solymosi, N and Stágel, A and Paholcsek, M and Posta, K and Gömbös, P and Ferenczi, S and Szőke, Z},
title = {Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113539},
pmid = {41079637},
issn = {2589-0042},
abstract = {Some mycotoxins and herbicide residues pose threats to animal health. These toxins might affect the gut microbiome of fallow deer. The analyzation of the intestinal content samples of this valuable game species exposed to varying levels of zearalenone (ZEA) and other toxic compounds such as aflatoxin B1, deoxynivalenol, fumonisin B1, and glyphosate residues was performed. Metagenomic analysis revealed significant alterations in the bacterial community composition. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. Changes in the abundance of antibiotic resistance genes (ARGs) were also observed, suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.},
}
@article {pmid41079385,
year = {2025},
author = {van Ede, JM and van der Steen, S and van der Kraan, GM and van Loosdrecht, MCM and Pabst, M},
title = {Discovery of microbial glycoside hydrolases via enrichment and metaproteomics.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41079385},
issn = {2633-0679},
abstract = {The immense microbial diversity on Earth represents a vast genomic resource, yet discovering novel enzymes from complex environments remains challenging. Here, we combine a microbial enrichment with metagenomics and metaproteomics to facilitate the identification of microbial glycoside hydrolases that operate under defined conditions. We enriched microbial communities on the carbohydrate polymer pullulan at elevated temperatures under acidic conditions. Pullulan is a natural polysaccharide composed of maltotriose units linked by α-1,6-glycosidic bonds. Pullulan, along with its hydrolyzing enzymes, has broad applications across various industries. The enrichment inocula were sampled from thermophilic compost and from soil from the bank of a pond. In both cases, Alicyclobacillus was identified as the dominant microorganism. Metaproteomic analysis of the enriched biomass and secretome enabled the identification of several pullulan-degrading enzyme candidates from this organism. These enzymes were absent in the metagenomic analysis of the initial inoculum, which is highly complex with a wide diversity of species. This underscores the effectiveness of combining microbial enrichment with multi-omics for uncovering novel enzymes and sequence variants that operate under defined conditions from complex microbial environments.},
}
@article {pmid41078880,
year = {2025},
author = {Goudarzi, R and Jahanshahi, DA and Kavousi, A and Ariaeenejad, S},
title = {Discovery and engineering of bifunctional enzymes for lignocellulose degradation: Metagenomic and computational approaches.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {48},
number = {},
pages = {e00926},
pmid = {41078880},
issn = {2215-017X},
abstract = {Efficient degradation of lignocellulosic biomass is vital for converting plant-based waste into renewable fuels and chemicals. Owing to its complex composition of cellulose, hemicellulose, and lignin, its enzymatic breakdown often requires multiple enzymes to act synergistically. Bifunctional enzymes that combine two catalytic activities in a single protein offer a promising solution. This review highlights recent advances in the identification and engineering of bifunctional enzymes for lignocellulose degradation, particularly through metagenomics, protein fusion and computational design. Functional pairings, such as cellulase/xylanase, were examined with a focus on their synergistic effects, substrate specificity, and stability. Promiscuous and naturally evolved bifunctional enzymes from extreme or uncultured environments are also discussed. Advances in silico modeling and directed evolution have enhanced enzyme properties such as thermostability and substrate range. The review concludes with an outlook on the challenges and opportunities of implementing bifunctional enzymes to improve the economic and technical viability of biomass conversion.},
}
@article {pmid41078518,
year = {2025},
author = {Liu, J and Wang, L and Su, L and Chen, J and Su, R},
title = {Exploring the gut microbiota-Parkinson's disease link: preliminary insights from metagenomics and Mendelian randomization.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654418},
pmid = {41078518},
issn = {1664-302X},
abstract = {INTRODUCTION: The relationship between the gut microbiome and Parkinson's disease (PD) has recently attracted significant attention, with most studies focused on analyzing microbial composition. However, our understanding of the potential causal relationship between the gut microbiota and PD remains limited.<br><br>METHODS: We extracted microbiome data from the metagenome for broad taxonomic coverage and accurate functional analysis. Subsequently, Mendelian randomization was employed to elucidate the causal relationship between the gut microbiome and PD.<br><br>RESULTS: The gut microbiota in PD patients was found to be systemically imbalanced, characterized by an abnormal enrichment of potential pathogenic bacteria, a significant reduction in key beneficial bacteria, and a reorganization of intestinal metabolic functions. This state of imbalance involves significant abnormalities in multiple metabolic and regulatory pathways, including the glucose metabolism, oxidative stress response, protein homeostasis regulation, and immune signaling pathways. These findings suggest that dysbiosis may influence host neural function through multilevel metabolic interventions. Additionally, specific microbial communities are clearly associated with disease risk, with some bacterial populations promoting disease onset and others demonstrating a potentially protective effect. Although metagenomic findings require validation in larger cohorts, the results of this study indicate that changes in gut microbiota composition and function are closely related to PD onset and progression.<br><br>CONCLUSION: This study revealed that certain microorganisms traditionally considered beneficial may contribute to PD risk. This finding challenges previous assumptions and highlights the complexity of host-microbiome interactions. The identification of altered metabolic and immune pathways, particularly those involving bacteria that produce short-chain fatty acids, underscores the critical role of the gut microbiota in PD pathophysiology. However, the relatively small sample size of the current metagenomic analysis limits the generalizability of these findings. Larger, more diverse cohorts are needed to validate these results. Despite this limitation, the study provides important insights into microbiome-targeted therapeutic strategies, emphasizing the need to reconsider the roles of both beneficial and harmful microorganisms in PD.},
}
@article {pmid41078512,
year = {2025},
author = {Li, Y and You, J and Liao, Y and Wang, D and Wang, H and Su, Y},
title = {Daily fluctuation of genus Prevotella in porcine colon under ad libitum feeding and its association with nutrient substrates.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1688301},
pmid = {41078512},
issn = {1664-302X},
abstract = {The circadian rhythms of the gut microbiota are biologically significant for the host. However, the association between fluctuations in the relative abundance of the microbiota and nutrient substrates in the gut remains incompletely understood. Using swine as a model, this study employed continuous sampling at 9 time points over 24 h via a colonic T-shaped fistula. It investigated the temporal dynamics of nutrient substrates and Prevotella abundance in the colon of pigs over a 24-h period and further explored dynamic interactions among KEGG level-3 pathways, genes, and Prevotella using metagenomic approaches. Results revealed a significant 24-h periodicity in Prevotella abundance, peaking at T06-T09 and declining to minimal levels at T18-T21, with the nadir at T18. Dynamic correlation network analysis uncovered significant temporal associations between Prevotella rhythms and nutrient substrates: negative correlations with true protein (TP) and ammonia nitrogen (NH3-N), in contrast to positive correlations with starch and cellulose, exhibiting time lags ranging from -2 to 4 h. Prevotella copri exhibited high relative abundance and pronounced daily fluctuations, while Prevotella sp. MGM2 showed relatively high abundance but lacked daily fluctuations. Furthermore, differences existed in the dynamic correlations of genes and KEGG level-3 metabolic pathways of these two Prevotella species with nutrient substrates. The results revealed that the two Prevotella species in the colon exhibited different response strategies to nutrient substrates: Prevotella copri likely adopted a "rhythmic substrate-responsive strategy," while Prevotella sp. MGM2 followed a "sustained response strategy," which may explain their distinct daily fluctuations.},
}
@article {pmid41078511,
year = {2025},
author = {Ren, G and Shi, W and Li, W and Wang, J and Wang, C and Zhao, G},
title = {Pyrolysis temperature shapes biochar-mediated soil microbial communities and carbon-nitrogen metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1657149},
pmid = {41078511},
issn = {1664-302X},
abstract = {INTRODUCTION: Biochar derived from agricultural residues has potential to improve soil quality and regulate microbial communities, but its effect depends strongly on pyrolysis temperature.<br><br>METHODS: In this study, biochar prepared from Flammulina velutipes residue at 200&#x202f;&#xb0;C, 300&#x202f;&#xb0;C, and 400&#x202f;&#xb0;C was applied to cucumber seedling cultivation to evaluate its influence on soil physicochemical properties, microbial community structure, and functional metabolism.<br><br>RESULTS: Results showed that soil pH increased significantly with biochar addition, from 5.00 in the control to 6.17 at 400&#x202f;&#xb0;C, while soil organic matter reached the highest level in the 400&#x202f;&#xb0;C treatment (90.03 g&#xb7;kg[-1]). Available phosphorus and potassium were also enhanced, with maximum values of 731.81 mg&#xb7;kg[-1] and 481.68 mg&#xb7;kg[-1], respectively. Seedling growth responded differently to pyrolysis temperatures: the 300&#x202f;&#xb0;C biochar treatment increased above-ground biomass to 0.18 g and total biomass to 0.214 g per plant, significantly higher than the control (0.124 g). Metagenomic sequencing revealed shifts in dominant microbial phyla, with Acidobacteriota enriched at higher temperatures, and alpha diversity indices (Chao1, ACE, Sobs) increased under 400&#x202f;&#xb0;C biochar. Functional analysis indicated that carbon metabolic genes (e.g., acetyl-CoA synthesis, TCA cycle) were optimized at moderate to high temperatures, whereas nitrogen metabolism showed divergent responses, with nitrate reduction favored at 300&#x202f;&#xb0;C and nitrite reduction at 400&#x202f;&#xb0;C. Regression analysis demonstrated a positive correlation between microbial diversity and carbon metabolism genes (R [2]&#x202f;=&#x202f;0.75), but a negative correlation with nitrogen metabolism genes (R [2]&#x202f;=&#x202f;0.56). Redundancy analysis further identified ammonium nitrogen, acid phosphatase, and catalase as key drivers of microbial community and functional gene structure.<br><br>DISCUSSION: Overall, these findings highlight that biochar from mushroom residue, particularly produced at 300-400&#x202f;&#xb0;C, improves soil fertility, regulates microbial community composition, and modulates carbon and nitrogen metabolic processes, thereby enhancing cucumber seedling growth.},
}
@article {pmid41078118,
year = {2025},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70379},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}
@article {pmid41078079,
year = {2025},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70102},
pmid = {41078079},
issn = {1398-9995},
support = {/NH/NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; //Massachusetts General Hospital/ ; //the Harvard University William F. Milton Fund/ ; //American Lung Association Innovation Award/ ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.<br><br>METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age <&#x2009;1&#x2009;year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24&#x2009;h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR]&#x2009;<&#x2009;0.05), regions (mbDMRs, FDR <&#x2009;0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6&#x2009;years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR <&#x2009;0.10).<br><br>RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).<br><br>CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}
@article {pmid41077897,
year = {2025},
author = {Rachtman, E and Jiang, Y and Mirarab, S},
title = {Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70055},
doi = {10.1111/1755-0998.70055},
pmid = {41077897},
issn = {1755-0998},
support = {2137603//National Science Foundation (ACCESS Program)/ ; 2138259//National Science Foundation (ACCESS Program)/ ; 2138286//National Science Foundation (ACCESS Program)/ ; 2138296//National Science Foundation (ACCESS Program)/ ; 2138307//National Science Foundation (ACCESS Program)/ ; ACI-1540112//National Science Foundation (NRP/Natulius Program)/ ; CNS-2100237//National Science Foundation (NRP/Natulius Program)/ ; ACI-1541349//National Science Foundation (NRP/Natulius Program)/ ; CNS-1730158//National Science Foundation (NRP/Natulius Program)/ ; CNS-2120019//National Science Foundation (NRP/Natulius Program)/ ; OAC-1826967//National Science Foundation (NRP/Natulius Program)/ ; OAC-2112167//National Science Foundation (NRP/Natulius Program)/ ; 1R35GM142725/NH/NIH HHS/United States ; //Minderoo Foundation/ ; //Schmidt Foundation/ ; },
abstract = {A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.},
}
@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.<br><br>METHODS: We performed metagenomic whole genome sequencing (mWGS; >&#x2009;25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.<br><br>RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p&#x2009;=&#x2009;0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p&#x2009;=&#x2009;0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p&#x2009;=&#x2009;0.05) but reduced compared to healthy individuals (0.20; p&#x2009;<&#x2009;0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p&#x2009;=&#x2009;0.06) and healthy (0.01; p&#x2009;=&#x2009;0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.<br><br>CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}
@article {pmid41077176,
year = {2025},
author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R},
title = {Microbiome Signatures and Their Role in Uveitis: Pathogenesis, Diagnostics, and Therapeutic Perspectives.},
journal = {Progress in retinal and eye research},
volume = {},
number = {},
pages = {101409},
doi = {10.1016/j.preteyeres.2025.101409},
pmid = {41077176},
issn = {1873-1635},
abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.},
}
@article {pmid41076761,
year = {2025},
author = {Jin, Y and Ping, J and Huang, X and Dai, J and Wang, X and Wang, S},
title = {Nanoscale zero-valent iron coupled with microorganisms enhances the removal of organochlorine pesticides in groundwater: Insights from the role of cascading effects and horizontal gene transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124745},
doi = {10.1016/j.watres.2025.124745},
pmid = {41076761},
issn = {1879-2448},
abstract = {Nanoscale zero-valent iron (nZVIs) represent a promising approach for the remediation of organic chlorine-contaminated groundwater. However, the interaction between nZVIs and indigenous dechlorinating microorganisms is complex, which may have unpredictable effects on the dechlorination of organic chlorine, necessitating further investigation. In this study, we investigated an abandoned pesticide factory in southwest China, combined with microcosm experiment to reconstruct the metabolic pathway of biological dechlorination, and quantified the functional contribution of dechlorination genes and microorganisms. The results showed that the combined treatment of nZVIs and microorganisms significantly enhanced the degradation efficiency of HCHs, DDTs, and their six isomers, achieving removal rates of up to 99 % for HCHs and 87.73 % for DDTs. The concentrations of Cl[-] and Fe[2+] had a direct positive effect on the enrichment of microbial communities harboring HCHs degradation genes. Haloalkane dehalogenase encoded by the dhaA gene was identified as a key enzyme in the degradation of β-HCH precursors, which not only promoted the growth of facultative dehalogenators (particularly Acidovorax and Methyloversatilis) but also enhanced overall dechlorination activity. Importantly, we successfully reconstructed 7 near-complete bacterial metagenome-assembled genomes (MAGs) carrying the dhaA gene, representing taxonomically diverse novel dechlorinating microorganisms. Additionally, nZVIs significantly increased the abundance of mobile genetic elements (MGEs), with 17 MGEs detected within scaffolds harboring dhaA in the 7 MAGs. Integrases and transposases were identified as key drivers facilitating the spread of dhaA. This finding was supported by the shift of dhaA-harboring hosts, and by the incongruent evolutionary patterns observed between the genome-based tree and the dhaA protein phylogenetic tree. To be specific, cascading effects and horizontal gene transfer synergistically promoted the proliferation of dechlorinating microbes, providing novel strategies for managing and remediating organic chlorine-contaminated ecosystems.},
}
@article {pmid41076729,
year = {2025},
author = {Burdon, IA and Psaltis, AJ},
title = {Changes in the sinus microbiome in health and chronic rhinosinusitis.},
journal = {Current opinion in otolaryngology &amp; head and neck surgery},
volume = {},
number = {},
pages = {},
pmid = {41076729},
issn = {1531-6998},
abstract = {PURPOSE OF REVIEW: This article synthesises the recent sinus microbiome literature, identifying common themes in research findings as well as surveying the varied methodological approaches used across these studies.<br><br>RECENT FINDINGS: While there remains no clear consensus as to which microbes define dysbiosis in chronic rhinosinusitis (CRS), certain trends are emerging. Increasingly, the evidence points towards a pathogenic role in the overabundance of Moraxella, Haemophilus and Pseudomonas species, whilst the genera Cutibacterium, Anaerococcus and Dolosigranulum tend towards commensalism. However, the roles of the most common genera in the sinus microbiome, Staphylococcus and Corynebacterium, remain uncertain. Given the diversity and abundance of species within these genera, species and function-level analyses are needed to clarify their contributions to the aetiopathogenesis of CRS. Comprehensive study of the sinus microbiome in healthy individuals further shows that community composition shifts with age, suggesting that dysbiosis may manifest differently across the lifespan. Beyond bacteria, growing evidence highlights the importance of fungi and viruses, underscoring the need to incorporate these microbionts into future analyses.<br><br>SUMMARY: Progress towards a clinically meaningful consensus will require standardised approaches to sequencing, species-level resolution in these analyses, and consideration of the heterogeneous clinical and immunological subgroups of CRS.},
}
@article {pmid41075638,
year = {2025},
author = {Yin, D and Wang, K and Sun, S},
title = {Efficient sulfide bio-chemical removal by different crystalline FeOOH (α, β, γ, δ and amorphous) in sewers.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140072},
doi = {10.1016/j.jhazmat.2025.140072},
pmid = {41075638},
issn = {1873-3336},
abstract = {H2S corrosion in sewers causes huge economic losses. However, effective control solutions have remained lacking for decades. This study proposes FeOOH as a long-lasting and cost-effective alternative to iron salts for H2S control in sewers. The effect of FeOOH crystalline structures, electrochemical activity, acid and thermal stability, and surface morphology on S and Fe microbial redox were investigated. δ-FeOOH exhibited nearly 100 % H2S removal efficiency and the highest S[2-] removal capacity of 369.6 mg S/g FeOOH (1.10 mol S/Fe) followed by α-, AMO-, β- and γ-FeOOH. α-FeOOH treatment showed the highest FeS-S precipitation (304.2 mg S/g) and longest duration for sulfide control. This was contributed to α-FeOOH's low surface area and high structure stability. SO4[2-]-S bio-reduction inhibition was highest in δ-FeOOH (92.4 mg S/g), attributed to its highest Fe(Ⅲ)/Fe(Ⅱ), abundant sulfide oxidation genes (fccB, soxY and SUOx), and minimal electron transfer resistance. Moreover, sewer microbes enhanced the sulfide removal capacity of FeOOH by up to 6.0 times. FeOOH redirected microbial electron transfer away from SO4[2-] reduction and formed hydrogen bond with proteins that influenced SO4[2-] transport and uptake. This study provides comprehensive insights into the impact of FeOOH crystalline structure on microbial sulfur metabolism and electron transfer in sewers.},
}
@article {pmid41075532,
year = {2025},
author = {Ghafoor, D and Hayakijkosol, O and Prasetsincharoen, N and Chen, CCM and Noman, M and Chomchat, P and Kinobe, R},
title = {Characterisation of the gut microbiome and surveillance of antibiotic resistance genes in green sea turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107605},
doi = {10.1016/j.marenvres.2025.107605},
pmid = {41075532},
issn = {1879-0291},
abstract = {Green sea turtles (Chelonia mydas) are globally endangered marine herbivores that maintain the health of seagrass and coastal ecosystems. Their populations are declining due to human activities, including environmental pollution, which can disrupt gut microbial communities and compromise nutrition, immunity, and overall health. In this study, cloacal swabs from 139 green sea turtles categorised as captive juveniles, captive adults and wild stranded animals in the Gulf of Thailand, were analysed via shotgun metagenomic sequencing to elucidate bacterial taxonomic diversity and ARG profiles. In captive juveniles, Pseudomonadota was the most abundant phylum, followed by Ascomycota and Basidiomycota. In captive adults, Pseudomonadota exhibited an even greater predominance, with only minor contributions from unclassified bacteria and other taxa. In wild stranded green sea turtles, Pseudomonadota was dominant in their gut microbiome, but this was accompanied by notable levels of Actinomycetota, Bacteroidota, and Bacillota. Stranded turtles exhibited highest microbial diversity and variability, while captive adult turtles showed the lowest. Resistome profiling also revealed significant differences in the relative abundance of antibiotic resistance genes across all three groups. MacB (macrolide resistance) was the most abundant gene overall, with the highest abundance observed in juveniles (4.8 %). Stranded turtles exhibited elevated levels of TetA(58) (tetracycline resistance, 2.6 %) and msbA (nitroimidazole resistance, 2.2 %), while adults showed the greatest enrichment of Ecol_fabG_TRC (triclosan resistance, 3.8 %) and TxR (tetracycline resistance, 3.6 %). These data demonstrate that marked variability existed in the gut microbiome and resistome of green sea turtles across different life stages in captive or wild environments. This offers critical insights for the development of targeted conservation strategies and health management practices for both wild and captive green sea turtles. Strategies to mitigate the spread of antibiotic resistance should be developed.},
}
@article {pmid41073934,
year = {2025},
author = {Zhu, X and Yan, J and Lai, X and Chen, M and Wang, Q},
title = {Hematogenous pulmonary abscess and septicemia due to infection with hypervirulent Pseudomonas aeruginosa in a nonimmunodeficient adolescent: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1280},
pmid = {41073934},
issn = {1471-2334},
support = {No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.2022KY927//, Health Science and Technology Planning Project of Zhejiang Province, China/ ; },
abstract = {BACKGROUND: Pseudomonas aeruginosa is a non-glucose-fermenting gram-negative bacillus and an opportunistic pathogen that typically causes localized or systemic infections in immunocompromised middle-aged and elderly individuals or children with congenital immune deficiencies. However, cases of pulmonary abscess with severe sepsis in normal individuals are rare and should be taken seriously.<br><br>CASE PRESENTATION: A 15-year-old nonimmunodeficient adolescent was hospitalized due to high fever and other clinical symptoms. The patient was diagnosed with a pulmonary abscess with severe sepsis. Etiological Examination showed that sensitive Pseudomonas aeruginosa. Subsequent inspection revealed this clinical isolate produces virulence factors ExoA and Pyocyanin, which was highly virulent. The patient&#x2019;s symptoms were improved after imipenem (IPM) treatment and discharged. At follow-up 3 months later, he had recovered well.<br><br>CONCLUSIONS: We report a case of a pulmonary abscess with severe sepsis caused by Pseudomonas aeruginosa in an immunocompetent patient. Compared with the vast majority of infections caused by P. aeruginosa, this patient was younger and had no immunodeficiency or basic diseases, and the characteristics of the lesions were also unique. For this P. aeruginosa isolate, the testings of antimicrobial drugs were generally sensitive, and the virulence factors ExoA and Pyocyanin by quantitative metagenomics next-generation sequencing may be the main factors for the severity.},
}
@article {pmid41075379,
year = {2025},
author = {Pichler, I and Krischer, E and Obenhuber, T and Hirsch, B and Reinhold, I and Wiedmer, C and Ziltener, G and Weller, D and Roth, P and Weiss, T and Kufner, V and Bloemberg, GV and Trkola, A and Müller, NJ and Huber, M},
title = {Viral metagenomic sequencing reveals rare pathogens and improves diagnostic accuracy in neuroinflammatory disorders.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117140},
doi = {10.1016/j.diagmicrobio.2025.117140},
pmid = {41075379},
issn = {1879-0070},
abstract = {BACKGROUND: Neuroinflammatory disorders are frequently of unknown aetiology. Unbiased metagenomic next-generation sequencing of cerebrospinal fluid could help bridge the current diagnostic gap by identifying more infectious pathogens inducing central nervous system disorders. This study examined the advantages of adding viral metagenomics to standard testing procedures.<br><br>METHODS: Patients presenting with symptoms indicative of a neuroinflammatory disorder were enrolled at a Swiss tertiary care hospital through prospective and retrospective recruitment. Participants were diagnosed with infectious or autoimmune neuroinflammatory disorders based on the results of routine diagnostics and viral metagenomic sequencing.<br><br>RESULTS: Of the 70 study participants, 50 were classified as having an infectious disorder. Among these, a total of 37 pathogens were identified in 29 individuals (56 %), including 32 viral, three bacterial, one fungal, and one prion infection. Conventional virus testing and viral metagenomic sequencing produced the same positive and negative results for 13 and 21 cases, respectively. This resulted in an overall percent agreement of 59 %. Disparate viral results were observed in 19 cases. Ten cases were detected only by conventional testing, and nine were detected only by viral metagenomics. Notably, we report the detection of Toscana virus by viral metagenomic sequencing, a relatively rare pathogen in Switzerland that is not routinely screened for, underscoring the advantages of integrating viral metagenomics with conventional testing.<br><br>CONCLUSIONS: Viral metagenomic sequencing as a first-line diagnostic tool in combination with conventional methods yields the most comprehensive results to diagnose patients with infectious neuroinflammatory disorders. Its unbiased approach enables the detection of rare or unconsidered viruses.},
}
@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}
@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}
@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf216},
pmid = {41074769},
issn = {1751-7370},
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}
@article {pmid41074341,
year = {2025},
author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z},
title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117155},
doi = {10.1016/j.foodres.2025.117155},
pmid = {41074341},
issn = {1873-7145},
mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; },
abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.},
}
@article {pmid41073968,
year = {2025},
author = {Onohuean, H and Choonara, YE},
title = {Epidemiological distribution of bacterial meningitis infections in South Africa: a systematic review and meta-analysis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1284},
pmid = {41073968},
issn = {1471-2334},
mesh = {Humans ; South Africa/epidemiology ; *Meningitis, Bacterial/epidemiology/microbiology ; Prevalence ; Child ; Adolescent ; Child, Preschool ; Female ; Male ; Adult ; Infant ; Middle Aged ; Young Adult ; },
abstract = {Scientific evidence from public health findings can enhance the management, treatment, and prevention policies for bacterial meningitis (BM) infections. However, comprehensive epidemiological data on BM prevalence in South Africa is limited. We aimed to assess the prevalence and characteristics of laboratory-confirmed BM cases at the national population level. Using PRISMA standards, we retrieved data from electronic databases and selected reference articles. Out of 115,626 participants, 57,964 (50.13%) were infected with BM, with the highest prevalence (7.67%) in the age group 6-17 years. Our meta-analysis of 19 studies revealed an overall pooled prevalence of 38.01%, 95% confidence interval (CI: 0.26-0.50), with significant heterogeneity (I[2] = 99.86%, Q = 13117.45, p < 0.0001). The Egger test indicated publication bias (z = 3.4977, p = 0.0005). Subgroup analyses showed a higher prevalence in studies with sample sizes over 1000 (60.22%, 95% CI: 0.3899-0.7819, I[2] = 99.92%), over long study years (37.50%, 95% CI: 0.2642-0.5005, I[2] = 99.84%), cross-sectional study design (58.69%, 95%CI: 0.4906-0.6770, I2 = 99.72%), and particularly in Gauteng province (60.42%, 95% CI: 0.4539-0.7371, I[2] = 98.45%). The infectious types included Listeria (83.33%, 95% CI: 0.1936-0.9905, I[2] = 0.00%) and Neisseria (62.64%, 95% CI: 0.6126-0.6400, I[2] = 0.00%). Significant heterogeneity was noted in study design (R[2] = 52.93%, p < 0.0001), sample size (R[2] = 0.00%, p = 0.0117), and province (R[2] = 0.0%, p < 0.0001). These findings underscore a high prevalence of BM infections in South Africa's epidemiological landscape, highlighting the urgent need for targeted surveillance for effective prevention and treatment strategies.},
}
@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth &amp; development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration &amp; dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}
@article {pmid41073868,
year = {2026},
author = {Leoni, C and Marzano, M and Filomena, E and D'Erchia, AM},
title = {Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2969},
number = {},
pages = {235-247},
pmid = {41073868},
issn = {1940-6029},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Gene Dosage ; DNA Copy Number Variations ; Fluorescent Dyes/chemistry ; },
abstract = {Digital Droplet PCR (ddPCR) is a quantitative PCR method that offers high sensitivity and accuracy in measuring the amount of nucleic acid in a sample, without the need of a standard curve. In ddPCR, a single sample is partitioned into up to 20,000 droplets, using the water-oil emulsion technology, and the amplification reaction occurs within each droplet using a fluorescent hydrolysis probe (Taqman) or a DNA-binding fluorescent dye. Following PCR, the emitted signals are individually measured in each droplet. Here, we describe a ddPCR optimized protocol for accurately quantifying the total copy number of the 16S rRNA gene in a metagenomic DNA sample. The protocol utilizes a primer pair, targeting the 16S V5-V6 hypervariable regions, in combination with a double-strand DNA-binding fluorescent dye.},
}
@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41073663},
issn = {2058-5276},
support = {K01-DK102771//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}
@article {pmid41073345,
year = {2025},
author = {Guo, WB and Wang, TT and Song, ZK and Liu, QY and Sun, JJ},
title = {[One case of occupational pulmonary anthrax].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {9},
pages = {705-707},
doi = {10.3760/cma.j.cn121094-20240719-00326},
pmid = {41073345},
issn = {1001-9391},
mesh = {Humans ; *Anthrax ; Male ; Bacillus anthracis ; *Occupational Diseases ; *Anthracosis ; Adult ; },
abstract = {Pulmonary anthrax is an acute zoonotic infectious disease caused by Bacillus anthracis infecting the human body. Humans can be infected by coming into contact with diseased animals and their products or by consuming diseased animals. According to the different infection routes, it can be classified into cutaneous anthrax, pulmonary anthrax and intestinal anthrax, etc. Among them, cutaneous anthrax is the most common, while case reports of pulmonary anthrax are rare. This article analyzes the clinical data of a case of occupational pulmonary anthrax diagnosed by metagenomic next-generation sequencing (mNGS) and successfully treated, so as to provide a reference for the clinical treatment of pulmonary anthrax.},
}
@article {pmid41072965,
year = {2025},
author = {Odukwe, C and Abdelrahman, A and Zaidi, AN and Love, B and El-Hamamsy, I and Ghesani, M and Hopkins, KA},
title = {Culture-Negative Transcatheter Pulmonary Valve Endocarditis.},
journal = {JACC. Case reports},
volume = {30},
number = {31},
pages = {105324},
doi = {10.1016/j.jaccas.2025.105324},
pmid = {41072965},
issn = {2666-0849},
abstract = {CLINICAL CONDITION: We present a case of transcatheter pulmonary valve endocarditis in a 38-year-old woman with a history of atrial septal defect, pulmonary stenosis, and bicuspid aortic valve, all previously repaired with mechanical and bioprosthetic valve replacements. Despite negative initial studies, [18]F-fluorodeoxyglucose positron emission tomography-computed tomography revealed septic pulmonary emboli and abnormal uptake at the pulmonary valve. Metagenomic sequencing identified Haemophilus parainfluenzae as the pathogen.<br><br>KEY QUESTIONS: What is the differential diagnosis of a cardiac mass in this context? How should imaging and laboratory testing be approached in prosthetic valve endocarditis with negative studies? What surgical factors matter in patients with prior cardiac repairs?<br><br>OUTCOME: The patient underwent successful replacement of the pulmonary and aortic valves and completed a course of antibiotics, with full recovery.<br><br>TAKE-HOME MESSAGE: Consider bioprosthetic valve endocarditis in patients with persistent fevers and negative cultures. Use advanced diagnostics early when the clinical suspicion is high.},
}
@article {pmid41072853,
year = {2025},
author = {Li, Y and Sun, C and Zhao, T and Ni, Y and Liu, Q and Song, M and Xu, X and Sun, W and Li, Y and Zhou, J and Li, D and Zhang, Q and Feng, C and Shi, J and Cao, M and Huang, B and Su, N and Lu, X and Wang, L and Lei, J and Sang, L and Zhou, W and Cai, X and Wang, J and Wang, Y and Cai, Y and Lu, Y and Zhong, J and Su, X},
title = {Etiology of Initial Treatment Failure in Non-immunosuppressed Adult Patients with Community-acquired Pneumonia.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108110},
doi = {10.1016/j.ijid.2025.108110},
pmid = {41072853},
issn = {1878-3511},
abstract = {OBJECTIVES: Initial treatment failure (ITF) of community-acquired pneumonia (CAP) is a significant clinical problem. The study aimed to explore the etiology of ITF using metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), and to provide optimized management strategies for patients with CAP.<br><br>METHODS: From June 2022 to August 2024, we conducted a prospective, multicenter study in 15 hospitals of non-immunosuppressed adult CAP patients with ITF in Jiangsu Province, China. Conventional microbiological tests (CMTs), mNGS, and tNGS were applied to detect microorganisms in bronchoalveolar lavage fluid.<br><br>RESULTS: ITF was mainly caused by responsible pathogens not covered by initial treatment (59.0%) despite the high compliance with guideline-recommended regimens. The top 5 responsible pathogens were Chlamydia psittaci (21.5%), Mycoplasma pneumoniae (16.7%), influenza virus (14.6%), SARS-CoV-2 (8.3%), and Pseudomonas aeruginosa (6.3%). The positive pathogen identification rate for mNGS and tNGS was 74.4% and 72.7%, respectively, while for CMTs it was 12.2%. Based on NGS results, treatment was optimized in 53.5% of patients, and 95.8% were improved or cured.<br><br>CONCLUSIONS: Atypical pathogens and viruses not covered by empirical treatment regimens were the main causes of ITF. mNGS and tNGS outperformed CMTs in identifying responsible pathogens and could optimize the treatment of patients with ITF.},
}
@article {pmid41072822,
year = {2025},
author = {Chen, Z and Zhang, J and Lin, L and Sun, Y and Li, XY and Li, B},
title = {Enhanced fermentation for lactic acid production from food waste via hydrothermal pretreatment: performance evaluation and metagenomic analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133456},
doi = {10.1016/j.biortech.2025.133456},
pmid = {41072822},
issn = {1873-2976},
abstract = {Mixed-culture lactic acid fermentation of food waste (FW) commonly requests low pH conditions. However, this can pose the challenge of insufficient substrate hydrolysis. To address this, we investigated hydrothermal pretreatment coupled with centrifugal supernatant recovery as a technical strategy to enhance the FW hydrolysis and lactic acid production. The study characterized the supernatant substrate after the pretreatment at different temperatures (80-140 °C), focusing on organic solubilization, supernatant-solid separation for organic recovery, grease removal, and subsequently evaluated lactic acid production in 8-day batch fermentation. The results showed that hydrothermal pretreatment significantly boosted FW hydrolysis, improved organic recovery in the supernatant, and enhanced lactic acid yields. Optimal lactic acid production (12.4 g/L) representing a 68 % increase over the control without hydrothermal pretreatment, was achieved at 120 °C, despite the maximum hydrolysis occurring at 140 °C. Metagenomic sequencing further revealed that the pretreated substrate fostered the development of a lactic acid bacteria-dominated microbial community at low pH, notably enriched with Lactobacillus amylolyticus and Lactobacillus delbrueckii, along with functional genes associated with lactic acid production. Crucially, the absence of genes related to propionate and butyrate pathways in the dominant bacteria would explain the reduced byproduct spectrum and enhanced fermentation stability. These findings indicate that hydrothermal pretreatment improves both the quantity and quality of FW supernatant substrate, promoting a lactic acid bacteria-dominated community that drives favorable metabolic pathways under low pH conditions for more efficient and stable lactic acid production.},
}
@article {pmid41072348,
year = {2025},
author = {Tang, Y and Khan, E and Gu, AZ and Tsang, DCW},
title = {Graphitic biochar-anammox achieved by multi-heme-based extracellular electron transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124704},
doi = {10.1016/j.watres.2025.124704},
pmid = {41072348},
issn = {1879-2448},
abstract = {The anammox process decarbonizes nitrogen removal by avoiding greenhouse gas emissions and organic carbon demand, yet its reliance on nitrification and denitrification undermines these advantages. To address this, we developed a biochar-assisted anammox system that leverages graphitic defects as redox-active sites to enable interspecies, multi-heme extracellular electron transfer (EET). Biochar produced at 800 °C for 4 h (BC800-4 h) exhibited the greatest graphitic defect density and the highest electron accepting capacity, uniquely exceeding the daily stoichiometric electron demand for complete ammonium oxidation in the present study. Metagenomic and in vitro assays revealed that BC800-4 h promoted hydroxylamine-dependent ammonium oxidation by anaerobic ammonia-oxidizing bacteria (AnAOB) via EET. A cooperative microbial network was identified: AnAOB in suspension supplied heme precursors, while ammonia-oxidizing and denitrifying bacteria colonizing the biochar facilitated heme assembly and transport. This partitioning enabled direct electron transfer to biochar, achieving 62 % nitrogen removal without exogenous nitrite and reducing N2O emissions by 28 %. The pore-size-dependent reduction in graphitic defects suggests that large molecular-weight biological channels (>10 kDa) are essential for electron transfer between anammox consortia and biochar. Our findings indicate an opportunity to develop a biochar-anammox reactor-with suspended AnAOB and a fixed-bed biochar biofilm-to exploit this synergy for efficient and low-emission nitrogen removal.},
}
@article {pmid41072344,
year = {2025},
author = {Yu, K and Xia, J and Zhu, D and He, B and Yu, Z and Zhu, DZ and Yao, Z},
title = {Public risk of sewage sediments in different functional areas - deciphered by metagenome assembly.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124691},
doi = {10.1016/j.watres.2025.124691},
pmid = {41072344},
issn = {1879-2448},
abstract = {Understanding public risk of sewage sediments, particularly those risks related to methane, sulfide emission and bio-risk, is critical for ensuring citizen safety. However, the underlying microbial mechanisms causing these risks remain unclear. This study employed metagenomic assembly to analyze methane/sulfur cycling pathways and bio-risks in sewage sediments from three typical functional areas: commercial, multifunctional, and residential. Results demonstrated that the sewage sediments in the multifunctional area exhibited the highest potential public risk levels, characterized by intensified methane/sulfur metabolic activity and increased abundance of mobile gene elements (MGEs) and high-risk antibiotic resistance genes (ARGs). In addition, the co-occurrence network complexity of ARGs, MGEs and pathogens were higher in the multifunctional sewage sediments. Intriguingly, we found genus Thiobacillus which participated in sulfur cycling, as the host of high risk ARGs, significantly enriched in the multifunctional area, also distributed in sewer systems around the world. Additionally, total organic carbon (TOC) emerged as key driver of sediment public risks. These findings highlight variations in sewage sediment public risks across different functional areas, providing a foundation for targeted risk mitigation strategies.},
}
@article {pmid41072198,
year = {2025},
author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E},
title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180681},
doi = {10.1016/j.scitotenv.2025.180681},
pmid = {41072198},
issn = {1879-1026},
abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.},
}
@article {pmid41072177,
year = {2025},
author = {Uribarri, A and Henriquez, L and Beguiristain, I and Rodriguez, I and Alfaro, M and Sancho, I and Portillo, ME},
title = {Toward a clinical algorithm for the detection of periprosthetic joint infections using targeted NGS.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117133},
doi = {10.1016/j.diagmicrobio.2025.117133},
pmid = {41072177},
issn = {1879-0070},
abstract = {OBJECTIVES: Periprosthetic joint infection (PJI) represents a severe surgical complication, and despite advances have been made in PJI diagnosis, many cases remain microbiologically negative. In this context, metagenomic Next-Generation Sequencing (mNGS) emerged as a promising diagnostic tool for PJI. This study aimed to establish objective, widely-usable methodology and criteria for diagnosing PJI based on sequence analysis.<br><br>METHODS: We retrospectively analyzed sonication fluid samples from 34 patients who underwent surgical treatment for PJI in 2022. A 16S rRNA-based targeted NGS (tNGS) approach was carried out amplifying 16S rRNA gene for 25 and 35 cycles. Sequencing was performed on the Illumina MiSeq platform and data was processed using nf-core/ampliseq.<br><br>RESULTS: A significantly higher number of classifiable reads was observed in PJI cases (p < 0.0001). A negative control database was created using negative tNGS controls and samples from patients classified as aseptic failure. The database was then employed to establish three tNGS diagnostic criteria. The diagnostic efficacy of tNGS employing these criteria was assessed through receiver operating characteristic (ROC) curve analysis, which revealed optimal results after 25 cycles of 16S rRNA amplification (AUC = 0.924, p < 0.0001). An optimal cut-off of >12 % was calculated, obtaining a sensitivity of 100 % (95 % CI 75.3 %-100 %) and a specificity of 90.5 % (95 % CI 69.9 %-98.8 %). In both of our culture-negative PJI cases potential pathogens were detected: Listeria and Cutibacterium.<br><br>CONCLUSIONS: To the best of our knowledge, this is one of the few studies that attempts to establish standardized criteria and diagnostic cut-offs for the analysis of PJI tNGS data. We believe that these results could serve as a valuable reference for future PJI metagenomics diagnostic studies.},
}
@article {pmid41071829,
year = {2025},
author = {Akanbi, DO and Abaye, BB and Averhoff, F and Berg, MG and Orf, GS and Lawan, KM and Beckett, GA and Omotoso, AB and Mata, M and Cloherty, GA and Chabuka, L and de Oliveira, T and Mac-Fisi, KW and Walter, A and Mark, II and Edeki, G and Sinayoko, A and Nasrullah, M and Justina, BI and Balogun, MS},
title = {Detection of dengue, malaria, and additional causes of acute febrile illness: The need for expanded testing, Bayelsa State, Nigeria.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {10},
pages = {e0013060},
doi = {10.1371/journal.pntd.0013060},
pmid = {41071829},
issn = {1935-2735},
abstract = {Dengue virus (DENV) infection has not been previously reported from Bayelsa State, Nigeria. We aimed to determine the prevalence of dengue virus (DENV) infection, malaria, and coinfection, and other pathogens among febrile patients in the capital city, Yenagoa.We conducted a cross-sectional study among persons aged ≥1 year who presented with acute febrile illnesses (AFI) at four hospitals in Bayelsa State during 20 May - 15 June 2022. Blood samples from 443 participants were tested for DENV seromarkers (NS1, IgM, IgG), using serology and RT-PCR, and malaria was diagnosed by thick smear microscopy. Sociodemographic and risk factor data were collected using electronic questionnaires administered via smart phones/tablets and analyzed using univariate and multivariate methods. Metagenomic libraries were prepared and enriched by viral target capture and sequenced by NGS. The seroprevalence of acute DENV infection was 14.5% (n = 64) while the prevalence of malaria was 42.4% (n = 188); 6.5% (n = 29) of participants were coinfected with acute DENV infection and malaria. An additional 17.6% (n = 78) of participants had markers for past DENV infection. Rural/suburban residence and age ≥ 31 years were significantly correlated with having any dengue seromarker. Residence in a larger household (≥5 persons), and borehole water-use were predictors for malaria fever. RT-PCR results revealed multiple DENV serotypes, with serotype 3 dominant. Sequencing of unknown AFI cases revealed numerous viral causes such as adenovirus, EBV, and hepatitis A, as well as additional dengue and malarial infections missed by conventional testing. Of interest were Coxsackievirus A5 (hand, foot and mouth disease; HFMD) which has been diversifying locally for years in Nigeria and an mPox clade IIb (lineage A.2.3) strain that emerged in Nigeria during the 2022 global outbreak. The results of this study provide the first documentation of human DENV infection in Bayelsa State, Nigeria and suggests that dengue is an emerging and important cause of febrile illness in this area. Our findings support the need for routine testing to identify DENV among patients who present with acute febrile disease. Metagenomic NGS results highlight the benefits of unbiased surveillance to identify circulating and emerging pathogens.},
}
@article {pmid41070991,
year = {2025},
author = {Brennan, C and Shaffer, JP and Belda-Ferre, P and Mohanty, I and Weng, Y and Cantrell, K and Ackermann, G and Allaband, C and Bryant, M and Farmer, S and González, A and McDonald, D and Martino, C and Meehan, MJ and Rahman, G and Salido, RA and Schwartz, T and Song, SJ and Tribelhorn, C and Tubb, HM and Dorrestein, PC and Knight, R},
title = {Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191225},
doi = {10.1128/spectrum.01912-25},
pmid = {41070991},
issn = {2165-0497},
abstract = {UNLABELLED: An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical sample collection alone cannot fully capture. At-home sample collection enables the inclusion of a larger and more diverse group of participants, accounting for differences in ethnicity, age, and other factors. However, managing large studies is challenging due to the complexities involved in sample acquisition, processing, and analysis. Building on our previous work demonstrating the effectiveness of single 1 mL barcoded, racked Matrix Tubes in reducing sample processing time and well-to-well contamination for paired DNA and metabolite extraction, we further validate this method against a previously benchmarked plate-based approach using the same extraction reagents. This validation focuses on samples from the built environment, human skin, human saliva, and feces from mice and humans. Importantly, we explore the impact of using a mix of bead sizes during bead-beating for cell lysis, demonstrating that it enhances taxonomic recovery compared to a single bead size. Finally, we assess the potential of 95% isopropanol for room-temperature sample preservation. Our results show that isopropanol performs comparably to 95% ethanol in many cases, suggesting it is viable as an alternative when ethanol is unavailable. Beyond minimizing contamination, halving processing time, eliminating human error during sample plating, and streamlining metadata curation, the Matrix tube approach produces metabolomic, 16S, and shotgun metagenomic data consistent with the Plate-based Method for both high- and low-biomass samples.<br><br>IMPORTANCE: Numerous studies have linked the microbiome to human and environmental health, yet many fundamental questions remain unanswered. Large-scale studies with robust statistical power are required to identify important covariates against a background of confounding factors. Cross-contamination, limited throughput, and human error have been identified as major setbacks when processing large numbers of samples. We present a streamlined method for sample accession and extraction of metabolites and DNA for both high- and low-biomass samples. This approach, previously shown to significantly reduce cross-contamination, employs an automation-friendly, single barcoded tube per sample. Additionally, we demonstrate that 95% isopropanol serves as an effective ambient-temperature storage solution for many sample types, providing an alternative in regions where ethanol is unavailable or restricted. This method has significant implications for the field, enabling large-scale studies to generate accurate insights with greater efficiency and expanded accessibility in situations in which ethanol is more costly or otherwise not available.},
}
@article {pmid41070134,
year = {2025},
author = {Li, Q and Liu, F and Zhong, J and Fang, X and Zhang, X and Xiong, H and Li, G and Chen, H},
title = {Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656016},
pmid = {41070134},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is strongly associated with alterations in the gut microbiome. While numerous studies have examined this association, most focus on genus- or species-level taxonomic classifications, overlooking functional heterogeneity at the strain level.<br><br>METHODS: We integrated 1,123 metagenomic samples from seven global CRC cohorts to conduct multi-level metagenome-wide association studies (MWAS). Fecal microbial load (FML) correction was applied to mitigate technical confounding. We evaluated the performance of taxonomic models at various resolutions strain, species, and genus levels in classifying CRC status both within and across cohorts.<br><br>RESULTS: Strain-level analysis revealed conspecific strains with divergent associations to CRC. For instance, distinct strains of Bacteroides thetaiotaomicron exhibited both protective and risk-increasing effects across different cohorts. Genomic functional annotation suggested potential mechanistic bases for these opposing roles. Correction for FML reduced confounding and significantly improved the performance of within-cohort and cross-cohort CRC classification models. Interestingly, genus- and species-level models demonstrated superior predictive robustness compared to strain-level models, likely due to higher microbial abundance and greater cross-population conservation at these taxonomic ranks.<br><br>CONCLUSION: Our study underscores the biological relevance of strain level analysis in elucidating functional diversity within the microbiome. However, higher taxonomic levels provide more robust and clinically translatable diagnostic markers for CRC. Integrating FML correction with multi-level taxonomic profiling enhances both mechanistic insight into microbiom CRC interactions and the generalizability of diagnostic models across diverse populations.},
}
@article {pmid41070121,
year = {2025},
author = {Long, C and Fu, X and Wu, Q and Wang, S and Zhou, X and Mao, J and Guo, L and Shi, W and Yang, H and Yang, T and Du, Y and Yue, J and Wu, D and Liu, H},
title = {Poncirus trifoliata vs. Citrus junos rootstocks: reshaping lemon rhizosphere microecology through microbial and metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650631},
pmid = {41070121},
issn = {1664-302X},
abstract = {INTRODUCTION: Trifoliate orange (Poncirus trifoliataL. Raf) and "Ziyang Xiangcheng" (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.<br><br>METHODS: Pot-cultured systems were established with lemon (Citrus&#x202f;&#xd7;&#x202f;limon "Eureka") saplings grafted onto trifoliate orange (PTL) and "Ziyang Xiangcheng" (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.<br><br>RESULTS: The results demonstrated no significant difference in rhizospheric microbial &#x3b1;-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. &#x3b2;-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-&#x3b2;-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance).<br><br>DISCUSSION: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.},
}
@article {pmid41070117,
year = {2025},
author = {He, C and Yang, S and Dong, S and Wang, S and Zhang, P and Yang, Y and Xu, D and Yang, R and Zeng, B and Hu, Y and Zhang, Q},
title = {Fermentation-driven microbial and metabolic shifts in filler tobacco leaves of different grades.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651289},
pmid = {41070117},
issn = {1664-302X},
abstract = {INTRODUCTION: Filler tobacco leaves (FTLs) serve as the primary raw material for cigar production, and notable differences in physicochemical properties and fermentation responsiveness exist across different grades. However, the underlying mechanisms governing microbial and metabolic evolution during FTL fermentation remain poorly understood. This study systematically investigated the microbial community structures and metabolomic profiles of FTLs of varying grades before and after fermentation using metagenomic sequencing and untargeted metabolomics.<br><br>RESULTS: Metagenomic analysis revealed marked differences in microbial composition among FTL grades at the onset of fermentation. The fermentation process further facilitated the enrichment of functional genera such as Bacillus, Escherichia, and Alternaria, while low-grade FTLs exhibited excessive accumulation of Corynebacterium, potentially contributing to off-flavors and undesirable odors. Untargeted metabolomics identified numerous significantly differential metabolites after fermentation, primarily enriched in pathways related to amino acid biosynthesis, sugar metabolism, and carotenoid biosynthesis. Principal component analysis and hierarchical clustering indicated partial continuity in metabolomic profiles within the same grade before and after fermentation. Correlation analysis further revealed strong positive associations between several dominant genera and flavor-related metabolites.<br><br>CONCLUSION: This study demonstrates that FTLs of different grades exhibit distinct patterns of microbial succession and metabolic remodeling during fermentation. The initial leaf grade plays a pivotal role in shaping microbial communities and metabolite accumulation. These findings offer mechanistic insights into the fermentation process of FTLs and provide theoretical and practical guidance for optimizing raw material grading and fermentation management in the cigar industry.},
}
@article {pmid41070051,
year = {2025},
author = {Zhang, Y and Chen, A and Yang, C and Guan, L and Wang, C},
title = {Metagenomic next-generation sequencing assists in diagnosing Pneumocystis Jirovecii pneumonia in non-HIV patients: a case report.},
journal = {Respiratory medicine case reports},
volume = {58},
number = {},
pages = {102289},
pmid = {41070051},
issn = {2213-0071},
abstract = {BACKGROUND: Pneumocystis jirovecii Pneumonia (PJP) is a pulmonary opportunistic fungal infection with an incompletely elucidated pathogenesis. In recent years, non-human immunodeficiency virus (HIV) -infected PJP patients have exhibited rapid progression, poor prognosis, and a greater mortality rate compared to their HIV equivalents, necessitating timely detection and management, which are both critical and problematic.<br><br>CASE REPORT: We report a young patient admitted with diabetic ketoacidosis characterized by rapidly progressing acute respiratory failure with negative pathogen blood cultures, serum antibodies and polymerase chain reaction results, and a normal CD4[+] lymphocyte count. Anti-HIV antibody were negative. A computed tomography scan of the chest revealed patchy opacities in both lower lungs, a nonspecific manifestation. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected high Pneumocystis jiroveci sequence counts and a markedly elevated 1,3-&#x3b2;-D-glucan test titer. Following the diagnosis of non-HIV-infected PJP, the patient was discharged after 13 days with a positive outcome, attained through systematic management involving Trimethoprim-sulfamethoxazole anti-infective medication and stringent glycemic control.<br><br>CONCLUSION: Insufficient glucose management may be an important susceptibility factor for immunocompetent persons with non-HIV-infected PJP patients. MNGS serves as an effective method for rapid diagnosis and medication adjustment when signs, symptoms, and imaging findings of PJP are nonspecific.},
}
@article {pmid41069861,
year = {2025},
author = {George, C and Dharan, HM and Drescher, L and Lee, J and Qi, Y and Wang, Y and Chang, Y and Teo, SLM and Wainwright, BJ and Yung, C and Lauro, FM and Hazen, TC and Pointing, SB},
title = {Tropical intertidal microbiome response to the 2024 Marine Honour oil spill.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100623},
pmid = {41069861},
issn = {2666-4984},
abstract = {Marine fuel oil (MFO) spills in tropical coastal environments are under-characterized despite increasing risk from maritime activities. Microbial and geochemical responses to the June 2024 Marine Honour MFO spill on Singapore's intertidal sediments were analyzed in real time over 185 days. Using metagenomics and hydrocarbon profiling, microbial community shifts and hydrocarbon degradation were quantified across visibly oiled (high-impact) and clean (low-impact) sites. Microbiomes at all sites adapted rapidly to the spill through increased diversity and abundance of genes encoding alkane and aromatic compound degradation, detoxification, and biosurfactant production. The dominant hydrocarbon-degrading bacteria differed markedly from those reported in other crude oil spills and in regions with different climates. Oil deposition intensity strongly influenced microbial succession and hydrocarbon-degrading gene profiles, and this reflected early toxicity constraints in heavily oiled areas. The persistence of hydrocarbon degradation genes beyond hydrocarbon detection in sediments suggested long-term functional priming may occur. The study provides novel genome-resolved insight into the microbial response to MFO pollution, advances understanding of marine environmental biodegradation, and provides urgently needed baseline data for oil spill response strategies in Southeast Asia and beyond.},
}
@article {pmid41069710,
year = {2025},
author = {Burakova, I and Smirnova, Y and Gryaznova, M and Morozova, P and Kotarev, V and Lyadova, L and Ivanova, N and Denisenko, L and Syromyatnikov, M},
title = {Effect of interferon on broilers' fecal microbiome composition.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {2},
pages = {487-496},
pmid = {41069710},
issn = {2311-7710},
abstract = {OBJECTIVE: The purpose of our study was to investigate the effect of chicken interferon on the intestinal microbiota of broiler chickens.<br><br>MATERIALS AND METHODS: The study used next-generation sequencing on the Ion Torrent pragmatic general multicast platform to target the V3 16S ribosomal ribonucleic acid hypervariable region gene, allowing us to analyze in detail changes in the composition of the broiler chicken microbiome.<br><br>RESULTS: Forty-one bacterial genera were identified in the studied groups of broilers. The highest abundance in both groups was observed for Lactobacillus, which was 31.08% &#xb1; 6.52 in the control group and 36.08% &#xb1; 7.25 in the interferon group. There was no clustering between the microbiome communities of the groups studied. We found a decrease or complete absence of Escherichia-Shigella, Eubacterium fissicatena group, Lachnospiraceae CHKCI001, and Pediococcus in the interferon-treated broiler group compared to the control group and an increase in the number of genera Ruminococcaceae CAG-352 and Turicibacter in the interferon group.<br><br>CONCLUSION: A decrease in E.-Shigella may indicate normalization of the intestinal microbiota of broilers, and it can also be concluded that the introduction of interferon helps to suppress opportunistic bacteria. In the interferon group, a sharp increase in the number of Turicibacter was observed. Representatives of this genus are among the most common members in the intestines of broilers.},
}
@article {pmid41069707,
year = {2025},
author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A},
title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf157},
pmid = {41069707},
issn = {2730-6151},
abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.},
}
@article {pmid41069598,
year = {2025},
author = {Wang, Z and Lin, X and Wu, J and Su, C and Luo, Y and Yu, G},
title = {Radix Pseudostellaria polysaccharides alleviate sepsis-induced liver injury by modulating the gut microbiota via the TLR4/NF-κB pathway.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1658147},
pmid = {41069598},
issn = {1663-9812},
abstract = {BACKGROUND: Sepsis-induced liver injury (SLI) is a life-threatening complication with limited therapeutic options. Radix Pseudostellariae polysaccharides (RPPS), a component of traditional Chinese medicine, exert immunomodulatory, anti-inflammatory, and antioxidant properties. Herein, we investigated the therapeutic effects and mechanisms of RPPS on SLI.<br><br>METHODS: A murine sepsis model was established using cecal ligation and puncture. Mice were pretreated with RPPS or saline for 14 days. Subsequently, multi-omics integration-including metagenomics, proteomics, and network pharmacology-was employed to elucidate the mechanisms of RPPS. Liver injury was assessed via serum biomarkers, histopathology, and transmission electron microscopy, while intestinal barrier integrity was evaluated through histopathological analysis. Gut microbiota composition and functional pathways were examined using metagenomic sequencing. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analyses of gut microbiota, liver proteomics, and network pharmacology data were integrated to predict key target pathways, which were experimentally validated in mice.<br><br>RESULTS: RPPS pretreatment significantly improved survival, reduced liver injury markers, attenuated hepatic necrosis and inflammation, and restored intestinal barrier integrity. RPPS also modulated the gut microbiota by enriching beneficial taxa and suppressing pathogens. Multi-omics integration identified the toll-like receptor 4 (TLR4)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-&#x3ba;B) pathway as the core mechanism, and experimental validation confirmed that RPPS inhibited TLR4 membrane expression, MyD88/IKK&#x3b1;/&#x3b2; activation, NF-&#x3ba;B p65 phosphorylation, and nuclear translocation. In conclusion, RPPS alleviates SLI by protecting the intestinal barrier, modulating gut microbiota, and suppressing the TLR4/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: This study provides a scientific foundation for RPPS as a potential therapeutic candidate in sepsis treatment.},
}
@article {pmid41069450,
year = {2025},
author = {Chen, W and Yang, P and Hu, J and Liu, X and Jiang, C and Wu, H and Wang, Y and Yan, Q and Lu, S and Xiong, J and Huang, X and Pan, Y and He, F and Chen, Q and Hu, S and Chen, M and Xiong, C},
title = {Echoes in the Deep: Revealing Influenza A Viruses' Persistence and Microbial Associations in Aquatic Ecosystems.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5586400},
pmid = {41069450},
issn = {1865-1682},
mesh = {*Influenza A virus/isolation &amp; purification/genetics/classification ; China/epidemiology ; Animals ; *Seawater/virology/microbiology ; Phylogeny ; Lakes/virology ; Ecosystem ; Humans ; *Water Microbiology ; Fresh Water/virology ; },
abstract = {BACKGROUND: Influenza A viruses (IAVs) are significant pathogens with complex transmission dynamics in aquatic ecosystems, yet their persistence, evolutionary relationships, and associations with environmental microorganisms remain poorly understood. This study aimed to elucidate the phylogenetic characteristics and ecological associations of IAV in freshwater and seawater ecosystems in Eastern China to inform public health strategies.<br><br>METHODS: Water samples were collected from three freshwater lakes and a coastal seawater site. Viral particles were concentrated, and nucleic acids were extracted for metatranscriptomic and metagenomic sequencing. Phylogenetic analyses, population dynamics assessments, and microbial association networks were constructed using bioinformatic tools. Statistical tests, including Tajima's D and Fu and Li's tests, were applied to evaluate evolutionary trends.<br><br>RESULTS: IAV fragments in seawater showed high homology with recent human H3N2 strains from North America (2021-2024), while freshwater-derived fragments aligned with historical avian strains from Asia. Microbial association networks revealed significant associations between IAV and environmental bacteria (e.g., Brevundimonas aurantiaca) and fungi (e.g., Thamnidium), implying potential ecological associations that may underpin viral persistence. Freshwater environments with higher abundances of Uroviricota exhibited more frequent IAV detection. PERMANOVA confirmed distinct overall microbial community compositions in IAV-positive versus IAV-negative samples across both freshwater and seawater ecosystems (p < 0.05).<br><br>CONCLUSION: Aquatic ecosystems, particularly freshwater habitats, may serve as reservoirs for IAV persistence and evolution, driven by complex microbial associations. Regional disparities in viral strain origins highlight the role of migratory waterfowl and environmental transmission routes. Integrated surveillance of aquatic IAV dynamics is critical to anticipate zoonotic risks and mitigate future outbreaks.},
}
@article {pmid41069107,
year = {2025},
author = {Ozel, B and Agirman, B and Simsek, O and Erten, H},
title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70003},
pmid = {41069107},
issn = {1097-0061},
support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; },
abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.},
}
@article {pmid41069041,
year = {2025},
author = {Koketsu, A and Fukase, S and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Kumada, K and Li, B and Shimada, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Bacterial Involvement in Oral Squamous Cell Carcinoma and Potentially Malignant Oral Disorders.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70115},
pmid = {41069041},
issn = {1601-0825},
abstract = {OBJECTIVE: To clarify the relationship between oral squamous cell carcinoma (OSCC), potentially malignant oral disease (OPMD), and bacterial flora using metagenomic analysis.<br><br>METHODS: This cross-sectional observational study included 50 patients in the control group and 77 patients with OPMDs, 41 with early OSCCs, and 20 with advanced OSCCs. Patient saliva samples were subjected to high-throughput sequencing of 16S rRNA gene amplicons to evaluate the composition and diversity of the oral microbiome.<br><br>RESULTS: No significant differences were observed in patient backgrounds, other than sex. Patients with advanced OSCCs had greater oral bacterial diversity than those with early OSCC or OPMD. The advanced OSCC group formed a distinct cluster separate from the other groups. Sixteen and 275 species were identified at the phylum and genus levels, respectively. Compared with the control group, Actinomycetia and Streptococcus were significantly elevated in the early OSCC and OPMD groups. Peptostreptococcus and Fusobacterium were significantly higher in the advanced OSCC group than in the control, OPMD, and early OSCC groups.<br><br>CONCLUSIONS: The composition and diversity of oral microbiota may be associated with OPMD development and progression to OSCC. Consequently, the salivary microbiome may serve as a biomarker for oral cancer and help predict cancer progression.},
}
@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.<br><br>RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.<br><br>CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}
@article {pmid41068590,
year = {2025},
author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B},
title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {653},
pmid = {41068590},
issn = {1471-2180},
support = {2023ZSLC24//Zhongshan Hospital/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Adult ; },
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.<br><br>METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.<br><br>RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio&#x2009;=&#x2009;0.29; 95% confidence interval&#x2009;=&#x2009;0.12-0.73; P&#x2009;=&#x2009;0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score&#x2009;=&#x2009;1.0; log2FoldChange&#x2009;=&#x2009;3.6) and Dolosigranulum (NetMoss score&#x2009;=&#x2009;0.6; log2FoldChange&#x2009;=&#x2009;1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.<br><br>CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.},
}
@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}
@article {pmid40704526,
year = {2025},
author = {Capps, B and Chadwick, R and Joly, Y and Lajaunie, C and Hauptmannova, I and Mackenzie, S and Mulvihill, JJ and Mumford, E and Rasmussen, SA and Sanghavi, K and Thaldar, DW and Yeates, J and Quinzin, MC and Lederman, Z},
title = {The Ecological Genome Project and the Promises of Ecogenomics for Society: Realising a Shared Vision as One Health.},
journal = {Bioethics},
volume = {39},
number = {9},
pages = {788-795},
doi = {10.1111/bioe.70020},
pmid = {40704526},
issn = {1467-8519},
mesh = {Humans ; *One Health/ethics ; *Genomics/ethics ; *Ecology/ethics ; *Metagenomics/ethics ; *Ecosystem ; },
abstract = {This paper develops a vision for The Ecological Genome Project: an aspirational, global endeavour to connect human genomic sciences with the ethos of ecological sciences. The Project's goal is to strengthen interdisciplinary networks that relate to diverse initiatives using genomic technologies, with respect to shared ethical frameworks and governance structures. To this end, this paper proposes a practical definition of ecogenomics to align various methodologies and values in a single environmental field using principles used to safeguard all forms of life in their habitats. We achieve this by using a One Health approach as a pretext for disparate disciplines to collaborate and also a lens to view the Ethical, Legal and Social Implications (ELSI) inherent in ecological systems.},
}
@article {pmid41068233,
year = {2025},
author = {Giovannini, N and Limena, A and Ercolino, C and Renteria, SCU and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D},
title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35306},
pmid = {41068233},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation &amp; purification ; *Pregnancy Complications, Infectious/microbiology/virology ; },
abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.},
}
@article {pmid41068119,
year = {2025},
author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y},
title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {196},
pmid = {41068119},
issn = {2055-5008},
support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; },
abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.},
}
@article {pmid41068096,
year = {2025},
author = {Wu, Y and Ji, G and Han, D and Zhang, Y and Zhu, X and Li, H and Li, M and Gao, Y and Xie, R and Xu, M and Lu, L and Deng, Z and Wei, Q and Qin, H and Bi, D},
title = {Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {197},
pmid = {41068096},
issn = {2055-5008},
support = {82072634//National Natural Science Foundation of China/ ; 82072236//National Natural Science Foundation of China/ ; SHDC2020CR2069B//Shanghai Municipal Hospital Development Center/ ; ZJ2022-ZD-005//Major Projects of Special Development Funds in Zhangjiang National Independent Innovation Demonstration Zone, Shanghai/ ; },
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Fusobacterium/genetics/classification/isolation &amp; purification/pathogenicity ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Male ; Female ; Fusobacterium nucleatum/genetics ; Real-Time Polymerase Chain Reaction ; Middle Aged ; Aged ; Metagenomics ; },
abstract = {Non-nucleatum Fusobacterium may play a nonnegligible role in colorectal cancer (CRC) and certain Fusobacterium lineages (namely, L1 and L5) have shown specific associations with CRC. We aim to clarify the complex connections between Fusobacterium and CRC. We found that the widely adopted quantitative PCR (qPCR) method could overestimate F. nucleatum abundance and, in fact, reflect L1 levels in clinical samples. A lineage-specific qPCR assay targeting L1/L5 was developed and validated using mock and clinical samples. Its application in independent cohorts confirmed that L1 was overabundant in CRC, whereas L5 correlated with lymphovascular invasion. Importantly, faecal L1 abundance was more predictive of CRC than F. nucleatum, supported also by cross-population metagenomic data. CRC-associated virulence and colonisation genes were found in various L1 species other than F. nucleatum. Our results highlight the clinical importance of L1/L5 in CRC with high-diversity Fusobacterium contexts and suggest that non-nucleatum Fusobacterium may also contribute to CRC.},
}
@article {pmid41067450,
year = {2025},
author = {Liu, N and Zhang, Y and Zhang, Y and Yang, Y and Long, H and Huang, A and Zeng, Y and Xie, Z},
title = {Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133459},
doi = {10.1016/j.biortech.2025.133459},
pmid = {41067450},
issn = {1873-2976},
abstract = {Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.},
}
@article {pmid41067299,
year = {2025},
author = {Feng, Y and Yuan, Q and Kang, Y and Zheng, M and Li, Z},
title = {Deciphering the mobility, pathogenic hosts, and co-selection of antibiotic resistance genes in untreated wastewater from three different hospitals.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105840},
doi = {10.1016/j.meegid.2025.105840},
pmid = {41067299},
issn = {1567-7257},
abstract = {OBJECTIVE: Antibiotic resistance genes (ARGs) in hospital wastewater pose significant environmental and public health risks, yet the co-selection mechanisms involving metal/biocide resistance genes (MRGs/BRGs) and the role of mobile genetic elements (MGEs) remain poorly characterized. This study aimed to comprehensively assess the abundance, mobility, pathogenic hosts, and co-selection patterns of ARGs, MRGs, and BRGs in untreated wastewater from three types of hospitals.<br><br>METHODS: Untreated wastewater samples from nine sources across three hospital types (general, traditional Chinese medicine, and dental) were analyzed using metagenomic sequencing and assembly. ARGs, MRGs, and BRGs were identified via the SARG and BacMet databases. ARG hosts, mobility, and MGE co-occurrence were analyzed using PlasFlow and MOB-suite, with risk levels evaluated alongside pathogenic bacteria databases.<br><br>RESULTS: A total of 1911 ARGs (222 subtypes), 1662 MRGs (167 subtypes), and 916 BRGs (139 subtypes) were detected. Tetracycline, multidrug, and &#x3b2;-lactam resistance genes were predominant, with 46.43&#x202f;% of ARGs being plasmid-associated. Key pathogens including Klebsiella pneumoniae and Enterococcus spp. harbored high-risk ARGs such as KPC-2 and NDM-1. Notably, 76.2&#x202f;% of ARGs in traditional Chinese medicine hospital wastewater were classified as high-risk. Significant co-occurrence of ARGs with MGEs (e.g., DDE recombinases) and MRGs/BRGs was observed, underscoring the role of horizontal gene transfer and co-selection.<br><br>CONCLUSION: Untreated hospital wastewater represents a significant reservoir of ARGs, with risks exacerbated by pathogenic hosts, MGE-mediated HGT, and metal/biocide co-selection. These findings underscore the urgent need for optimized wastewater treatment strategies to curb the spread of antibiotic resistance and inform future intervention efforts.},
}
@article {pmid41067045,
year = {2025},
author = {Li, LH and Pabst, M and van Loosdrecht, MCM and Pronk, M},
title = {Distinct roles of granules and flocs in aerobic granular sludge processes.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124671},
doi = {10.1016/j.watres.2025.124671},
pmid = {41067045},
issn = {1879-2448},
abstract = {Aerobic Granular Sludge (AGS) is an innovative and efficient biotechnology for wastewater treatment that has been successfully applied on full-scale worldwide. Full-scale municipal AGS systems typically contain both granular sludge (granules) and flocculent sludge (flocs). Studies on the different roles of granules and flocs remain limited. In this study, a laboratory-scale AGS reactor fed with complex synthetic wastewater was operated to simulate full-scale AGS systems and to study the different functional roles of granules and flocs. The laboratory reactor achieved a coexistence of granules and flocs with a floc mass fraction of 17 %. The activities of different size fractions were evaluated using batch experiments and compared for carbon, nitrogen, and phosphorus removal: flocs (FL; <0.2 mm), small granules (SG; 0.2∼1.0 mm), medium granules (MG; 1.0∼2.0 mm), and large granules (LG; >2.0 mm). During feeding, large granules and medium granules exhibited more substrate uptake than small granules and flocs due to preferential substrate access. For aerobic conversion, flocs and small granules showed higher biomass-specific nitrification rates, while medium granules and large granules showed higher phosphorus uptake and denitrification capacity. Furthermore, large granules and medium granules showed stronger mass transfer limitation of oxygen, which limits their nitrification capability. Microbial community analysis using metagenomics and metaproteomics was performed across size fractions, and distinct communities in granules and flocs were shown. Granules showed a high abundance of Candidatus Accumulibacter (polyphosphate-accumulating organisms, PAOs) and Candidatus Competibacter (glycogen-accumulating organisms, GAOs). Flocs showed a high abundance of Nitrosomonas (ammonium-oxidizing bacteria, AOB) and Tetrasphaera (fermentative PAOs) and a low abundance of Ca. Accumulibacter. The distribution of microbial activities and microbial community over sludge size fractions in the laboratory reactor is similar to full-scale AGS systems, indicating that this laboratory setup can simulate full-scale systems and can be used for future research. Overall, this study highlights the importance of maintaining a good balance between different granule sizes and flocs to optimize nutrient removal.},
}
@article {pmid41067043,
year = {2025},
author = {Xu, D and Liu, T and Fan, J and Chen, W and Li, Y and Zhang, M and Zheng, P and Guo, J},
title = {Mechanical resistance of higher EPS contents in larger granules restricts anammox bacterial growth.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124705},
doi = {10.1016/j.watres.2025.124705},
pmid = {41067043},
issn = {1879-2448},
abstract = {Extracellular polymeric substances (EPS) are core granular components, playing critical roles in its structural stability. However, little is known about the effect of EPS on bacterial growth due to physical and mechanical resistances posed by EPS matrix. Herein, anaerobic ammonium oxidation (anammox) granules with different sizes and EPS contents were collected from a full-scale plant. Using [13]C isotope labelling and qPCR assays, we confirmed that larger granules with higher EPS content exhibited the higher maximum nitrogen removal activity but much lower bacterial growth yield, resulting in a significantly lower maximum specific growth rate (-26.8%), compared to smaller granules. Metagenomic sequencing revealed that anammox species were identical in different granules, and actual EPS production yields were similar in 15-day incubation, ruling out the possibility that more energy was diverted to produce additional EPS in larger granules. Interestingly, the EPS mechanical strength was significantly greater in large granules, which reduced cell membrane fluidity and severely deformed bacterial cells. These mechanical constraints imposed by the dense EPS matrix limited anammox bacterial proliferation and reduced their growth yield. Using low-intensity ultrasound to loosen EPS structure improved the growth yield of anammox bacteria in large granules, while also enhancing nitrogen removal activity. These together contributed to a substantial increase in bacterial growth rate (+153.3%). The findings highlight that physical and mechanical resistance imposed by EPS plays a previously overlooked role in bacterial growth, and provide the basis for promoting anammox bacterial proliferation within granules.},
}
@article {pmid41066987,
year = {2025},
author = {Zhang, C and Zhang, Y and Diao, G and Hou, N and Zhao, X and Li, D},
title = {Decoding pyrene-induced reactive oxygen species production in the rhizosphere and their role in biodegradation: The repair mechanism of symbiotic driving by Fe(II) and microorganisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140073},
doi = {10.1016/j.jhazmat.2025.140073},
pmid = {41066987},
issn = {1873-3336},
abstract = {Reactive oxygen species (ROS) are considered key drivers of biogeochemical processes. However, there is limited research on the factors influencing ROS generation in the rhizosphere due to polycyclic aromatic hydrocarbon (PAHs) pollution during plant-microbe joint remediation, as well as their role in biodegradation. This study demonstrated that exposure to pyrene at a concentration of 100 mg/kg significantly enhanced the release of hydrogen peroxide (H2O2), hydroxyl radicals (•OH), and superoxide anions (O2•[-]) in the rhizosphere of ryegrass during root development. The concentrations of these reactive oxygen species were 1.5-7.8 times higher than those in the control group. Additionally, the Fe(II) concentration increased by 37.5 ± 3.2 %, and the pyrene degradation rate reached 26.8 ± 1.4 %. These results indicate that pyrene serves as a major factor stimulating ROS generation in ryegrass. Among these processes, Fe(II) catalyzes the production of •OH, which directly attacks the benzene ring structure of pyrene. High-throughput analysis further revealed that ROS enhanced the diversity, cohesion, and robustness of the rhizosphere microbial community structure. Furthermore, Pseudomonas, Marmoricola, Nocardioides and Dietzia were identified as core microbial genera involved in pyrene degradation and ecological restoration. Metagenomics analysis suggests that rhizosphere microorganisms respond to ROS-induced oxidative stress by enhancing ATP synthesis, which provides energy for antioxidant-related protein production and damage repair, thereby accelerating pyrene degradation. These results elucidate the ROS-mediated driving mechanism behind microbial pyrene degradation in plant-microbe combined remediation systems, thereby providing a theoretical basis for optimizing bioremediation strategies for organically contaminated soils.},
}
@article {pmid41066873,
year = {2025},
author = {Hou, J and Liu, M and Li, Y and Li, L and Yao, Y and Xu, H and An, Y},
title = {Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109840},
doi = {10.1016/j.envint.2025.109840},
pmid = {41066873},
issn = {1873-6750},
abstract = {Heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in mitigating heavy metal stress and reducing heavy metal accumulation in plants. However, the origins and transmission mechanisms of PGPB and their associated heavy metal resistance genes (MRGs) in plants remain unclear. To fill this knowledge gap, we collected rice and related environmental samples from heavy metal-contaminated paddy fields. The microbial DNA was recovered from these rice and environmental samples and then analyzed using shotgun metagenomics at the metagenome-assembled genomes (MAGs) level. As a result, 805 MRG-PGPB combinations were detected in rice tissues and related environments under heavy metal contamination conditions. Core MRG-PGPB combinations shared across seed-rice (42.46%) and environment-rice (13.34%) interfaces collectively constituted 55.80% of the detected combinations, demonstrating that environmental translocation and seed-borne vertical transmission jointly drive over half of MRG-PGPB colonization in rice systems. Subsequent source-tracking analysis indicated that PGPBs present in rice primarily originated from seeds, with a substantial proportion also attributed to translocation within rice tissues. Phylogenetic analysis of dominant MRGs further demonstrated the seed-borne vertical transmission of MRGs-PGPB, while simultaneously elucidating that MRGs harbored by PGPB in rice could also be acquired via horizontal gene transfer (HGT) from environmental or seed-borne MRG-PGPB, particularly from atmospheric microbes such as Methylophilus and Serratia. These findings provide valuable insights into harnessing PGPB to enhance rice resilience against heavy metal contamination, thereby contributing to improved food security and sustainable agricultural practices.},
}
@article {pmid41066697,
year = {2025},
author = {Li, Y and Gao, Y and Liu, X and Mao, Y and Wang, M and Qin, Y and Zhang, C and Chen, Q and Ning, K and Wang, Z and Han, M},
title = {Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/bib/bbaf535},
pmid = {41066697},
issn = {1477-4054},
support = {82300645//National Natural Science Foundation of China/ ; 41877409//National Natural Science Foundation of China/ ; U23A2059//National Natural Science Foundation of China/ ; 2408085Y039//Outstanding Youth Program of Anhui Provincial Natural Science Foundation/ ; YQZD202406//Key Project for cultivating outstanding young teachers of Higher Education in Anhui Province/ ; tsqn202312094//Taishan Scholars Program of Shandong Province/ ; 2023KJ034//Shandong Provincial Higher Education Institution Youth Innovation Teams/ ; XJ201916//Grants for Scientific Research of BSKY/ ; 2022zhyx-B15//Anhui Medical University, Research Fund of Anhui Institute of translational medicine/ ; },
mesh = {Humans ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Risk Assessment ; Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Feces/microbiology ; },
abstract = {The global dissemination of antibiotic resistance genes (ARGs) represents a critical challenge to One Health. Existing ARG risk assessment tools (e.g. MetaCompare, ARRI) are constrained by short-read sequencing data, limiting their utility for long-read platforms. To address this gap, we developed the Long-read based Antibiotic Resistome Risk Assessment Pipeline (L-ARRAP), which calculates the Long-read based Antibiotic Resistome Risk Index (L-ARRI) to quantify antibiotic resistome risks. Building upon our previous ARRI framework, L-ARRAP leverages long-read sequencing advantages to concurrently identify ARGs, mobile genetic elements, and human bacterial pathogens, integrating their interactions for risk scoring. Our results showed that L-ARRAP was not only able to accurately identify ARGs and evaluate the antibiotic resistance risk scores in samples of hospital wastewater (HWW), Chaohu lake, and human fecal samples, but also significantly distinguish the ARG risk in HWW samples between before and after disinfection groups, demonstrating the performance of L-ARRAP. Furthermore, L-ARRAP scores exhibited strong concordance with those generated by our laboratory-adapted MetaCompare variant (L-MetaCompare), corroborating its methodological reliability. Overall, to our knowledge, L-ARRAP is the first assessment pipeline of antibiotic resistome for long sequencing reads and has a great potential for monitoring the risk of ARGs in various environmental niches.},
}
@article {pmid41066275,
year = {2025},
author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S},
title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002065},
pmid = {41066275},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; },
abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.},
}
@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}
@article {pmid41066109,
year = {2025},
author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y},
title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2511071122},
doi = {10.1073/pnas.2511071122},
pmid = {41066109},
issn = {1091-6490},
support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; },
abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.},
}
@article {pmid41065113,
year = {2025},
author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC},
title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251376911},
doi = {10.1177/13872877251376911},
pmid = {41065113},
issn = {1875-8908},
abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.},
}
@article {pmid41064842,
year = {2025},
author = {Kuswandi, W and Budiman, C and Khaerunnisa, I and Sumantri, C},
title = {Rearing system and immune status influence the small intestinal microbiota of IPB-D3 chickens: A full-length 16S rRNA metagenomic approach.},
journal = {Veterinary world},
volume = {18},
number = {8},
pages = {2206-2221},
pmid = {41064842},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The small intestinal microbiota plays a pivotal role in poultry digestion and immune function. Rearing systems can influence their composition, thereby affecting the overall health and performance of the birds. This study aimed to investigate how rearing systems (intensive [IN] vs. free-range [FR]) and immune status, reflected by leukocyte profiles, influence the small intestinal microbiome of IPB-D3 chickens, a genetically improved Indonesian local breed.<br><br>MATERIALS AND METHODS: Ninety IPB-D3 chickens were reared for 12 weeks under either IN or FR systems. Hematological profiling was conducted to assess health status, with leukocyte counts used to stratify birds. Microbiota samples from the small intestine were analyzed using full-length 16S ribosomal RNA (V1-V9) sequencing on the Oxford Nanopore platform. Taxonomic identification was performed using the SILVA database. Statistical comparisons were made using t-tests, and microbial diversity was assessed through alpha and beta diversity metrics.<br><br>RESULTS: While most hematological parameters did not differ significantly between rearing systems, total leukocyte counts were higher in intensively reared chickens (p = 0.002). FR chickens exhibited significantly greater microbial diversity (p < 0.05) across multiple alpha diversity indices. A total of 1,294 unique species were identified in FR birds versus 720 in the IN group, with 1,761 shared species. Leukocyte level further influenced microbial profiles; chickens with high leukocyte (HL) counts were dominated by Ligilactobacillus aviarius, whereas low-leukocyte chickens had a higher abundance of Bacteroides caecigallinarum. Gallibacterium anatis, a potential pathogen, dominated in IN systems with elevated leukocytes.<br><br>CONCLUSION: This study demonstrates that both the rearing environment and immune status substantially influence small intestinal microbial composition in IPB-D3 chickens. FR systems promoted richer, more beneficial microbial communities, while IN systems, especially with HL levels, were associated with opportunistic pathogens. Leukocyte profiling may serve as a non-invasive biomarker for gut health, supporting future development of precision poultry management strategies and immune-responsive probiotics.},
}
@article {pmid41064771,
year = {2025},
author = {Giraldo-Badillo, I and Pineda-Vélez, E and Carbonell-Medina, BA and Ardila, CM},
title = {Microbiological and Pharmacological Aspects Involved in Dentin-Pulp Complex Regeneration: A Scoping Review.},
journal = {Journal of clinical and experimental dentistry},
volume = {17},
number = {9},
pages = {e1149-e1158},
pmid = {41064771},
issn = {1989-5488},
abstract = {BACKGROUND: The regeneration of the dentin-pulp complex represents a pivotal challenge in endodontics, requiring a delicate balance between microbial eradication and tissue repair. This scoping review, conducted in accordance with PRISMA-ScR guidelines, synthesizes current evidence on microbiological and pharmacological factors influencing regenerative outcomes.<br><br>MATERIAL AND METHODS: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library identified 242 studies, with 15 meeting inclusion criteria after screening.<br><br>RESULTS: The review highlights the dominance of anaerobic biofilm-forming pathogens (Enterococcus faecalis, Porphyromonas gingivalis) in periapical lesions, their virulence mechanisms (e.g., proteolytic enzymes, immune evasion), and the rising threat of antibiotic resistance driven by &#x3b2;-lactamases and efflux pumps. Pharmacologically, while triple/double antibiotic pastes promote dentin thickening, their cytotoxicity at high concentrations and disruption of commensal microbiota underscore the need for optimized dosing. Emerging alternatives-such as antimicrobial peptides, calcium hypochlorite, and immunomodulatory biomolecules-demonstrate superior biocompatibility and dual action against pathogens while supporting stem cell viability.<br><br>CONCLUSIONS: Future directions emphasize microbiome-targeted therapies, advanced biomaterials, and personalized approaches leveraging metagenomics. This review underscores the imperative to integrate selective antimicrobial strategies with regenerative biology to advance endodontic outcomes. Key words:Dentin-pulp regeneration, endodontic infections, biofilm, antimicrobial resistance, regenerative endodontics.},
}
@article {pmid41064045,
year = {2025},
author = {Zhao, S and Wang, F and Song, L and Zhu, S and Liu, S and Zhao, K and Liu, R and Li, YY},
title = {Interspecies electron transfer as one of key drivers of methanogenic consortia succession within quorum sensing regulation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf165},
pmid = {41064045},
issn = {2730-6151},
abstract = {Robust interspecies interactions are essential for efficient methanogenesis in anaerobic digestion. This study investigated the impact of quorum sensing (QS) enhancement on the succession of methanogenic communities during anaerobic digestion. The QS stimulation via exogenous N-acyl-homoserine lactones enhanced methane production by 18.8%-22.1%. Moreover, QS shaped microbial community succession toward a more deterministic assembly, selectively enriching key syntrophs (Pelotomaculum, Smithella), and methanogens (Methanobacterium, Methanothrix). Metagenomic analysis revealed that QS induced genes related to transcription, transport, and cofactor biosynthesis instead of directly regulating carbon metabolism. In this context, interspecies electron transfer emerges as a critical factor regulating interspecies interactions under QS regulation. Specifically, QS enhancement boosted redox mediator secretion, and the concentration of 2-amino-3-carboxy-1,4-naphthoquinone and phenazine increased by 7.8- and 4.8-fold, respectively. QS enhancement also induced higher abundance of c-type cytochromes. Moreover, the higher electron transfer coefficients were detected with 40.2%-89.9% increase. Further, QS also enhanced relative abundance of genes involved in Complex I/III and ferredoxin-dependent hydrogenases, promoting electron flow from syntrophs to methanogens. These effects induced higher relative abundance of genes associated with syntrophic propionate/butyrate oxidation and hydrogenotrophic/acetotrophic methanogenesis. Collectively, given that the similar regulation pathway is widely distributed in anaerobes, these findings identify QS as a critical ecological signal that drives functional microbial succession.},
}
@article {pmid41063294,
year = {2025},
author = {Sun, S and Wang, H and Han, B and Wu, H and Wang, Y and Xu, T},
title = {Combined effects of low temperature, hyperosmolarity and seawater-conditioned pathogens on open fracture healing in a rat model simulating circumpolar environments.},
journal = {Journal of orthopaedic surgery and research},
volume = {20},
number = {1},
pages = {875},
pmid = {41063294},
issn = {1749-799X},
mesh = {Animals ; Rats, Sprague-Dawley ; Male ; *Seawater/microbiology/adverse effects ; Rats ; *Fracture Healing/physiology ; *Cold Temperature/adverse effects ; *Fractures, Open/microbiology/diagnostic imaging ; Disease Models, Animal ; *Femoral Fractures/microbiology/diagnostic imaging ; },
abstract = {OBJECTIVE: To investigate the factors influencing the healing of open fractures in circumpolar latitude region seawater immersion conditions.<br><br>MATERIALS AND METHODS: A femoral fracture model was established in ninety 6-to-8-week-old male Sprague-Dawley rats, randomly assigned to five groups (n&#x2009;=&#x2009;18 per group): (1) fracture only, (2) fracture with circumpolar seawater immersion, (3) fracture with low-temperature isotonic solution immersion, (4) fracture with aseptic circumpolar seawater immersion, and (5) fracture with low-temperature aseptic circumpolar seawater immersion. Fractures were confirmed postoperatively by radiographs on days 7, 21, and 42. Micro-CT and H&amp;E staining were performed on day 42 to assess bone healing. Bacterial cultures from internal fixation devices were analyzed on day 3. Blood samples were collected on days 3, 7, and 14 to assess leukocyte and neutrophil counts, and serum ALP and VEGF levels were measured on days 7, 14, and 21. Pathogenic microorganisms in the seawater were identified by metagenomic analysis. Fracture healing and callus formation rates were compared using the Log-rank test.<br><br>RESULTS: X-ray, micro-CT, and histological analyses revealed significantly impaired fracture healing in the group exposed to circumpolar seawater immersion compared to the fracture-only group (P&#x2009;<&#x2009;0.05). Bacterial colony counts on internal fixation devices were highest in the circumpolar seawater group (P&#x2009;<&#x2009;0.05). Leukocyte and neutrophil levels were significantly elevated in this group on days 3 and 7 (P&#x2009;<&#x2009;0.05), with no significant differences observed on day 14 (P&#x2009;>&#x2009;0.05). Serum ALP and VEGF levels were significantly reduced on days 7, 14, and 21 (P&#x2009;<&#x2009;0.05), although ALP levels on day 21 showed no significant difference (P&#x2009;>&#x2009;0.05). Log-rank analysis indicated that the bone union and callus maturation rates were significantly lower in the circumpolar seawater group compared to the other four groups. Metagenomic analysis identified Flavobacterium, Rhodobacter, and Bacteroides as the dominant pathogens in circumpolar seawater.<br><br>CONCLUSIONS: This study demonstrates that hyperosmolarity, low temperature, and exposure to opportunistic pathogens under circumpolar seawater conditions collectively delay open fracture healing. Among these factors, opportunistic pathogens exert the most significant impact, highlighting microbial contamination as the primary barrier to bone regeneration in such environments and providing direction for future therapeutic strategies.<br><br>CLINICAL TRIAL NUMBER: not applicable.},
}
@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}
@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}
@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R15LM013460//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}
@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}
@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The Sex Related Differences in Health and Disease: A Systematic Review of Sex-Specific Gut Microbiota and Possible Implications for Microbial Pathogenesis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.<br><br>METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.<br><br>RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.<br><br>CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}
@article {pmid41061960,
year = {2025},
author = {Wang, H and Sheng, J and Zhang, Y and Lan, H and Lu, X and Li, X and Zhao, X},
title = {Detection of zoonotic Coxiella burnetii causing chronic Q fever endocarditis in a Chinese geriatric patient by mNGS.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.015},
pmid = {41061960},
issn = {2213-7173},
abstract = {OBJECTIVES: Q (query) fever, caused by Coxiella burnetii, is often linked to negative bacterial cultures. Infective endocarditis with negative cultures is difficult to diagnose and treat. Our case demonstrates that metagenomic next-generation sequencing (mNGS) can provide a rapid and accurate method for pathogenetic diagnosis in infectious diseases.<br><br>CASE PRESENTATION: We reported a case of infective endocarditis with negative blood cultures in a male patient with a history of sheep farming and previous aortic valve replacement (AVT) and atrial septal defect atrial septal defect (ASD) repair. Blood tests showed positive serum immunofluorescent antibodies to rickettsia, while mNGS of perivalvular abscess tissue suggested C. burnetii. Doxycycline 0.1 g q12h and hydroxychloroquine 0.2 g q12h were used for postoperative antibiotic treatment. The genome of the C. burnetii C2245173Z was assembled on the Illumina platform, and no known antibiotic resistance genes were detected. Phylogenetic analysis of C. burnetii genomes shows a genetic relationship between animal-derived strains and human-derived strains.<br><br>CONCLUSIONS: The application of mNGS could provide a rapid and accurate assay in clinical diagnosis and play a decisive role in the pathogenetic diagnosis of some infectious diseases. Doxycycline plus hydroxychloroquine remains an effective treatment for chronic Q fever endocarditis. In addition, phylogenetic tree analysis indicates that C. burnetii infection may pose a potential risk to humans working with livestock.},
}
@article {pmid41061540,
year = {2025},
author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W},
title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140065},
doi = {10.1016/j.jhazmat.2025.140065},
pmid = {41061540},
issn = {1873-3336},
abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.},
}
@article {pmid41061488,
year = {2025},
author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N},
title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111479},
doi = {10.1016/j.ijfoodmicro.2025.111479},
pmid = {41061488},
issn = {1879-3460},
abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.},
}
@article {pmid41060906,
year = {2025},
author = {Sawyer, FM and Stossi, F and Nachman, E and Britton, RA and Bolt, MJ and Mancini, MA and Estes, MK and Blutt, SE},
title = {A pipeline for rapid, high-throughput imaging and quantitative analysis of human intestinal organoids.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332418},
doi = {10.1371/journal.pone.0332418},
pmid = {41060906},
issn = {1932-6203},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestinal Mucosa/cytology ; *High-Throughput Screening Assays/methods ; Microscopy, Confocal/methods ; Image Processing, Computer-Assisted/methods ; *Intestines/cytology ; Cell Proliferation ; },
abstract = {Human intestinal organoids (HIOs) are a model system for studying human intestinal epithelium. Utilizing HIOs for high-throughput studies remains inefficient, as analyzing their cellular composition and responses to varying experimental conditions requires extensive time and labor. We describe a 96-well plate-based automated pipeline for rapidly imaging and quantifying fluorescent labeling in HIOs using a high-throughput confocal microscope and image analysis software. The pipeline was leveraged to quantify varying levels of cell proliferation among donor HIO lines in response to microbial products. Cytoplasmic fluorescence via antibody labeling was also quantified with the pipeline, enabling measurement of the prevalence of specific cell types in HIOs. This platform offers a novel approach to efficiently and rapidly image and quantify fluorescent staining and immunolabeling in HIOs and has many potential applications, including drug screening, toxicity testing, intestinal barrier integrity and transport studies, microbiome and host-pathogen interaction studies, and lineage tracking.},
}
@article {pmid41060725,
year = {2025},
author = {Liu, Y and Tang, J and Wang, Y and Cui, F and Yang, Y},
title = {Intracranial infection caused by Mycoplasma hominis after neurosurgical operation: an easily overlooked but serious condition.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {9},
pages = {1425-1431},
doi = {10.3855/jidc.20729},
pmid = {41060725},
issn = {1972-2680},
mesh = {Humans ; Male ; *Mycoplasma hominis/isolation &amp; purification/genetics ; *Mycoplasma Infections/diagnosis/drug therapy/microbiology ; Aged ; Anti-Bacterial Agents/therapeutic use ; *Neurosurgical Procedures/adverse effects ; *Postoperative Complications/microbiology/diagnosis/drug therapy ; },
abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) is a commensal that mainly colonizes in the microflora of the genitourinary tracts and is associated with urogenital tract infections. There are reports of central nervous system (CNS) infections in neonates caused by M. hominis. Nevertheless, M. hominis CNS infections in non-neonatal patients are extremely rare. Herein, we have reported a case of a man who suffered from intracranial infection secondary to M. hominis after neurosurgical operation. Additionally, we reviewed the relevant published literature to raise awareness on such infections and highlight the importance of proper treatments.<br><br>CASE PRESENTATION: A 68-year-old man underwent emergence craniotomy for intracerebellar hemorrhage. He presented with a moderate fever unresponsive to piperacillin-tazobactam on the seventh day after the surgery. His body temperature continued to increase, and he presented with signs of CNS infection. The antimicrobial therapy was switched to meropenem and vancomycin. No obvious reduction in the body temperature was observed. The cerebrospinal fluid (CSF) obtained previously revealed tiny point colonies which were morphologically consistent with M. hominis and subsequently confirmed by metagenomic next-generation sequencing (mNGS). Thus, M. hominis induced intracranial infection was diagnosed, and a combination therapy with moxifloxacin and minocycline was implemented. Fortunately, the patient's body temperature decreased to normal range after effective antibiotic therapy.<br><br>CONCLUSIONS: Based on the lesson of our case and a thorough review of published literature, the possibility of M. hominis induced CNS infections after neurosurgical intervention should not be ignored, especially when there is no response to standard antimicrobial therapy.},
}
@article {pmid41060484,
year = {2025},
author = {Khan, MF},
title = {Enhancing stability of enzymes for industrial applications: molecular insights and emerging approaches.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {362},
pmid = {41060484},
issn = {1573-0972},
support = {82930-NP//University College Dublin/ ; },
mesh = {Enzyme Stability ; *Enzymes/chemistry/metabolism/genetics ; Protein Engineering/methods ; Hydrogen-Ion Concentration ; Biocatalysis ; Biotechnology ; },
abstract = {The growing demand for robust biocatalysts in industrial bioprocesses has intensified the pursuit of enzymes capable of functioning under extreme physicochemical conditions. This work critically examines the molecular determinants of enzyme stability, including thermostability, pH tolerance, halotolerance, resistance to solvents and oxidative stress, mechanical resilience to shear and pressure, and storage stability. These traits are essential for sustained catalytic performance in sectors such as bioenergy, pharmaceuticals, food, textiles, and environmental remediation. Recent advances in structure-guided engineering, molecular dynamics, and mutational profiling have enabled rational strategies to enhance enzyme resilience. By adopting a multi-parametric lens, this study bridges specific molecular adaptations with industrial challenges, offering a systems-level framework often lacking in single-condition analyses. It also explores emerging frontiers, including AI-assisted enzyme design, metagenomic discovery from extremophiles, and synthetic reconstruction of adaptive pathways, paving the way for next-generation biocatalysts optimised for scalability, performance, and sustainability. The novelty of this work lies in its integrative approach combining molecular insight, environmental origin, and computational tools to guide the development of industrially robust enzymes.},
}
@article {pmid41060313,
year = {2025},
author = {Hays, MD and Fuchsman, CA},
title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf221},
pmid = {41060313},
issn = {1751-7370},
abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in 6 ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep sub-ecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b sub-ecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.},
}
@article {pmid41060304,
year = {2025},
author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N},
title = {High strain-level diversity of Bradyrhizobium across Australian soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf222},
pmid = {41060304},
issn = {1751-7370},
abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.},
}
@article {pmid41059692,
year = {2025},
author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF},
title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258324},
doi = {10.1128/spectrum.02583-24},
pmid = {41059692},
issn = {2165-0497},
abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.},
}
@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}
@article {pmid41059063,
year = {2025},
author = {Hu, J and Cyle, KT and Yuan, W and Shi, W},
title = {Metagenomic evidence clarifies the texture-dependent cascading effects of organic degradation on soil hypoxia and N2O emission.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670657},
pmid = {41059063},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil pore-scale aeration is a crucial yet often overlooked factor influencing the effectiveness of nitrous oxide (N2O) emission mitigation strategies. Our previous work revealed a hundred-fold variation in N2O emissions among soils under apparently aerobic conditions and texture-dependent mitigation effects of biochar-manure co-compost (BM) compared to manure compost (M).<br><br>METHODS: We analyzed soils of three textures-clay loam (CL), silt loam (SL), and sand (SA)-amended with BM or M. Metagenomic sequencing was used to profile microbial community composition and functional genes, with a focus on aeration-sensitive taxa and pathways.<br><br>RESULTS: We demonstrate that these changes of N2O emissions are aligned with variations in aeration-sensitive microbes and genes. SA, with the highest N2O emissions, was most abundant in obligate and facultative anaerobes and denitrification-related genes, while CL, with the lowest emissions, had more genes related to fermentation and dissimilatory nitrate reduction. Compared to M, BM in CL favored genes for microbial processes requiring a more reducing environment, likely because biochar-induced finer pores, exacerbating oxygen diffusion limitations. This severe oxygen restriction in CL after BM addition was substantiated by greater reductions in CO2 efflux and C-cycling genes than in the other soils.<br><br>DISCUSSION: Our findings suggest that hypoxic pore abundance and the severity of pore anaerobiosis imparted by degradation of organic amendments varied with soil texture and are the overriding factors of soil greenhouse gas (GHG) emissions. Metagenomic traits provide a sensitive tool for detecting pore-scale environmental shifts, improving our mechanistic understanding of soil-dependent GHG emissions following organic amendments.},
}
@article {pmid41059058,
year = {2025},
author = {Wang, Y and Bai, Z and Liu, Y and Wang, Y and Xu, J and Lai, Z},
title = {Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616985},
pmid = {41059058},
issn = {1664-302X},
abstract = {INTRODUCTION: Tacrolimus is crucial for immunosuppression after liver transplantation, but its pharmacokinetics vary markedly among individuals. Emerging evidence suggests that the gut microbiota may influence its metabolism, although the underlying mechanisms remain unclear.<br><br>METHODS: This study analyzed the fecal microbiota from 38 postliver transplant patients and 31 healthy controls via 16S rDNA amplicon and shotgun metagenomic sequencing. Patients were stratified into three groups on the basis of oral tacrolimus dosage and blood concentration: LDLBC (low dose, low blood concentration), LDHBC (low dose, high blood concentration), and SDLBC (standard dose, low blood concentration).<br><br>RESULTS: Posttransplant patients presented significantly reduced gut microbial diversity. Specific bacterial taxa, including Enterococcus raffinosus, Intestinibacter bartlettii, and Bacteroides fragilis, were enriched in patients with lower tacrolimus blood concentrations. In contrast, Phascolarctobacterium faecium and Streptococcus salivarius were associated with increased drug levels. Functional analysis revealed differences between patient subgroups in ATP-binding cassette (ABC) transporters and drug efflux pumps, suggesting a potential microbial influence on tacrolimus absorption and metabolism. Additionally, antibiotic resistance genes were more abundant in patients with lower tacrolimus blood concentrations, particularly in the Escherichia coli-enriched groups.<br><br>DISCUSSION: These findings underscore the influence of the gut microbiota on tacrolimus pharmacokinetics and support the potential of microbial composition as a biomarker for optimizing immunosuppressive therapy.},
}
@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.<br><br>METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by &#x3b1;-diversity, &#x3b2;-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.<br><br>RESULTS: Overall, no significant differences in viral and bacterial &#x3b1;- or &#x3b2;-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.<br><br>CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}
@article {pmid41059035,
year = {2025},
author = {Huang, Y and Zhang, M and Tian, Y and Lan, X and Jin, W and Bai, Y and Zang, Q and Chen, M and Su, Z and Zhang, W and Aishan, G and Geng, M and Xie, J and Tong, P},
title = {A novel broad-spectrum lytic phage vB_EcoM_P3322: isolation, characterization, and therapeutic potential against avian pathogenic Escherichia coli.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1645263},
pmid = {41059035},
issn = {2235-2988},
mesh = {Animals ; *Escherichia coli/virology/pathogenicity ; *Escherichia coli Infections/therapy/veterinary/microbiology ; *Myoviridae/isolation &amp; purification/classification/ultrastructure/genetics/physiology ; Host Specificity ; *Phage Therapy/methods ; Wastewater/virology ; *Coliphages/isolation &amp; purification/classification/ultrastructure/physiology/genetics ; Columbidae/microbiology ; Genome, Viral ; Phylogeny ; Poultry Diseases/therapy/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {INTRODUCTION: The widespread misuse of antibiotics has accelerated the emergence of multidrug-resistant bacterial strains, presenting a major threat to global public health. Bacteriophages (phages), owing to their host-specific lytic activity and self-replicating nature, have emerged as promising alternatives or adjuncts to conventional antibiotic therapies.<br><br>METHODS: In this study, a lytic phage targeting avian pathogenic Escherichia coli (APEC) was isolated from farm wastewater. The phage's morphological characteristics, host range, optimal multiplicity of infection (MOI), one-step growth curve, pH stability, thermal stability, chloroform sensitivity, and in vitro antibacterial activity were determined. Subsequently, the therapeutic efficacy of the phage was evaluated in a pigeon model.<br><br>RESULTS: In this study, we isolated and characterized a lytic phage, designated vB_EcoM_P3322, from farm wastewater targeting APEC. Transmission electron microscopy classified vB_EcoM_P3322 within the Myoviridae family. The phage exhibited broad lytic activity against five Escherichia coliserotypes (O8:H10, O15:H18, O51:H20, O149:H20, and O166:H6). Optimal biological parameters included a multiplicity of infection (MOI) of 1, a latent period of 10 minutes, an 80-minute burst period, and a burst size of 252 PFUs/cell. vB_EcoM_P3322 maintained stable lytic activity across a pH range of 5-9 and temperatures from 4&#xb0;C to 50&#xb0;C, although it was sensitive to chloroform. In vitro, the phage effectively suppressed bacterial growth within 6 hours at MOIs of 0.1, 1, and 10. Whole-genome sequencing revealed a 151,674 bp double-stranded DNA genome encoding 279 predicted open reading frames. No virulence factors, toxin genes, antibiotic resistance genes, or lysogeny-related elements were identified, affirming its safety for therapeutic application. Phylogenetic analysis indicated 98.44% nucleotide identity (97% coverage) with phage vB_EcoM_Ro121c4YLVW (GenBank: NC_052654), suggesting a close evolutionary relationship. In a pigeon infection model, vB_EcoM_P3322 treatment significantly improved survival and reduced histopathological damage in the liver and spleen. Metagenomic analysis of duodenal contents revealed a marked reduction (P < 0.01) in E. coli abundance in the treatment group, indicating selective pathogen clearance and modulation of gut microbiota.<br><br>DISCUSSION: In summary, vB_EcoM_P3322 displays broad-spectrum lytic activity, robust environmental stability, potent antibacterial efficacy both in vitro and in vivo, and a safe genomic profile. These attributes support its potential as a novel biocontrol agent for managing APEC infections in poultry farming.},
}
@article {pmid41058886,
year = {2025},
author = {Liu, Y and Li, L and Yang, L and Yang, Y and An, H and Li, D and Wang, X},
title = {Clinical Features and Treatment Strategies of Q Fever Spinal Infection: A Pooled Analysis of 39 Cases and Narrative Review of the Literature.},
journal = {Open forum infectious diseases},
volume = {12},
number = {10},
pages = {ofaf584},
pmid = {41058886},
issn = {2328-8957},
abstract = {BACKGROUND: The incidence of spinal infections is increasing; However, pathogen identification remains challenging. Although Q fever spinal infection is reported infrequently, its accrual incidence is likely underestimated. The causative agent, Coxiella burnetii, cannot be routinely cultured. Consequently, physicians often misdiagnose Q fever spinal infection as spinal tuberculosis, leading to severe patient harm. Thus, improving clinicians' awareness of the clinical characteristics of Q fever spinal infection is urgently needed.<br><br>METHODS: We present a case of Q fever spinal infection and conducted literature searches in PubMed and the Chinese core journals of the Wanfang Database using keywords including "Q fever," "Coxiella burnetii," "spinal infection," "osteomyelitis," "spondylodiscitis," and "psoas abscess." Additional reports were identified through cross-referencing, with a cutoff date of 6 November 2024. Cases were included if patient age, sex, and baseline medical history were documented. Clinical data were retrospectively analyzed, and clinical features were compared between the aneurysm-associated group and the isolated spinal infection group. Fisher's exact probability test was used to evaluate the incidence difference.<br><br>RESULTS: A total of 39 adult patients were enrolled (mean age: 67.82 &#xb1; 10.51 years, male: 34,87.2%), Eleven cases reported potential pathogen exposure. Thirty-three cases presented with early-onset of lower back pain, and 13 developed fever during the disease course. Thirty-four cases involved the lumbar spine, exhibiting continuous lesions of 1-3 vertebral bodies, with imaging features of vertebral osteomyelitis, discitis, paravertebral soft-tissue swelling, and/or adjacent aneurysmal changes. Among 21 cases with routine blood tests, 2 showed elevated leukocyte counts, 5 had mild anemia, and the remainder were normal. Serological testing was performed in 34 cases, with 29 testing positive on the first time; PCR testing was conducted in 25 cases, with 23 cases detecting positive specimens; and rapid diagnosis confirmed in all 3 cases via metagenomic next-generation sequencing (mNGS). Inflammatory reactions were identified in all 21 biopsied cases, with inflammatory granulomas reported in 7 and explicitly excluded in 4. There were 24 cases complicated with aneurysm and 15 cases with isolated spinal infection. A significant difference in CRP elevation rate was observed between the two groups (14/15, 93.33% vs 4/8, 50.00%, P = .033). Early local lesion debridement combined with doxycycline-based multidrug therapy showed favorable outcomes. Serological monitoring demonstrated low sensitivity for assessing therapeutic efficacy.<br><br>CONCLUSIONS: This study systematically summarizes the clinical characteristics of Q fever spinal infection and, for the first time, reports features associated with its distinct clinical subtypes. Q fever should be considered in case of chronic spinal infections-especially those complicated with vascular lesions. Based on clinical history evaluation, rapid diagnosis may be achieved through mNGS of specimens from local lesions. Combined with early initiation of doxycycline-based regimens, timely debridement of necrotic tissues and purulent material may improve treatment outcomes. Further investigations are needed to identify reliable biomarkers for monitoring therapeutic efficacy and to establish optimal treatment strategies for subtypes of Q fever spinal infection.},
}
@article {pmid41058622,
year = {2025},
author = {Cai, ZZ and Zeng, DM and Lei, LW and Xiao, S},
title = {Rotavirus gastroenteritis complicating meningitis caused by Bacteroides uniformis detected using mNGS: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1601953},
pmid = {41058622},
issn = {2296-858X},
abstract = {This case report describes a rare instance of pediatric meningitis caused by Bacteroides uniformis (B. uniformis) following rotavirus gastroenteritis in a 1-year-4-month-old boy, diagnosed using metagenomics next-generation sequencing (mNGS). Bacterial meningitis (BM) is a life-threatening disease in children, particularly those under 5 years old, and early identification of the pathogen is crucial for reducing mortality and improving prognosis. B. uniformis, a Gram-negative, non-spore-forming, obligate anaerobic bacillus and common gut commensal, is rarely implicated in human infections, particularly pediatric meningitis. The child presented with vomiting, diarrhea, convulsions, and syncope, and was initially treated for meningitis and rotavirus gastroenteritis. Despite negative bacterial cultures, mNGS identified B. uniformis in the cerebrospinal fluid (CSF). Treatment was switched from ceftriaxone to meropenem (0.45 g, IV every 8 h) based on its good blood-brain barrier penetration and likely susceptibility of B. uniformis. The child's condition improved significantly, with follow-up lumbar puncture showing normal CSF parameters and no detectable pathogens. The case suggests that rare anaerobic meningitis may occur against the backdrop of rotavirus gastroenteritis and underscores the importance of using mNGS for accurate pathogen detection in bacterial meningitis, as well as the need for early initiation of appropriate antimicrobial therapy.},
}
@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}
@article {pmid41058431,
year = {2025},
author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV},
title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimce.2025.09.011},
pmid = {41058431},
issn = {2529-993X},
abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.},
}
@article {pmid41057946,
year = {2025},
author = {Ren, Y and Wu, YH and Chen, J and Luo, ZH and Xu, XW},
title = {New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {127},
pmid = {41057946},
issn = {2524-6372},
support = {42376133//National Natural Science Foundation of China/ ; 2021YFF0501303//National Key R&amp;D Program of China/ ; },
abstract = {Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.},
}
@article {pmid41057624,
year = {2025},
author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y},
title = {Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.},
journal = {NPJ digital medicine},
volume = {8},
number = {1},
pages = {599},
pmid = {41057624},
issn = {2398-6352},
support = {2023YFC2308300//Key Technologies Research and Development Program/ ; 82472371//National Natural Science Foundation of China/ ; },
abstract = {Recent advances in unbiased metagenomic next-generation sequencing (mNGS) enable simultaneous examination of microbial and host genetic material. We developed a multimodal machine learning-based diagnostic approach to differentiate lung cancer and pulmonary infections by analyzing 402 bronchoalveolar lavage fluid (BALF) mNGS datasets, including lung cancer (n = 123), bacterial infections (n = 114), fungal infections (n = 79), and pulmonary tuberculosis (n = 86). The training cohort revealed differences in microbial profiles, bacteriophage abundance, host gene and transposable element expression, immune cell composition, and tumor fraction derived from copy number variation (CNV). The integrated model (Model VI) achieved an AUC of 0.937 (95% CI, 0.910-0.964) in the training cohort and 0.847 (95% CI, 0.776-0.918) in the test cohort. A rule-in/rule-out strategy further improved accuracy in differentiating lung cancer from tuberculosis (accuracy = 0.896), fungal (accuracy = 0.915), and bacterial (accuracy = 0.907) infections. These findings highlight the potential of mNGS-based multimodal analysis as a cost-effective tool for early and accurate differential diagnosis.},
}
@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Human Gut Microbiome (Shotgun Metagenomics) and Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
support = {U01 AI169298/AI/NIAID NIH HHS/United States ; T32 AI005284/AI/NIAID NIH HHS/United States ; R01 GM126479/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; P01 AI179406/AI/NIAID NIH HHS/United States ; R01 HG011035/HG/NHGRI NIH HHS/United States ; },
abstract = {UNLABELLED: Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual omics models. We evaluate performance across 588 binary and 735 continuous models using human gut microbiome-derived metabolomics and taxonomic data derived from metagenomics shotgun sequencing data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.<br><br>KEY POINTS: A total of 1,323 models were developed to comprehensively evaluate prediction performance and the robustness of feature selection for human gut microbiome (metabolomics and taxonomy from metagenomics shotgun sequencing) datasets. These models included three widely used machine learning algorithms - Elastic Net, Random Forest and XGBoost - applied across five integration strategies and single-omics approaches on datasets with binary and continuous outcomes.For continuous outcomes, Random Forest combined with NNLS integration achieved the highest performance and maintained strong predictive performance across full-dimensional and feature-reduced datasets.For binary outcomes, Random Forest consistently performed well regardless of the integration strategy. Notably, single-omics models, especially those using metabolomics data, outperformed integrative approaches.Tree-based models demonstrated greater consistency in feature selection across different dimensionalities and integration strategies.},
}
@article {pmid39764050,
year = {2025},
author = {Nasr, E and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, K and Ferrari, E and Griffin, TJ and Gruening, B and Hiltemann, S and Hyde, CJ and Jagtap, P and Mehta, S and Métris, KL and Momin, S and Nelson, TM and Oba, A and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, A and Van Heusden, P and Vohra, M and , and Zierep, P and Batut, B},
title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.23.629682},
pmid = {39764050},
issn = {2692-8205},
support = {U24 AI183870/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).},
}
@article {pmid41059288,
year = {2023},
author = {Cameron, ES and Blaxter, ML and Finn, RD},
title = {plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets.},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {475},
pmid = {41059288},
issn = {2398-502X},
abstract = {The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.},
}
@article {pmid41056780,
year = {2025},
author = {Chang, X and Ma, Y and Zhang, J and Wang, T and Li, H and Wang, L},
title = {Size-specific effects of polyethylene microplastics (100-10,000 nm) on the soil resistome and pathogens revealed via metagenomics and machine learning.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127517},
doi = {10.1016/j.jenvman.2025.127517},
pmid = {41056780},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are widespread, persistent environmental contaminants. However, the influence of MP particle size on ARGs dissemination and soil ecosystem health remains unclear. Herein, polyethylene MPs of three sizes (100, 1,000, and 10,000 nm) were incubated in ARG-contaminated soils for 45 days to evaluate their effects on soil physicochemical properties, microbial communities, ARGs, mobile genetic elements (MGEs), and pathogen abundance. MP exposure significantly increased soil water (up to 4.07-fold), total nitrogen (up to 50.34 %), and ammonium nitrogen (up to 38.54 %) contents. Conversely, soil organic carbon content decreased with increasing MP size. MPs markedly reduced the activities of key enzymes, including alkaline phosphatase (by 87.65 %), sucrase (by 10.96 %), and urease (by 54.17 %). Microbial α-diversity increased; however, the abundance of potentially pathogenic Pseudomonadota increased by up to 41.88 %, whereas that of beneficial Actinobacteria and Chloroflexi declined. MPs promoted the expression of 44 ARGs and 15 MGEs, with smaller MPs exhibiting stronger enrichment. They also increased the expression of virulence factors and the abundance of human- and plant-associated pathogens. Random forest modeling revealed that smaller MPs primarily drove these changes by altering soil physicochemical properties and microbial dynamics. Collectively, these findings demonstrate that MPs, especially smaller particles, simultaneously alter soil chemistry, suppress enzyme activities, reshape microbial communities, and enhance ARGs expression and pathogen proliferation, underscoring their significant ecological and human health risks in agricultural soils.},
}
@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}
@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).<br><br>METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.<br><br>RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p&#x2009;=&#x2009;0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p&#x2009;=&#x2009;0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p&#x2009;=&#x2009;0.056 and 1.11 [0.58, 1.64] unadjusted p=&#x2009;<&#x2009;.001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p&#x2009;=&#x2009;0.001 for each 10% increase in virome score).<br><br>CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}
@article {pmid41055380,
year = {2025},
author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W},
title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.},
journal = {mBio},
volume = {},
number = {},
pages = {e0244725},
doi = {10.1128/mbio.02447-25},
pmid = {41055380},
issn = {2150-7511},
abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.},
}
@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164224},
doi = {10.1128/msystems.01642-24},
pmid = {41055333},
issn = {2379-5077},
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}
@article {pmid41054501,
year = {2025},
author = {Wang, W and Mo, Q and Ding, X and Pan, J},
title = {Metagenomic Next-Generation Sequencing Reveals Tannerella forsythia in Lung Abscesses: A Retrospective Case Series Linking Smoking, Oral Health, and Diagnostic Challenges.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5193-5205},
pmid = {41054501},
issn = {1178-6973},
abstract = {PURPOSE: Tannerella forsythia (T. forsythia) is a Gram-negative anaerobic bacterium commonly found in the oral cavity of patients with periodontitis, but lung abscesses caused by this pathogen are extremely rare in the literature. This study aimed to characterize the clinical features, diagnostic challenges, and treatment outcomes of T. forsythia-associated lung abscesses through four case analyses.<br><br>PATIENTS AND METHODS: We retrospectively reviewed four patients treated between April 2023 and May 2024 with lung abscesses confirmed by chest computed tomography (CT) and T. forsythia detection via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Conventional cultures were performed but yielded negative results. Clinical data, including demographics, symptoms, imaging findings, and treatment regimens, were analyzed.<br><br>RESULTS: All patients had oral diseases, and 75% were long-term smokers. The primary clinical manifestations were nonspecific respiratory symptoms, including cough, fever, chest pain, and hemoptysis. Chest CT revealed consolidation and cavitation in the upper lobes of the lungs. T. forsythia was successfully detected by mNGS of BALF, while conventional cultures failed to identify pathogens in all cases. All patients received combination antibiotic therapy based on metronidazole and piperacillin-tazobactam, with some cases requiring additional antibiotics. Following treatment, significant clinical improvement was observed, and follow-up imaging demonstrated gradual resolution of the lesions.<br><br>CONCLUSION: This study is limited by its small sample size and the lack of confirmatory tests, which warrant validation in larger prospective cohorts. Our findings highlight the advantages of mNGS in detecting fastidious pathogens (such as the anaerobic bacterium T. forsythia), providing new insights for the diagnosis of similar infections in the future. Additionally, the results identify smoking and poor oral health as common features that may be associated with the development of T. forsythia-associated lung abscesses.},
}
@article {pmid41053880,
year = {2025},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {126},
pmid = {41053880},
issn = {2524-6372},
support = {CRP/ZAF22-03)//ICGEB, Italy/ ; NRF//South African National Research Foundation/ ; },
abstract = {BACKGROUND: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.<br><br>METHOD: The entire DNA sample&#xa0;was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.<br><br>RESULTS: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.<br><br>CONCLUSION: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.},
}
@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}
@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}
@article {pmid41052966,
year = {2025},
author = {Tang, W and Hexter, C and Dai, R and Fortin, SG and Tracey, JC and Intrator, N and Kunes, MA and Wan, XS and Jayakumar, A and Shi, D and Ward, BB},
title = {Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70187},
doi = {10.1111/1462-2920.70187},
pmid = {41052966},
issn = {1462-2920},
support = {OCE-1946516//National Science Foundation/ ; 675459//Simons Foundation/ ; //University of South Florida/ ; },
mesh = {*Nitrification ; *Nitrous Oxide/metabolism ; *Urea/metabolism ; *Archaea/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ammonia/metabolism ; Nitrites/metabolism ; },
abstract = {Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N2O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia-oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rates, and the relative rates of N2O production from the two substrates, is correlated with the ratio of the substrate concentrations. By examining all reported measurements of urea and ammonium concentrations and the paired urea and ammonia oxidation rates, we show that this relationship likely holds across the global ocean. Examination of newly acquired and previously published metagenomic data shows that the fraction of AOA with the genetic capability for urea oxidation increases with the urea:ammonium ratio, rather than depending on the urea or ammonium concentration alone. These results corroborate the correlation between substrate ratios and oxidation rate ratios, and extend it to N2O production. This may help explain the distribution of nitrification rates and N2O production in the ocean.},
}
@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}
@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}
@article {pmid41052251,
year = {2025},
author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y},
title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000548822},
pmid = {41052251},
issn = {1421-976X},
abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.<br><br>METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide (EPS) production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy (CLSM) and scanning electron microscopy (SEM). Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.<br><br>RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.<br><br>CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anti-caries therapies.},
}
@article {pmid41051042,
year = {2025},
author = {Nancy, and Lakhawat, SS and Kumar, R and Sharma, PK},
title = {Cloning, Expression, Purification, and Characterization of Superoxide Dismutase from the Soil Metagenome.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665415743250926072254},
pmid = {41051042},
issn = {1875-5305},
abstract = {INTRODUCTION: Superoxide Dismutases (SODs) are enzymes that catalyze the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.<br><br>MATERIALS AND METHODS: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector and subcloned into an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.<br><br>RESULTS: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40&#xb0;C and pH 8, respectively. The enzyme remains completely stable at 40&#xb0;C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50&#xb0;C and 60&#xb0;C for 3 h. The biophysical investigation revealed stable confirmation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.<br><br>DISCUSSION: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn2+ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.<br><br>CONCLUSION: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, which include its therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.},
}
@article {pmid41050906,
year = {2025},
author = {Wiese, M and Klaassens, ES and Hatt, V and Kreikamp, A and Baak, ML and Heerikhuisen, M and Van Der Vossen, JMBM},
title = {Demonstration of phage inhibitory action against Clostridium perfringens LMG 11264 within a complex chicken cecal microbiota in vitro.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1599939},
pmid = {41050906},
issn = {2813-2467},
abstract = {INTRODUCTION: Clostridium perfringens strains may cause foodborne illness, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection may cause necrotic enteritis, and infections are associated with high mortality rates partially due to antibiotic resistance, which hampers efficient treatment. In-vitro screening approaches of alternative treatment options, for instance, specific phages, represent a promising strategy for the selection of novel interventions to combat infections.<br><br>MATERIAL AND METHODS: In this study, we explored the application of a C. perfringens strain LMG 11264-specific phage #7 introduced at 10[4] pfu/mL to inhibit the growth of C. perfringens at 10[6] cfu/mL compared to two antibiotics (amoxicillin at 10 &#xb5;g/mL and clindamycin at 10 &#xb5;g/mL) within complex chicken cecal microbiota in vitro. Samples for gDNA isolation, qPCR, and metagenome sequencing were taken at the beginning and after 24 and 48 h of incubation.<br><br>RESULTS: The C. perfringens strain LMG 11264 proliferated within the untreated complex microbiota and reached levels of approximately 10[8] and 10[9] genome equivalents per mL after 24 and 48 h of incubation, respectively. The phage intervention with phage #7 inhibited the growth of C. perfringens LMG 11264 significantly; the inhibitory effects were similar to those exerted by the antibiotic intervention with amoxicillin and stronger than the inhibitory effects with clindamycin. In the absence of the C. perfringens challenge, we found a significant effect of amoxicillin (p = 0.040) or clindamycin (p = 0.000017) compared to the untreated control after 24 h of incubation, and the phage addition did not affect the alpha diversity expressed as Chao index significantly (p = 1). In addition, the endogenous C. perfringens in the chicken microbiota appeared insensitive to phage #7. The phage titer of phage #7 only increased in the presence of the inoculated C. perfringens strain LMG 11264. In conclusion, the i-screen model can be implemented to test the efficacy and specificity of phage therapy in vitro.},
}
@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.<br><br>METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6&#xa0;L. crispatus strains (LC106) or 15&#xa0;L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of &#x2265; Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance &#x2265;5&#xa0;% of any LBP strain or &#x2265;10&#xa0;% of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.<br><br>CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.<br><br>TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).<br><br>PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}
@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation &amp; purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}
@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}
@article {pmid41050203,
year = {2026},
author = {Wang, Q and Shan, S and Sun, Q and Zhao, X and Yuan, C and Mou, Y and Wang, J and Yan, C and Wang, Q and Rui, Q and Li, C},
title = {The coupling effect of Penicillium baileys W2 in the Aspergillus flavus inhibition and peanut growth promotion.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {127-140},
pmid = {41050203},
issn = {2405-805X},
abstract = {Aspergillus flavus is a significant plant pathogen, and peanut crops are particularly vulnerable to aflatoxin contamination. This vulnerability underscores the need for more effective control methods. In this study, the strain Penicillium baileys W2 was isolated from the rhizosphere soils of healthy peanut seedlings. The fermentation extract exhibited concentration-dependent inhibition of pathogenic A. flavus growth, with a minimum inhibitory concentration (MIC) of 55 % and a minimum fungicidal concentration (MFC) of 60 %. Physiological data and transcriptome analysis demonstrated that the W2 fermentation supernatant inhibited A. flavus growth by disrupting membrane permeability. Metabolomics analysis identified active compounds, including propylparaben, taxifolin, and phloretin, which exhibited significant antagonistic effects against A. flavus. Additionally, we evaluated the impact of the W2 fermentation broth on peanut growth promotion and on rhizosphere microbial community structure using metagenomic sequencing. The reduction of harmful soil microorganisms contributed to the maintenance of soil health, whereas the increased abundance of beneficial microorganisms enhanced peanut seedling growth by facilitating soil nutrient cycling. These findings indicate that the development and application of P. baileys strain W2 or its fermentation extract aligns with sustainable agricultural principles and offers a promising biological control approach.},
}
@article {pmid41049781,
year = {2025},
author = {Wang, B and He, T and Cheng, Y and Chen, H and Hu, Y and Liu, Y and Wang, F and Chen, L},
title = {Targeted enhancement strategies for Sojae Semen Praeparatum: Impact of Aspergillus oryzae and Bacillus subtilis on microbial communities, flavor substances, and functional components.},
journal = {Food chemistry: X},
volume = {30},
number = {},
pages = {102931},
pmid = {41049781},
issn = {2590-1575},
abstract = {Sojae Semen Praeparatum (SSP), a traditional Chinese fermented soybean product, was optimized through novel single/double enhancement fermentation using Aspergillus oryzae and Bacillus subtilis. Enhanced fermentation significantly increases the production of flavor amino acids. Using headspace solid-phase extraction microextraction gas chromatography-mass spectrometry (HS-SPEM-GC-MS) technology, 51 critical flavor substances were identified, confirming that enhanced fermentation improves the flavor profile of SSP. Isoflavone quantification revealed that enhancement strategies promoted isoflavone conversion. Enzyme inhibition and antioxidant activities were superior in the double enhancement fermentation group. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated a significant increase in SSP's enrichment in the flavone and flavonol biosynthesis pathway. Screening identified 19 key flavonoid components strongly correlated with bioactivity, and enhancement fermentation notably enhancing their accumulation. Metagenomic sequencing revealed 14 key differential microorganisms, essential to flavor development and activity enhancement in SSP. This study offers valuable insights for optimizing fermentation processes to enhance product quality.},
}
@article {pmid41049190,
year = {2025},
author = {Liu, C and Li, B and Wu, Q and Chen, D and Zhou, W and Ao, J},
title = {The effects and mechanism of urease inhibitor and its combination with nitrification inhibitor on nitrous oxide emission across four soil types.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1663261},
pmid = {41049190},
issn = {1664-462X},
abstract = {Nitrogen (N) fertilization is essential for ensuring crop productivity, while excessive N application significantly increases greenhouse gases (GHGs) emissions, particularly nitrous oxide (N2O). Urease inhibitors (UI) and combined urease and nitrification inhibitors (UN) have demonstrated potential in mitigating GHGs emission, though their efficiency with great variation across different soils types. In this study, controlled incubation experiments were conducted using four types of agricultural soils to evaluate the mitigation potential of UI and UN application and to investigate their underlying mechanisms. N fertilization significantly increased N2O emissions by 5.1~99.9-fold and elevated CO2 emissions by 13.6~65.4% across all soil types. The UI treatment decreased the peak of NO2 [-] concentrations in two alkaline soils, while the UN treatment decreased both NO2 [-] and NO3 [-] concentrations in all four soils. In terms of GHG mitigation, UI treatment reduced N2O emissions by 16.5~57.4% in alkaline soils and reduced CO2 emissions by 6.5~49.3% across four soil types. The UN treatment demonstrated superior efficacy, reducing N2O emissions by 52.5~92.4% and CO2 emissions by 4.2~87.2% across all soils. Metagenomic sequencing revealed that both UI and UN significantly inhibited the relative abundances of key functional genes associated with nitrification (hao and nxrAB), dissimilatory nitrate reduction (narGHI/napAB), nitrite reduction (nirS/nirK), and nitric oxide reduction (norBC). Random forest identified key factors influencing the N2O mitigation efficiency of UI and UN. These included soil properties such as soil pH, total nitrogen, organic matter, available potassium, water-filled pore space, texture. Additionally, partial functional genes related to nitrification, denitrification, carbon and methane metabolism, sulfur and phosphorus cycling were also identified as key contributors. Overall, these findings provide valuable insights for the region-specific application of UI and UN to effectively mitigate GHGs emissions. The identification of key soil abiotic and biotic factors offers a theoretical foundation for optimizing inhibitors application and enhancing their mitigation efficiency.},
}
@article {pmid41049022,
year = {2025},
author = {Cohodes, M and Fernandez, A and Ashkin, D and Reed, C and Park, S and Banaei, N and Fung, M and Jacobson, K and Goswami, ND},
title = {Curated cases from the TB expert network: Unplugged! Series: Use of plasma microbial cell-free DNA metagenomic sequencing to diagnose Mycobacterium tuberculosis.},
journal = {Journal of clinical tuberculosis and other mycobacterial diseases},
volume = {41},
number = {},
pages = {100563},
pmid = {41049022},
issn = {2405-5794},
abstract = {A 52-year-old U.S.-born man with diabetes and a kidney transplant 3 months prior presented with fever of unknown origin and left-sided weakness. On admission, he was found to have right internal carotid artery thrombus and cerebral infarct. He developed respiratory failure and underwent treatment for Pseudomonas bacteremia. Fevers continued through hospital day 30 and computed tomography (CT) scans demonstrated an esophageal mass, hepatic lesions, and pulmonary nodules, which were new compared to pre-transplant imaging 2 years prior. While awaiting results from acid-fast bacilli (AFB) cultures from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). Based on the results of mcfDNA sequencing, clinical presentation, and radiographic findings, a diagnosis of tuberculosis disease was made, and anti-tuberculosis treatment was initiated. While awaiting results from acid-fast bacilli (AFB) cultures and molecular studies from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). The patient was discharged on hospital day 60; 27 days after discharge, 58 days after the Mtb PCR resulted positive from tissue biopsy, and 60 days after the positive mcfDNA, sputum cultures returned positive for Mycobacterium tuberculosis.},
}
@article {pmid41048510,
year = {2025},
author = {Mieremet, A and van der Wurff, M and Pagan, L and Ferrer-González, E and Seo, J and Schuren, FHJ},
title = {Taxonomic and functional profiling of the vulvar microbiome indicates variations related to ecological signatures, aging, and health status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633147},
pmid = {41048510},
issn = {1664-302X},
abstract = {INTRODUCTION: The vulvar microbiome is adjacent to that of the skin and the vagina and connects microbiomes present on a stratified epithelial barrier to that of a mucosal barrier. Yet, the characterization of the microbiome in the vulvar region of the body is understudied, although dysbiosis in the microbiome of the skin or vagina have been linked to impairments in women's health.<br><br>METHODS: To better understand the role of the vulvar microbiome during healthy aging or during presentation of vulvar diseases, we analyzed the vulvar microbiome by shotgun metagenomic sequencing on composition at species level and for functional capacity. This was performed in a large population enrolled in the Vulvar Microbiome Leiden Cohort (VMLC), including a total of 58 healthy women in a broad age range (22-82 years). Moreover, we analyzed vulvar microbiome derived from 9 participants presenting a vulvar disease, including vulvar lichen sclerosus (LS; N = 6), or high-grade squamous intraepithelial lesion (HSIL; N = 3).<br><br>RESULTS: Compositional analyses showed a skin-, vagina-, or multispecies mixture- dominant bacterial signature, which revealed differences in the alpha diversity and functional capacity of the microbiome. Upon aging the presence of Lactobacillus iners, L. crispatus, and L. gasseri in the vulvar microbiome shifted toward reduction. In the microbiome of individuals with a vulvar disease, higher abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium amycolatum, and Corynebacterium simulans was detected, and an altered functional capacity for the L-histidine pathway.<br><br>DISCUSSION: In conclusion, we identified variations in microbial taxa and functional capacities in the vulvar microbiome that are associated with age and disease (LS and HSIL), which can be targeted to develop microbiome-based vulvar therapies promoting women's health.},
}
@article {pmid41048504,
year = {2025},
author = {Ai, X and Huang, C and Liu, Q and Duan, R and Ma, X and Li, L and Shu, Z and Miao, Y and Shen, H and Lv, Y and Jiang, Z and Luo, H and Long, Z},
title = {Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629811},
pmid = {41048504},
issn = {1664-302X},
abstract = {INTRODUCTION: Population aging represents a significant challenge in contemporary society. The gut microbiome plays a critical role in maintaining host health and physiological functions, and its alterations with advancing age are closely associated with the process of healthy aging.<br><br>METHODS: This study conducted a comprehensive analysis of the gut microbiome in hundred healthy elderly individuals (aged &#x2265;60) residing in Changshou Town, Zhongxiang City, Hubei Province, utilizing metagenomic sequencing technology. The primary objective was to investigate the changes in the gut microbiome and its potential functions during the latter stages of life. Participants were categorized into three distinct age groups: the Young-Old group (YO, ages 60-74), the Middle-Old group (MO, ages 75-89), and the Long-Lived Old group (LO, ages 90-99).<br><br>RESULTS: The findings indicate that the diversity of the gut microbiome tends to diminish with age. However, a significant reversal was observed among healthy longevity elderly individuals. Our analysis specifically focused on the trends in the alterations of gut microbiome species and their potential functions as age increases, revealing that the changes in major differential functions closely align with the trends in major differential species, demonstrating a strong positive correlation. The YO group exhibited a more diverse array of differential microbial characteristics and functional traits. Notably, there was a significant enrichment of Bacteroides stercoris in the YO group, which displayed a continuous decline with age, alongside a marked enrichment of pathways associated with xenobiotic biodegradation and metabolism. Furthermore, species significantly linked to aging-related pathways, such as oxidative phosphorylation, were identified through species functional correlation analysis. Specifically, Collinsella bouchesdurhonensis and Prevotella stercorea were enriched in the LO and YO groups, respectively. In total, we successfully obtained two hundred and thirty eight high-quality bins through metagenomic assembly, which included the identification of four species with 100% completeness, as well as the genomic information of the Methanobrevibacter smithii A across all groups.<br><br>DISCUSSION: This study characterizes the age-associated trends in gut microbiome composition and function during later-life healthy aging, providing exploratory insights that may inform future microecological intervention strategies, pending validation in longitudinal studies.},
}
@article {pmid41048502,
year = {2025},
author = {Peng, X and Wei, Y and Zhou, X},
title = {Enhancing pathogen identification through AI-assisted metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634194},
pmid = {41048502},
issn = {1664-302X},
abstract = {INTRODUCTION: To address the limitations of current metagenomic identification approaches, we proposed a principled AI-assisted architecture that enhances accuracy, scalability, and biological interpretability through three core innovations.<br><br>METHODS: Firstly, we developed a structured probabilistic model that formulates pathogen detection as a hierarchical and compositional inference task under taxonomic and ecological constraints. This framework enables the integration of phylogenetic priors and sparsity-aware mechanisms, reducing noise and ambiguity. By modeling taxonomic structure and ecological dependencies, the approach ensures more accurate identification, especially in complex or low-abundance microbial communities. Secondly, we introduced the Taxon-aware Compositional Inference Network (TCINet), a deep learning model that processes sequencing reads to produce taxonomic embeddings. TCINet estimates abundance distributions via masked neural activations that enforce sparsity and interpretability, while also propagating uncertainty through log-normal variance modeling. Designed to respect microbial phylogeny and co-occurrence patterns, TCINet enables scalable, biologically plausible inference across diverse clinical and environmental datasets. Thirdly, we presented the Hierarchical Taxonomic Reasoning Strategy (HTRS), a post-inference module that refines predictions by enforcing compositional constraints, propagating evidence across taxonomic hierarchies, and calibrating confidence using entropy and variance-based metrics. HTRS includes context-aware thresholding and co-occurrence priors to adaptively optimize performance based on dataset characteristics.<br><br>RESULTS: Together, these innovations create a unified framework for metagenomic identification that combines probabilistic modeling, deep learning, and structured reasoning.<br><br>DISCUSSION: The architecture delivers robust and interpretable results, making it suitable for applications in clinical diagnostics, environmental monitoring, and ecological research.},
}
@article {pmid41048492,
year = {2025},
author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J},
title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633379},
pmid = {41048492},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.<br><br>METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.<br><br>RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.<br><br>DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.},
}
@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}
@article {pmid41048206,
year = {2025},
author = {Tao, H and Zheng, W},
title = {Non-Tuberculous Mycobacterial Infections of the Skin and Soft Tissue in a Chinese Population: A Retrospective Analysis of 15 Cases.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5139-5147},
pmid = {41048206},
issn = {1178-6973},
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) skin and soft tissue infections (SSTIs) are increasingly recognized but underdiagnosed in China.<br><br>METHODS: This retrospective study analyzed 15 confirmed cases of NTM SSTIs treated at a southern Chinese hospital from 2012 to 2022. Clinical data, including demographics, clinical presentations, comorbidities, diagnostic methods, treatment regimens, and outcomes, were collected and analyzed. Diagnostic efficacy of conventional culture and metagenomic next-generation sequencing (mNGS) was compared.<br><br>RESULTS: The median age of patients was 57 years, and 66.7% were farmers. Pathogens identified included Mycobacterium abscessus (20.0%), M. marinum (13.3%), and rapidly growing mycobacteria (13.3%). Immunocompromised states, such as anti-interferon-gamma autoantibody positivity, were present in 40.0%. mNGS demonstrated superior diagnostic performance, achieving a detection rate of 86.7% (13/15 cases), compared to 26.7% for culture. Treatment regimens, including clarithromycin, rifampin, ethambutol, and moxifloxacin, lasted 1-24 months. Outcomes showed cure in 8 patients (53.3%), improvement in 6 (40.0%), and 1 lost to follow-up.<br><br>CONCLUSION: NTM SSTIs present significant diagnostic and therapeutic challenges, with clinical variability and frequent association with immunocompromised states. M. abscessus, M. marinum, and M. avium were the predominant pathogens. mNGS improves detection but still should complement culture. Precise pathogen identification and tailored therapy are essential for achieving optimal outcomes, and further studies are needed to refine diagnostics and treatment strategies.},
}
@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}
@article {pmid41046791,
year = {2025},
author = {Wang, H and Chen, H and Ruan, C and Liao, J and Schwarz, C and Shi, B and Alvarez, PJJ and Yu, P},
title = {Nanoplastics induce prophage activation and quorum sensing to enhance biofilm mechanical and chemical resilience.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124712},
doi = {10.1016/j.watres.2025.124712},
pmid = {41046791},
issn = {1879-2448},
abstract = {Despite the prevalence of nanoplastics (NPs) in natural and engineered water systems and their association with microbial risks, bacterium-phage interactions have been largely overlooked in the context of biofilm formation. Here, we investigated the effects of positively (PS-NH2) and negatively (PS-COOH) charged polystyrene nanoplastics (PS-NPs) on dual-species biofilms composed of Escherichia coli (λ+) and Pseudomonas aeruginosa. PS-NPs promoted biofilm formation and stability at environmentally relevant concentrations (e.g., 100-1000 ng/L), with PS-NH2 exhibiting higher influence. The cellular internalization of PS-NPs increased the reactive oxygen species (ROS) levels by 2.18-2.25 folds, triggered prophage λ activation followed by lysis of E. coli (λ+) after exposure to PS-NPs. Transcriptomic analyses revealed that PS-NPs, especially PS-NH2, activated the SOS response (2.35-2.63-fold), λ phage replication (2.68-3.97-fold), and interspecies quorum sensing (2.24-5.13-fold), which was verified by the proteomic analyses. Therefore, PS-NPs stimulated protective extracellular polymeric substances (EPS) secretion with eDNA content increased to 325.8-433.8 μg/cm[2]. Enhanced EPS production contributed to improved biofilm mechanical properties (1.46-1.57-fold as measured by atomic force microscopy) and increased resistance to chlorine disinfection. Metagenomic analysis of pipeline biofilm demonstrated that PS-NPs promoted bacterium-phage interactions and enhanced bacterial antiviral defense systems, which stimulated multi-species biofilm formation and enhanced environmental resilience. Overall, our findings provide novel insights into the interplay between nanoplastics and bacterium-phage dynamics, highlighting increased microbial risks associated with waterborne nanoplastics.},
}
@article {pmid41046720,
year = {2025},
author = {Yang, J and Wang, S and Heal, KV and Chen, L and Zhou, C},
title = {Microbial functional groups activate insoluble rhizosphere phosphorus to mitigate P limitation of Chinese fir plantations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127503},
doi = {10.1016/j.jenvman.2025.127503},
pmid = {41046720},
issn = {1095-8630},
abstract = {The decline in soil phosphorus (P) reserves and its low solubility pose significant challenges in long-term plantation cultivation. In P-limited subtropical environments, the rhizosphere microbial community and associated genes play a crucial role in driving P cycling and availability during the long-term development of forest plantations. Using the space-for-time substitution method, we investigated rhizosphere P cycling in Chinese fir (Cunninghamia lanceolata) plantations at different growth stages in Fujian Province, southern China. We utilized the modified Hedley fractionation method and metagenomic sequencing for rhizosphere soil samples from stand ages of 6, 26, 45, and 102 years. The results revealed that, with stand development, rhizospheric concentrations of total, stable and moderately labile P decreased significantly, whereas labile P became progressively enriched (P < 0.05). Genes involved in organic P mineralization and P transport were positively correlated with labile P concentrations in the rhizosphere (P < 0.05), whereas P metabolism regulatory genes were negatively correlated with moderately labile P (P < 0.05). Additionally, the dominant P-solubilizing bacteria-Bacteroidetes and Rudaea-exerted significant positive effects on labile P and negative effects on stable P, respectively (P < 0.05). Overall, rhizospheric P reserves were significantly depleted in the Chinese fir plantations during their developmental progression. However, this unsustainable trend in P reserves was mitigated through synergistic interactions between P-solubilizing bacteria and P metabolism genes, which catalyzed the conversion of insoluble P into labile P, while enhancing plant P uptake efficiency. Consequently, we propose science-informed management practices-such as optimizing P fertilization management, inoculating P-solubilizing microbial agents, utilizing organic fertilizers, and introducing native broadleaf species-to sustain functional stability and long-term productivity of subtropical plantation ecosystems.},
}
@article {pmid41000811,
year = {2025},
author = {Konnaris, MA and Saxena, M and Lazar, N and Silverman, JD},
title = {Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000811},
issn = {2692-8205},
abstract = {Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.},
}
@article {pmid41046693,
year = {2025},
author = {Theysgeur, S and Dugardin, C and Louvel, B and Lemière, S and Muchembled, J and Taminiau, B and Daube, G and Siah, A and Ravallec, R and Hilbert, JL and Lucau-Danila, A},
title = {Assessment of health effects of potato crop phytopharmaceuticals and storage products in a murine model.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180630},
doi = {10.1016/j.scitotenv.2025.180630},
pmid = {41046693},
issn = {1879-1026},
abstract = {Potatoes are among the most widely consumed staple foods worldwide, but their cultivation and storage frequently involve multiple phytopharmaceutical products (PPPs), raising concerns about the health risks of dietary pesticide residues. The health effects of multi-residue PPPs used in potato cultivation were assessed in an in vivo murine model, involving 36 mice, and evaluated through omics analyses. Two field cultivation methods (conventional and organic) and two post-harvest storage conditions (using 1,4-dimethylnaphthalene and mint essential oil as sprout inhibitor treatments) were considered. Potato tubers were processed into flour and administered to the animals at a moderate daily dose for 20 consecutive days. Nutrigenomic analyses revealed significant gene deregulations, with 70 genes affected in the liver, 56 in the jejunum, and 52 in the brain, suggesting disturbances in cellular proliferation, nervous system functions, lipid and carbohydrate metabolism, reproductive health, and immune responses. Metagenomic analyses indicated microbiota imbalances, including a shift in the Firmicutes/Bacteroidota ratio and changes in 2 bacterial genera with potentially adverse effects. The main residues suspected of producing these effects include propamocarb, carfentrazone, 1,4-dimethylnaphthalene, copper derivatives, and peppermint essential oil. These findings highlight the importance of large-scale omics approaches in uncovering potential biological disruptions, underscore the health risks associated with chronic dietary exposure to pesticide residues, particularly in mixtures, and emphasize the need to reassess regulatory standards to promote agricultural practices that minimize pesticide residues to better protect the environment and human health.},
}
@article {pmid41046691,
year = {2025},
author = {Zhang, N and Li, W and Wang, H and Lv, G},
title = {Metabolomic insights into rhizosphere microbial dynamics in desert plants under drought stress.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180653},
doi = {10.1016/j.scitotenv.2025.180653},
pmid = {41046691},
issn = {1879-1026},
abstract = {Drought hinders plant growth and development. However, studies on rhizospheric metabolism and microbial composition of desert plants under drought stress are limited. This study used untargeted metabolomics to detect that the differential metabolites included mainly alkaloids and their derivatives, benzenoids, lipids, and lipid molecules under drought stress. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the differences between drought stress in the rhizosphere environment were usually reflected in microbial metabolism, plant hormone biosynthesis, and secondary metabolite biosynthesis in different environments. Metagenomic analysis showed that the relative abundances of Chloroflexi, Firmicutes, and Gemmatimonadetes in the mild drought rhizosphere group (MiR) were significantly higher than those in the severe drought rhizospheric soil group (SR) in the phylum of the microorganisms; the relative abundance of Proteobacteria in the SR group was also significantly higher. Through the analysis of the correlation network, it is found that there is a significant correlation between microorganisms and differential metabolites. During drought stress, plants can indirectly influence the support of soil microbes by modifying the structure and concentration of metabolites, which helps to enhance drought tolerance. This study provides a theoretical basis for exploring new stress adaptation strategies and protecting soil microecology.},
}
@article {pmid41046678,
year = {2025},
author = {Alhaboub, A and Deschenes, NM and Li, XX and Williams, VR and Katz, KC and Park, SY and Aftanas, P and Wong, H and Sjaarda, C and Tozer, K and Maguire, F and Leis, J and Sheth, P and Kozak, R},
title = {Some assembly required: Comparison of bioinformatic pipelines for analysis of viral metagenomic sequencing from nosocomial respiratory virus outbreaks.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {181},
number = {},
pages = {105877},
doi = {10.1016/j.jcv.2025.105877},
pmid = {41046678},
issn = {1873-5967},
abstract = {INTRODUCTION: Metagenomic sequencing (mGS) is a useful tool for identifying pathogens in patient samples. During nosocomial outbreaks of respiratory viruses, mGS allows for the identification of viral strains and provides insight into their genetic relatedness. Multiple bioinformatics analysis assembler are available for processing data, but a comprehensive comparison of their performance in for respiratory virus outbreaks has not been conducted.<br><br>METHODS: This study sequenced samples from five separate nosocomial outbreaks of RNA respiratory viruses. RNA was extracted from the samples, and cDNA was synthesized using random hexamers, and then sequenced on an Illumina Miniseq following Nextera DNA Flex library preparation. The data from each outbreak were analyzed using four different assemblers: MEGAHIT, rnaSPAdes, rnaviralSPAdes, and coronaSPAdes, to evaluate their analytical performance.<br><br>RESULTS: The mGS confirmed the viral identification and provided accurate strain identification for both coronavirus and parainfluenza virus samples. However, differences were observed between the assemblers in terms of the largest contigs produced and the proportion of the viral genome aligned with reference genomes. Notably, coronaSpades outperformed the other pipelines for analyzing seasonal coronaviruses, generating more complete data and covering a higher percentage of the viral genome.<br><br>CONCLUSION: Achieving a higher percentage of the viral genome sequence is crucial for a more detailed characterization, which is especially valuable for outbreak analysis where viral strains may only differ by a few genetic changes. Comparison of assemblers will allow for clinical laboratories to determine the bioinformatic pipeline that is optimal for helping clinicians better manage outbreaks.},
}
@article {pmid41046586,
year = {2025},
author = {Kwiatkowska, AM and Guzmán, JA and Lafaurie, GI and Castillo, DM and Cardona, AF},
title = {Exploring the role of the oral microbiome in saliva, sputum, bronchoalveolar fluid, and lung cancer tumor tissue: A systematic review.},
journal = {Translational oncology},
volume = {62},
number = {},
pages = {102557},
doi = {10.1016/j.tranon.2025.102557},
pmid = {41046586},
issn = {1936-5233},
abstract = {OBJECTIVE: To explore the association between the oral microbiome and the presence or progression of lung cancer (LC) using metagenomic sequencing techniques.<br><br>METHODS: Databases, including PubMed and EMBASE, were reviewed. Eligible studies included the study of oral microorganisms via genomic sequencing and molecular mechanisms associated with LC in saliva, sputum, bronchoalveolar lavage fluid (BALF), or tumor tissue from LC patients. A quality analysis of the studies was carried out, and a qualitative synthesis was performed according to the localization and sample type. Meta-analysis was performed on alpha diversity indexes.<br><br>RESULTS: Of the 1880 scrutinized articles, 50 studies were selected, comprising 29 cross-sectional, 7 case-control, and 14 cohort studies. The quality analysis sheds light on potential biases. The findings revealed a conspicuous overgrowth of specific microbial taxa in LC patients' saliva BALF samples of Veillonella and Streptococcus. Conversely, the Bacteroides genus, related to periodontal disease, exhibited no significant correlation with LC. Microorganisms in tumoral tissue were associated with poor prognosis. Veillonella was associated with a better response to ICIs therapy. Oral microorganisms were related to metabolic reprogramming with xenobiotic biodegradation, amino acid, sugar, sucrose, and lipidic metabolism, immune modulation, and proinflammatory responses.<br><br>CONCLUSION: Overgrowth of specific oral microorganisms in the saliva and BALF is associated with diagnosis, poor prognosis, and low response to immunotherapy. Veillonella could be a marker for response to ICIs therapy. Further well-designed studies should evaluate the impact of the oral microbiome on the response to ICIs.},
}
@article {pmid41045990,
year = {2025},
author = {Liu, Y and Zheng, Y and Wang, L and Guo, Y and Huang, G and Yuan, Z and Wang, F and Gai, W and Xing, J},
title = {Bacteriophage combined with mNGS enhances the specificity of bacterial infection diagnosis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106618},
doi = {10.1016/j.jinf.2025.106618},
pmid = {41045990},
issn = {1532-2742},
abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is an important tool for enhancing pathogen detection in infected patients. However, distinguishing between specimens that are infected or colonized is still a major challenge.<br><br>OBJECTIVES: To explore the composition of bacteriophages in the blood and respiratory tract of the human body, the association between bacteriophage detection and bacterial infections, and whether bacteriophages can assist in differentiating infectious pathogens according to mNGS results.<br><br>METHODS: Clinical samples from hospitalized patients were collected between January 2023 and February 2024. DNA and cell-free DNA were extracted from BALF and plasma retrospectively to identify the pathogens present, and bacteriophage annotations were conducted.<br><br>RESULTS: A total of 299 samples, comprising 136 blood samples and 163 BALF samples, were obtained from 218 patients. Compared with the samples negative for bacteria, both blood and bronchoalveolar lavage fluid (BALF) samples infected with Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and S. aureus showed a corresponding increase in the proportions of phages related to these pathogens. In BALF samples with Acinetobacter baumannii infection, the proportions of Autographiviridae, Siphoviridae, and Myoviridae were significantly greater than those in the Acinetobacter baumannii colonization group. The sensitivity of Myoviridae for differentiating between infection and colonization was 86.36%, and the specificity was 52.94%.<br><br>CONCLUSION: In sepsis, compared with conventional mNGS methods alone, the use of bacteriophages combined with mNGS was more effective in identifying causative pathogens and had higher specificity. These findings may provide new ideas and tools for improving clinical infection diagnosis.},
}
@article {pmid41045972,
year = {2025},
author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X},
title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104408},
doi = {10.1016/j.ibmb.2025.104408},
pmid = {41045972},
issn = {1879-0240},
abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.},
}
@article {pmid41045941,
year = {2025},
author = {Alcolea-Medina, A and Snell, LB and Humayun, G and Al-Yaakoubi, N and Ward, D and Alder, C and Patel, V and Vivian, F and Meadows, CIS and Wyncoll, D and Paul, R and Barratt, N and Batra, R and Edgeworth, J and Nebbia, G and Whitehorn, J},
title = {Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101174},
doi = {10.1016/j.lanmic.2025.101174},
pmid = {41045941},
issn = {2666-5247},
abstract = {BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs).<br><br>METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation.<br><br>FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae.<br><br>INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies.<br><br>FUNDING: None.},
}
@article {pmid41045876,
year = {2025},
author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M},
title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180614},
doi = {10.1016/j.scitotenv.2025.180614},
pmid = {41045876},
issn = {1879-1026},
abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.},
}
@article {pmid41045656,
year = {2025},
author = {Tuffou, R and Windal, L and Delmotte, S and Skorski, G and Metton, I and Voisin, SN and Surribas, A and Beytur, S and Leborgne, M and Blanquart, H and Salducci, X and Feugier, A},
title = {Combining fermentation and vermicomposting for sustainable pet food waste management: Effects of waste profile and inoculum source.},
journal = {Waste management (New York, N.Y.)},
volume = {208},
number = {},
pages = {115176},
doi = {10.1016/j.wasman.2025.115176},
pmid = {41045656},
issn = {1879-2456},
abstract = {Ingredient production is the main driver of pet-food GHGs and land use. Indeed, the pet food industry uses nearly 495,000 km[2] of land annually. Yet, waste streams from production and declassified products remain underexplored as resources to produce high quality soil amendment. This study proposes an integrated approach to valorise such organic wastes through microbial fermentation prior to vermicomposting. Two experiments were conducted. (1) the effects of kibble incorporation ratio (15 % vs. 30 %), fibre source (spruce flakes, SF vs. beech sawdust, BS), and container size (50 L vs. 500 L) on fermentation dynamics, worm preference, and vermicompost properties were assessed. (2) the functional equivalence of commercial inoculum (EM®) and locally sourced indigenous microorganisms (IMO) was evaluated. Results showed that fibre type significantly influenced fermentation outcomes at low kibble incorporation, with BS lowering pH (from 9 in SF30% to 5.2 in BS15%, P < 0.001) and increasing redox potential (+213 %, P < 0.001). Electroconductivity was strongly affected by both kibble ratio (+110 %, P < 0.001) and fibre source (+130 %, P < 0.001). Worms displayed strong preference for BS-based substrates (+493 % density in 7 days, P < 0.001). Vermicompost derived from SF exhibited slower nitrogen and carbon mineralisation than BS. Container size had no effect on fermentation. EM® and IMO performed equivalently in fermentation efficiency, worm attraction, and functional microbial activity (metagenomic/metaproteomic analyses). This work demonstrates that combining microbial pre-digestion with vermicomposting can upcycle pet food waste into valuable soil amendments, while supporting local circular bioeconomy and sustainable waste management.},
}
@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//K&#xe4;ppalaf&#xf6;rbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}
@article {pmid41044758,
year = {2025},
author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H},
title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {105},
pmid = {41044758},
issn = {2524-4671},
support = {PRE2020-093762//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; },
abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.<br><br>RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.<br><br>CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.},
}
@article {pmid41044750,
year = {2025},
author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M},
title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {104},
pmid = {41044750},
issn = {2524-4671},
support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.<br><br>RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.<br><br>CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.},
}
@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; },
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}
@article {pmid41044010,
year = {2025},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}
@article {pmid41043962,
year = {2025},
author = {Sessions, AL and Magnabosco, C and Barton, HA and Burkhardt, C and Dworkin, JP and Freissinet, C and French, KL and Glavin, DP and Leys, N and Maixner, F and Olsson-Francis, K and Probst, AJ and Quitté, G and Rampe, E and Steele, A and Carrier, BL and Hays, LE and Thiessen, F and Paardekooper, D and Hutzler, A and Harrington, AD and Teece, BL},
title = {Planning Considerations Related to Contamination Control for the Return and Analysis of Martian Samples.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15311074251382157},
pmid = {41043962},
issn = {1557-8070},
abstract = {The joint National Aeronautics and Space Administration and European Space Agency Mars Sample Return (MSR) Campaign is a proposed multi-mission effort to bring selected geological samples from Mars to Earth for the purpose of scientific investigation. Significant parts of these investigations could be affected by Earth-sourced contamination that is either misinterpreted as having a martian origin or that masks a martian signal. The Mars 2020 Perseverance rover implemented strict contamination control requirements to limit contamination of the samples during sample collection. Contamination control and contamination knowledge requirements have not yet been established for the samples after they arrive on Earth. The MSR Sample Receiving Facility (SRF) Contamination Panel (SCP) was tasked with defining the terrestrial biological, organic, and inorganic contamination limits for martian samples during their residence inside the SRF. To reach our recommendations, the SCP studied (i) the previously proposed limits and rationale of the Organic Contamination Panel, (ii) cleanliness levels achieved for sampling hardware by the M2020 mission, (iii) recent improvements in analytical technology and detection limits, (iv) updated information regarding the organic content of martian samples (e.g., from the Sample Analysis at Mars instrument on the Curiosity rover and laboratory analyses of martian meteorites), and (v) information about the composition and geologic context of samples being collected by the Perseverance rover for return to Earth.},
}
@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.<br><br>RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-&#x3b1; (TNF-&#x3b1;)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.<br><br>CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.},
}
@article {pmid41043636,
year = {2025},
author = {Ba, XQ and Wang, MF and Huang, WL and Ye, XF and Xu, YY and Li, MM and Jiang, RF and Chen, CN},
title = {Talaromyces Marneffei Infection Involving the Central Nervous System in a Patient with Acquired Immunodeficiency Syndrome: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108096},
doi = {10.1016/j.ijid.2025.108096},
pmid = {41043636},
issn = {1878-3511},
abstract = {BACKGROUND: Talaromycosis, an opportunistic deep invasive mycosis, is caused by the fungus Talaromyces marneffei and is predominantly observed in individuals with acquired immunodeficiency syndrome (AIDS). Involvement of the central nervous system (CNS) is exceedingly rare and presents significant diagnostic challenges, often associated with high mortality rates.<br><br>CASE PRESENTATION: This report details a case of CNS Talaromyces marneffei infection in an AIDS patient who initially presented with epileptic seizures. Neuroimaging identified a ring-enhancing lesion within the right frontal lobe, concurrent with a marked elevation in serum &#x3b2;-D-glucan levels. The diagnosis was confirmed through a multimodal approach, including histopathological examination and metagenomic next-generation sequencing (mNGS). Postoperative management involved a sequential regimen of amphotericin B followed by voriconazole, leading to a favorable recovery. The patient is currently on a maintenance elvitegravir-based antiretroviral therapy regimen.<br><br>CONCLUSIONS: CNS Talaromyces marneffei infection in AIDS patients often lacks specific clinical manifestations, which complicates diagnosis and treatment. This case report contributes to the existing body of knowledge by presenting a successfully managed case, thereby enhancing the understanding of diagnostic and therapeutic strategies for similar future presentations.},
}
@article {pmid41043345,
year = {2025},
author = {Yu, C and Zhu, H and He, Y and Weng, R},
title = {Comparison of sulfur cyclings coupled with anaerobic ammonium oxidation in response to different river remediations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127523},
doi = {10.1016/j.jenvman.2025.127523},
pmid = {41043345},
issn = {1095-8630},
abstract = {The evolution from 'malodor' to 'algae bloom' in remediated urban rivers has received an ever-increasing attention due to relatively high nitrogen (N) loadings. As pivotal autotrophic processes, anaerobic ammonium oxidation (anammox) and sulfur-driven denitrification (SDD) represent promising candidates for N removal in remediated rivers with low C/N ratios. However, how and to what extent SDD is coupled with anammox remained largely unknown. Our investigations of four remediated urban rivers revealed that SDD was more prevalent than anammox, with Thiobacillus (0.13 %-2.51 %) dominating over Candidatus_Brocadia (0-0.02 %). The injection of Ca(NO3)2 greatly enhanced the coupling of SDD and anammox (SDDA) in anaerobic environments, achieving a maximum total nitrogen (TN) removal of 93.89 %. Metagenomic and metatranscriptomic analyses identified Thiobacillus, Thermomonas, and Candidatus_Brocadia as key microbial players, with their activities increased by 0.060 %, 0.015 %, and 0.498 %, respectively. Differently, Sulfurisoma, Dechloromonas, and Candidatus_Scalindua emerged as key players in Na2S2O3-group, while Sulfurisoma, Sulfurimonas, and Candidatus_Scalindua played pivotal roles in FeS2-group. Additionally, river simulations revealed that Na2S2O3-group showed the strongest SDDA coupling, supported by the highest abundances of soxB (0.14 %), narG (0.05 %), nirS (5.92 %), and hzsB (6.14 %). The FeS2-group demonstrated moderate coupling, whereas the Ca(NO3)2-group displayed the weakest performance. Moreover, Na2S2O3-group also exhibited excellent TN removal (87.58 %) in real river scenarios, indicating its potential as one promising N removal strategy for practical application. This study contributes to the understanding of S-N cyclings in river ecosystems and provides insights into manipulating N-reduction for possible application in remediated urban rivers.},
}
@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
doi = {10.1016/j.identj.2025.103929},
pmid = {41043307},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.<br><br>METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-&#x3b1;) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.<br><br>RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.<br><br>CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.<br><br>CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}
@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}
@article {pmid41042849,
year = {2025},
author = {Shen, LQ and Lin, D and Ye, YQ and Liu, Y and Ni, B and Wu, D and Wang, L and Zhu, D},
title = {Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {40},
pages = {e2516722122},
doi = {10.1073/pnas.2516722122},
pmid = {41042849},
issn = {1091-6490},
support = {2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 42207013//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {*Bacteriophages/genetics ; *Nitrogen ; *Soil Microbiology ; *Pesticides/toxicity ; Soil/chemistry ; Bacteria/genetics/virology/drug effects ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Phage-mediated dissemination of antibiotic resistance genes (ARGs) intensifies health threat in the environment. Increasing amounts of pesticides are entering the soil ecosystem, yet their potential influence on phage-mediated ARG spread, particularly under conditions of global change, remains poorly understood. In this study, we performed a long-term field experiment simulating pesticide contamination under nitrogen deposition and examined the role of soil phages in ARG spread and host adaptation using metagenomic and viromic sequencing. Combined pesticide markedly elevated the abundance of phage-encoded ARGs under nitrogen deposition. By enhancing phage-host interactions and increasing the co-occurrence of auxiliary metabolic genes with ARGs, phages may further facilitate the transfer of ARGs to bacterial hosts, conferring hosts a competitive edge in intensified microbial competition driven by combined pesticide exposure under nitrogen deposition. The phage-driven mechanism was supported by in vitro cultivation experiments, demonstrating that phages harboring ARGs, shaped by long-term combined pesticide exposure under nitrogen deposition, can infect bacterial hosts and confer resistance. Collectively, our findings underscore the pivotal role of phages in ARG mobilization under environmental stressors, reinforcing the importance of accounting for phage activity in ARG risk assessments under global change.},
}
@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}
@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}
@article {pmid41041976,
year = {2025},
author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA},
title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/mec.70126},
pmid = {41041976},
issn = {1365-294X},
support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; },
abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.},
}
@article {pmid41041810,
year = {2025},
author = {Oskolkov, N and Jin, C and Clinton, SL and Guinet, B and Wijnands, F and Johnson, E and Kutschera, VE and Kinsella, CM and Heintzman, PD and van der Valk, T},
title = {Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf108},
pmid = {41041810},
issn = {2047-217X},
support = {KAW 2021.0048 [P.D.H., F.W.]//Knut and Alice Wallenberg Foundation/ ; KAW 2022.0033 [P.D.H.]//Knut and Alice Wallenberg Foundation/ ; //National Bioinformatics Infrastructure Sweden at SciLifeLab/ ; VR 2020-04808//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab and Wallenberg Data Driven Life Science Program/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *DNA, Ancient/analysis ; Animals ; Phylogeny ; Archaea/genetics/classification ; },
abstract = {Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.},
}
@article {pmid41041613,
year = {2025},
author = {Ma, R and Xu, B and Chen, X and Sun, Q and Li, Y and Zheng, Q and Jiao, N and Zhang, R},
title = {Prophages in marine Citromicrobium: diversity, activity, and interaction with the host.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf148},
pmid = {41041613},
issn = {2730-6151},
abstract = {Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine Citromicrobium strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the "Piggyback-the-Winner" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual "Kill-the-Relatives" and "Colonize-the-Relatives" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.},
}
@article {pmid41041524,
year = {2025},
author = {Happi, A and Sijuwola, A and Omah, IF and Ogunsanya, O and Saibu, F and Ayinla, A and Adedokun, O and Fadele, J and Nwofoke, C and Adelabu, A and Ogundana, E and Lawal, O and Elias, O and Okokoh, E and Colquhoun, R and Achonduh-Atijegbe, O and Nta, H and Onimajesin, A and Momoh, F and Mari-Saez, A and Redding, D and Murray, K and Hanefeld, J and Sesay, AK and Rambaut, A and Happi, C},
title = {Metagenomics reveals cryptic circulation of zoonotic viruses in Nigeria.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7630852/v1},
pmid = {41041524},
issn = {2693-5015},
abstract = {Zoonotic spillover events pose an ongoing threat to global health, with historic and recent viral diseases of international concern emerging from animal reservoirs 1-6. In Nigeria, limited surveillance of animal hosts at the human and animal interface continues to hinder our understanding of viruses that are cryptically circulating in animals near human dwellings with potential for consequential spillover events. We performed unbiased metagenomic next‑generation sequencing (mNGS) on tissue and swab samples collected from 240 individual animals across 11 taxa (rodents, shrews, bats, goats, sheep, pigs, dogs, cats, chickens, cattle egrets, and lizards) in two Lassa‑affected Nigerian states (Ondo and Ebonyi). Host‑depleted sequencing reads were assembled into contigs, taxonomically classified, and subjected to phylogenetic analyses to characterize viral diversity, host associations, and evidence of cross‑species transmission. Across all samples, we identified 214 distinct viral taxa spanning 33 families, of which 41% (n = 83) represent novel species by ICTV criteria. Positive‑sense RNA viruses dominated (Coronaviridae, Picornaviridae, Astroviridae), followed by negative‑sense RNA, single‑ and double‑stranded DNA, and double‑stranded RNA viruses. Notably, human‑associated enteroviruses-including Hepatitis A virus (genotype 1b), echoviruses, coxsackieviruses, and noroviruses-were detected in goats, pigs, dogs, and chickens, indicating cryptic circulation of human pathogens in peridomestic and domesticated animals. Phylogenetic reconstructions revealed multiple cross‑species viral sharing events, particularly among rodents, goats, sheep, and pigs, and extensive recombination within Nigerian Betacoronavirus 1 lineages. Interestingly we found a putative novel avian like coronavirus in rodents, goats and sheep. Ecological modelling demonstrated that host species identity, sample type, and sampling effort were primary drivers of viral richness and abundance, and that higher overall viral diversity strongly predicted cross‑species transmission potential. Our integrated mNGS approach uncovered a rich and dynamic virome within animals inhabiting human‑dominated environments in Nigeria, including undetected circulation of human enteric viruses. These findings underscore the importance of broad‑taxonomic, real‑time surveillance at human-animal interfaces to inform early‑warning systems and pandemic preparedness, particularly in low‑resource settings.},
}
@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.<br><br>METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000&#x202f;mg lees/kg body weight for 14&#x202f;days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.<br><br>RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.016) showing both a potentially sex-dependent responses to dietary intervention.<br><br>CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}
@article {pmid41040987,
year = {2025},
author = {Li, Y and Zhang, L and Ma, G and Li, C and Hu, W and Ren, R and Zang, Y and Ying, D and Qiu, S and Jin, S and Qiu, C and Cao, X},
title = {Optimization of decision thresholds for Mycobacterium tuberculosis can effectively improve the performance of mNGS in tuberculosis diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646194},
pmid = {41040987},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis (TB) diagnosis remains challenging due to limitations in traditional methods. This study aimed to optimize the metagenomic next-generation sequencing (mNGS) threshold for Mycobacterium tuberculosis complex (MTBC) detection and evaluate its efficacy compared to standard diagnostic approaches.<br><br>METHODS: A total of 264 bronchoalveolar lavage fluid (BALF) samples were collected from patients with suspected pulmonary TB at Yongkang First People's Hospital between January 2022 and June 2023. After excluding patients with incomplete data, 59 clinically confirmed TB patients and 111 with non-tuberculous conditions were enrolled. mNGS data were analyzed to calculate reads per million (RPM) for MTBC, and thresholds of 0.02, 0.05, and 0.10 RPM were evaluated for diagnostic efficacy using clinical diagnosis as the gold standard.<br><br>RESULTS: The area under the receiver operating characteristic (ROC) curve (AUC) for mNGS in diagnosing TB at RPM thresholds of &#x2265;0.02, &#x2265;0.05, and &#x2265;0.10 were 0.881, 0.873, and 0.814, respectively. The optimal detection threshold was found at RPM &#x2265; 0.05. Comparative analysis showed mNGS (AUC = 0.873) outperformed routine culture (0.718), PCR (0.741), and Xpert (0.763). Combining mNGS with these methods improved AUC values to 0.837, 0.868, and 0.873, respectively.<br><br>CONCLUSION: Optimizing the mNGS threshold to &#x2265;0.05 significantly enhances MTBC detection in pulmonary TB. Combining mNGS with traditional methods further improves diagnostic efficacy, suggesting a potential role for mNGS in clinical TB management.},
}
@article {pmid41040929,
year = {2025},
author = {Cho, HY and Park, HJ and Choi, JS and Kim, SH and Ryu, MO and Seo, KW},
title = {Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1571107},
pmid = {41040929},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiome is a vital component of an organism's health, influencing metabolism, immune function, and overall homeostasis. In this study, we aimed to characterize the gut microbiota of healthy domestic short-hair cats in South Korea and evaluate the effects of age, body condition score (BCS), sex, and diet on microbial composition.<br><br>METHODS: From August to December 2023, 40 healthy cats aged 1-14&#x202f;years with a body condition score (BCS) of 5-9 were selected. Cats were excluded if they had taken probiotics or antibiotics, exhibited gastrointestinal symptoms within the last 6&#x202f;months, or had blood work abnormalities. DNA quantification was performed, and libraries targeting the V3 and V4 regions were prepared according to the Illumina 16S metagenomic sequencing protocol with a read length of 2&#x202f;&#xd7;&#x202f;300 bp. The relative abundance of bacteria at the phylum, genus, and species levels was assessed according to the age, sex, diet, and BCS of the cats, with major bacterial groups selected for chart analysis.<br><br>RESULTS: Examination of the fecal samples from 40 healthy cats (aged 0.5-14&#x202f;years) using 16S rRNA gene sequencing revealed 2,721 bacterial amplicon sequence variants. The predominant phyla were Bacillota, Bacteroidota, and Actinomycetota. Although age did not significantly affect alpha diversity, a trend toward increased diversity was observed in cats aged 7-14&#x202f;years. Phocaeicola was more abundant in older cats, suggesting a possible association with age-related conditions. Furthermore, Verrucomicrobiota was enriched in cats with a BCS of 8-9, and Ruminococcus torque was positively correlated with higher BCS. Sex-based differences indicated increased levels of Pseudomonadota, Finegoldia magna, and Sutterella massiliensis in neutered males, potentially linked to inflammatory pathways. Dietary analysis revealed an increased abundance of Blautia and Lachnoclostridium following a combination of dry and wet food.<br><br>CONCLUSION: Our findings provide critical insights into the core microbiota of domestic short-hair cats in South Korea, emphasizing the influence of geographic, physiological, and environmental factors on gut microbial diversity. The results offer a valuable foundation for advancing feline gut health research and enhancing health management strategies for felines, particularly in South Korea.},
}
@article {pmid41040912,
year = {2025},
author = {Matsumura, M and Mitsui, H and Woo, T and Suzuki, T and Arai, H and Koike, C and Kataoka, T and Motooka, D and Fukushima, K and Okudela, K},
title = {Identification of key molecules in micropapillary progression of lung adenocarcinoma: A comprehensive gene expression analysis study using the spatial gene expression solution methodology.},
journal = {Oncology letters},
volume = {30},
number = {5},
pages = {533},
pmid = {41040912},
issn = {1792-1082},
abstract = {The micropapillary histological subtype is a high-grade element and a poor prognostic marker in lung adenocarcinoma (LUAD). This subtype develops through the lepidic-filigree micropapillary (filigree)-conventional/overt micropapillary (mPAP) pathway. The present study aimed to identify key molecules that promote this progression. To this end, gene expression profiles specific to lepidic, filigree and mPAP elements were investigated in histological sections obtained from 4 different LUAD cases. The 10× Genomics Visium Spatial Gene Expression Solution was used due to its superior resolution compared with conventional microdissection techniques. Cellular retinoic acid binding protein 2 (CRABP2), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) and mucin 21 (MUC21) were identified as common molecules with significantly elevated levels along the lepidic-filigree-mPAP pathway. Furthermore, the present findings indicated that CRABP2 may serve an important role in the early stage of this process, as its level significantly increases during the transition from the lepidic to the filigree substage. Immunohistochemical analysis of the expression of CRABP2, CEACAM5 and MUC21 proteins in 207 surgically resected LUAD samples (expanded sample size) was performed. The present study revealed an increase in the expression levels of CRABP2 between the lepidic and filigree elements, and between filigree and mPAP for CEACAM5 and MUC21. Thus, these three proteins were demonstrated to serve roles in the lepidic-filigree-mPAP pathway at different stages. Notably, these molecules were associated with poor prognosis, characterized by an elevated recurrence rate and poor survival rate. In conclusion, crucial molecules that promote the lepidic-filigree-mPAP pathway, and exhibit potential clinical utility as prognostic markers and molecular therapeutic targets, were identified.},
}
@article {pmid41040880,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Li, B and Zhang, M and Jiang, F and Song, P and Liang, C and Fan, Q and Xu, Y and Zhang, R},
title = {Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659661},
pmid = {41040880},
issn = {1664-302X},
abstract = {Understanding the composition and function of gut microbiota is essential for elucidating how wild animals adapt to arid environments. The Mongolian wild ass (Equus hemionus hemionus), which inhabits harsh desert ecosystems, offers an ideal model for such investigations. This study employed metagenomic sequencing of fecal samples to characterize the composition and structure of the gut microbiota in adult, subadult, and juvenile Mongolian wild asses, with functional annotation based on the KEGG, CARD, and CAZy databases. Our study revealed that Bacillota and Bacteroidota were the dominant phyla, together accounting for over 85% of relative abundance, with their ratio (B/B value) showing clear age-dependent shifts. Juveniles were dominated by Bacillota (high B/B value), consistent with adaptation to a milk-based, protein- and lactose-rich diet, whereas adults shifted toward Bacteroidota dominance (low B/B value), with relative abundance increasing from 39.53% to 64.92%, reflecting enhanced polysaccharide and fiber degradation, thereby providing microecological support for adaptation to low-energy, high-fiber desert vegetation resources. Alongside this transition, α-diversity significantly increased with age, while β-diversity patterns shifted from dispersed to clustered, indicating a more complex, stable, and mature gut community. Over 58% of predicted genes were assigned to metabolic pathways, highlighting the essential contribution of gut microbes to herbivore digestion. Polysaccharide lyases, enriched in adults and subadults, were positively correlated with Bacteroidota abundance, highlighting their central role in fiber degradation and stable energy supply, thereby supporting adaptation to arid desert habitats. In contrast, juveniles were characterized by enrichment of the galactose metabolism pathway, high abundance of Pseudomonadota (LEfSe LDA > 4), and the largest number of antibiotic resistance genes (AROs), including 17 potential key AROs, reflecting greater microbial plasticity and higher environmental exposure risks during early development. This study provides the first systematic characterization of age-related gut microbiome dynamics and functional adaptations in the endangered Mongolian wild ass, offering novel insights into microbial contributions to host energy optimization and resilience in arid ecosystems, with implications for conservation strategies.},
}
@article {pmid41040879,
year = {2025},
author = {Hoepfner, C and Guzmán, D and Vidal-Veuthey, B and Foronda, V and Beggs, A and Cárdenas, JP and Vargas, VA and Alfaro, FD},
title = {Functional stratification and enzymatic arrangement in microbial communities across a hypersaline depth gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1624058},
pmid = {41040879},
issn = {1664-302X},
abstract = {Extreme environments comprise a significant portion of Earth's terrestrial surface, posing challenges, such as extreme temperatures, pressure, pH extremes, oxygen and nutrient scarcity, and high salinity. Hypersaline ecosystems, such as those in the Andean Cold Deserts, exemplify extreme environments where microbial life has evolved specialized survival mechanisms. The Central Andean Mountains host extensive salt flats exposed to extreme temperature fluctuations, intense ultraviolet radiation, and high soil salinity. While most studies focus on surface layers, the impact of soil depth on functional diversity remains poorly understood. This study utilized shotgun metagenomics and functional annotation to explore enzymatic diversity across a 8-meter depth gradient in the Uyuni Salt Flat aiming to understand microbial adaptations to depth and abiotic stress. Our findings revealed a complex, stratified microbial ecosystem. Surface layers showed high abundance of amylases, enzymes that degrade accessible carbohydrates, likely derived from photosynthetic communities or surface-imported organic matter. These patterns suggest a dominance of strategies for rapid carbon decomposition. Intermediate depths exhibited elevated lipase and peroxidase activity, reflecting the presence of complex lipids and oxidative stress management, essential for survival in oxygen-limited, high-salinity zones. Lipase support lipid utilization as a carbon source, while peroxidase activity points to redox adaptations for microbial resilience under fluctuating oxidative conditions. Deeper sediment layers showed a shift toward protease and peptidase activity, indicating organic nitrogen recycling in nutrient-deprived environments and suggesting an efficient protein degradation system among halophilic archaea. Peroxidases remained abundant even at these depths, supporting sustained redox regulation and biogeochemical cycling thus enabling microbes to manage redox imbalances in high-salinity, low-oxygen settings. The enzymatic diversity across the depth gradient demonstrates functional stratification and remarkable microbial adaptability to hypersaline conditions. This functional resilience underpins nutrient cycling and organic matter decomposition deep in the salt flats. Notably, the identified halophilic enzymes, stable and active under high-salinity conditions, hold significant potential for biotechnological applications. This study contributes to our understanding of microbial life's complexity in hypersaline environments, enhancing our ability to harness extremophilic enzymes for biotechnological applications while underscoring the ecological value of these unique habitats.},
}
@article {pmid41040656,
year = {2025},
author = {Wilkins, L and Yuen, B and Petersen, J and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {435},
pmid = {41040656},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Ctena decussata (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1,658.05 megabases. Most of the assembly (97.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 53.28 kilobases in length. The genome of Candidatus Thiodiazotropha sp. CDECU1, a bacterium associated with C. decussata was also assembled.},
}
@article {pmid41040369,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.22.677880},
pmid = {41040369},
issn = {2692-8205},
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and therefore the most important bioenergetic process on earth, and the greatest diversity in photosynthetic systems are found in microorganisms. However, understanding of the biophysical and biochemical processes that transduce light to chemical energy has derived from the relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of microbial DNA sequences encoding proteins that catalyze the initial photochemical reactions that has been deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90° C) springs available through the JGI IMG database, to generate a resource of diverse sequences that potentially are adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}
@article {pmid41040146,
year = {2025},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.16.633031},
pmid = {41040146},
issn = {2692-8205},
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collected Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}
@article {pmid41039672,
year = {2025},
author = {Silvester, R and Webster, G and Perry, WB and Farkas, K and Rushton, L and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL},
title = {Genome-resolved metagenomics uncovers antimicrobial resistance gene carriers in hospital and municipal wastewater environments.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180607},
doi = {10.1016/j.scitotenv.2025.180607},
pmid = {41039672},
issn = {1879-1026},
abstract = {Wastewater-based epidemiology (WBE) is a powerful approach to study antimicrobial resistance (AMR) dynamics at the population level. Using genome-resolved metagenomics, we recovered 3978 metagenome-assembled genomes (MAGs) from archived metagenome sequences generated under the national wastewater surveillance programme across Wales, UK. Taxonomic profiling of MAGs revealed a diverse bacterial community, with significant compositional shifts observed across seasons and sample sources. Approximately 13.6 % of the MAGs carried one or more antimicrobial resistance genes (ARGs), with genes conferring resistance to tetracycline and oxacillin being the most prevalent within the wastewater microbiomes. We also recovered yet-uncultivated microbial genomes- often referred to as "microbial dark matter" harbouring clinically relevant ARGs, offering insights into previously uncharacterised resistance reservoirs in wastewater. ARG-host associations shifted between untreated influent and treated effluent, with effluent profiles also varying significantly between secondary and tertiary treatments, revealing the impact of treatment type on ARG host composition. This study represents the first comprehensive genome-resolved metagenomic characterisation of ARG carriers across both hospital and municipal wastewater in Wales, effectively bridging clinical and environmental compartments. Our findings highlight the need to integrate high-resolution genome-resolved metagenomic surveillance into national AMR monitoring frameworks to track emerging threats, characterise ARG reservoirs and inform targeted public health interventions.},
}
@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}
@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth &amp; development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.<br><br>RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.<br><br>CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}
@article {pmid41039197,
year = {2025},
author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI},
title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {601},
pmid = {41039197},
issn = {1471-2180},
support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; },
abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.<br><br>RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.<br><br>CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.},
}
@article {pmid41039183,
year = {2025},
author = {Al-Shaibani, MM and Zin, NM and Remali, J and Sidik, NM and Al-Mekhlafi, NA and Mariappan, V and Sukri, A},
title = {Anticancer compounds from Streptomyces: insights from metagenomics and mechanistic perspective.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41039183},
issn = {1874-9356},
support = {FRGS/1/2016/STG05/UKM/02/5//Ministry of Higher Education/ ; },
abstract = {Cancer continues to be a leading cause of death globally, driving the ongoing search for novel bioactive compounds with therapeutic potential. Metagenomic sequencing has revolutionized this pursuit by enabling the direct detection and genomic assembly of previously uncultured Streptomyces species from environmental DNA, circumventing traditional cultivation limitations. This review explores recent advances in metagenomics-driven discovery of anticancer compounds derived from Streptomyces, with a focus on identifying biosynthetic gene clusters (BGCs) responsible for producing bioactive secondary metabolites. Over the past decade, metagenomic approaches have been adopted to uncover new species of Streptomyces and anticancer compounds. Although metagenomics has been adopted in research and discovery of new Streptomyces, its application in the discovery of Streptomyces-related pathways pertaining to anticancer compounds remains limited. Furthermore, clinical translation remains limited, highlighting the need for further research. By examining metagenomic methodologies and the mechanisms of action of these compounds, this review provides an updated and focused perspective on Streptomyces-derived anticancer agents and their potential for future drug development.},
}
@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}
@article {pmid41038529,
year = {2025},
author = {Liu, J and Dong, Y and Huang, Y and Xie, M and Wang, H and Wang, Q and Wang, S and Wang, N and Jiang, Y and Zhang, W and Wang, M and Chen, J and Huang, L and Cai, H},
title = {Clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections in ICU: A multicenter retrospective study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.ijid.2025.108094},
pmid = {41038529},
issn = {1878-3511},
abstract = {BACKGROUND: Central nervous system (CNS) infections impose a substantial global burden of morbidity and mortality, necessitating accurate and timely diagnosis for optimal clinical management. Metagenomic next-generation sequencing (mNGS) has been demonstrated as a valuable tool for pathogen detection in patients with suspected CNS infections.<br><br>METHODS: From December 2019 to June 2023, we conducted a comprehensive analysis of 520 cerebrospinal fluid samples collected from patients with suspected intracranial infections across six intensive care units. All pathogen-positive results identified through metagenomic next-generation sequencing were subsequently validated by an independent laboratory.<br><br>RESULTS: Metagenomic NGS detected 105 microbial species in 520 clinical samples, comprising 64 bacterial species (61.0%), 16 DNA viruses (15.2%), 13 fungal species (12.4%), and 7 RNA viruses (6.7%). The 30-day mortality rate among all study participants was 18.5%. Metagenomic NGS identified 172 infection cases, whereas conventional culture methods detected only 31 cases. For CNS infections, mNGS demonstrated diagnostic sensitivity, specificity, and accuracy rates of 59%, 90.5%, and 72.5%, respectively.<br><br>CONCLUSIONS: Metagenomic NGS testing facilitates accelerated diagnosis of CNS infections and informs evidence-based clinical management decisions.},
}
@article {pmid41038519,
year = {2025},
author = {Surgers, L and Lafont, C and Lamoureux, C and Demontant, V and N'Debi, M and Cheval, J and Boizeau, L and Trawinski, E and Pawlotsky, JM and Woerther, PL and Rodriguez, C and , },
title = {Shotgun metagenomics for the diagnosis of infections: A prospective study.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106619},
doi = {10.1016/j.jinf.2025.106619},
pmid = {41038519},
issn = {1532-2742},
abstract = {BACKGROUND: Shotgun metagenomics (SMg) promises to significantly improve the microbiological diagnosis of infectious diseases. However, the prospective evaluation of its clinical utility in different infectious syndromes remains poorly documented.<br><br>METHODS: We conducted a prospective study including all patients who underwent SMg as part of their care at the French Henri Mondor Hospital National Reference Laboratory for accredited SMg between February 2018 and January 2020. Patients were categorized as having either a "high likelihood" or "low likelihood" of infection based on their clinical presentation. The contribution of the SMg to the final diagnosis was assessed by a multidisciplinary team of infectious disease specialists.<br><br>FINDINGS: 202 patients were enrolled in the study. Of the 123 patients considered to have a high likelihood of infection, SMg confirmed the cause of infection in 38 cases (30.9%), including 12 cases (9.8%) diagnosed exclusively by this method. In the 79 patients classified as having a "low likelihood" of infection, SMg did not detect any microorganisms compatible with an infectious cause. In particular, patients undergoing immunosuppressive treatment within the latter group showed no deterioration after 6 months.<br><br>INTERPRETATION: SMg facilitated microbiological diagnosis in over 30% of complex cases, regardless of sample type or site of infection. Compared with conventional techniques, SMg provided diagnoses in 10% more cases, highlighting its broad utility across different infectious diseases. Our results suggest that SMg is a promising tool for documenting complex infectious diseases alongside traditional microbiology tools. Furthermore, negative SMg results are useful for the management of patients with a low likelihood of infection.<br><br>FUNDING: This study was conducted as part of patient care.},
}
@article {pmid41038405,
year = {2025},
author = {Jin, H and Feng, B and Gong, W and Chen, X and Wang, D and Li, Y and Huang, W and Peng, W},
title = {Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease.},
journal = {Genomics},
volume = {},
number = {},
pages = {111126},
doi = {10.1016/j.ygeno.2025.111126},
pmid = {41038405},
issn = {1089-8646},
}
@article {pmid41038354,
year = {2025},
author = {Qing, Z and Haibei, H and Hanxue, Y and Juan, S},
title = {Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133416},
doi = {10.1016/j.biortech.2025.133416},
pmid = {41038354},
issn = {1873-2976},
abstract = {The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD600 > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.},
}
@article {pmid41038122,
year = {2025},
author = {Zhao, F and Yang, Z and Xiao, Y and Han, G and Hardie, KR and Bartlam, M and Wang, Y},
title = {Enantioselective interactions of silver nanoparticles and chiral antibiotics in driving resistance evolution in activated sludge.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124656},
doi = {10.1016/j.watres.2025.124656},
pmid = {41038122},
issn = {1879-2448},
abstract = {The stereochemistry of antibiotics significantly affects resistance development. With rising antibiotic resistance, nanotechnology is emerging as a promising solution, potentially increasing the likelihood of nanoparticle coexistence with antibiotics in wastewater treatment plants (WWTPs). However, the influence of nanoparticles on chiral antibiotics induced resistance remains unclear. This study employed chemical characterization, metagenomics, and molecular docking to comprehensively elucidate the resistance mechanisms induced by the combination of silver nanoparticles (AgNPs) and chiral antibiotics (ofloxacin: OFL and levofloxacin: LEV). AgNPs significantly altered the abundance and composition of antibiotic and metal resistance genes, as well as the conjugative transfer of the RP4 plasmid among activated sludge communities, with the OFL_AgNPs combination exhibiting a higher resistance potential than LEV_AgNPs. Mechanistic studies revealed that chiral antibiotics selectively interact with AgNPs, promoting Ag[+] release, enhancing antibiotic uptake, and forming stable complexes. These interactions reshaped microbial functions, including cell membrane permeability, oxidative stress response, quorum sensing, and extracellular secretion, thereby shaping resistance profiles. This study reveals previously overlooked enantiomer-specific risks associated with nanoparticle-antibiotic interactions and provides a foundation for strategies to mitigate ARG dissemination in wastewater treatment and broader environmental systems.},
}
@article {pmid41037216,
year = {2025},
author = {Pan, F and Yu, F and Zhang, H and Chen, P and Weng, W},
title = {Clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected bloodstream infection.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41037216},
issn = {1435-4373},
abstract = {BACKGROUND: Accurate and comprehensive pathogen diagnosis methods are urgently required for the diagnosis of bloodstream infection (BSI).This study retrospectively evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected BSI.<br><br>METHODS: Between July 8, 2021 to December 31, 2022, mNGS tests and conventional methods tests (CMTs) were performed simulataneously on samples from children with suspected BSI. The diagnostic performance of mNGS was assessed in comparison CMTs .<br><br>RESULTS: A total of 191 patients with suspected BSI were included in the final analysis after excluding 9 patients due to lost to follow-up or duplicated entries. The mNGS yielded positive results in 111 cases, with a positive rate of 58.1% (111/191), significantly higher than that of CMTs (13.1%, 25/191) (P&#x2009;<&#x2009;0.05). Using CMTs as standard, the sensitivity, specificity, positive predictive value and negative predictive value for mNGS and CMTs were 73.8% vs. 25.0%, 54.2% vs. 96.3%, 55.9% vs. 84.0%, and 72.5% vs. 62.0%, respectively. Among 111 mNGS-positive cases, 46 cases (41.4%) showed ploymicrobial infections, with Torque teno virus, human betaherpesvirus 5, and human gammaherpesvirus 4 being most frequently identified pathogens. Of them, 62 cases (55.9%) were clinically diagnosed as BSI regarded as true positive results, while 49 cases (44.1%) positive for pathogens were diagnosed as non-BSI. The diagnostic time of mNGS was significantly shorter than that of CMTs (30.6&#x2009;&#xb1;&#x2009;7.7&#xa0;h vs. 70.5&#x2009;&#xb1;&#x2009;11.6&#xa0;h, P&#x2009;<&#x2009;0.05). It is worth noting that mNGS results guided adjustments to antimicrobial therapy in 50.8% (97/191) patients, including escalation in 74 cases and de-escalation in 23 cases.<br><br>CONCLUSIONS: The mNGS significantly improves the detection rate for the pathogens in children with suspected BSI, especially for viruses, which serve as a complement to CMTs.},
}
@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}
@article {pmid41036867,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Mazza Rodrigues, JL and Peay, KG and Tsai, SM},
title = {A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0064225},
doi = {10.1128/mra.00642-25},
pmid = {41036867},
issn = {2576-098X},
abstract = {The Amazon rainforest is facing multifaceted anthropogenic pressures, and we previously showed that forest-to-pasture conversion has led to soil microbial communities with distinct genomic traits. Here, we present 69 archaeal and bacterial metagenome-assembled genomes and detail their virulence- and antimicrobial resistance-associated genes.},
}
@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023425},
doi = {10.1128/msphere.00234-25},
pmid = {41036845},
issn = {2379-5042},
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}
@article {pmid41036842,
year = {2025},
author = {Zeng, J and Hu, W and Chang, L and Hua, Z and Wu, G and Fang, Y and Wang, G and Xiao, C and Liu, J},
title = {Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117825},
doi = {10.1128/msystems.01178-25},
pmid = {41036842},
issn = {2379-5077},
abstract = {The WOR-3 phylum is widely distributed in various environments, including hot springs, marine ecosystems, and hydrothermal vents, yet its ecological roles and metabolic capabilities remain poorly understood. In this study, we analyzed 181 medium- to high-quality metagenome-assembled genomes, including 59 newly reconstructed from environmental samples and 122 retrieved from public databases. Phylogenetic analyses resolved the WOR-3 lineage into four subgroups (subgroup 1-4). Metabolic reconstruction revealed significant divergence of the carbon, sulfur, nitrogen, and hydrogen metabolism pathways among the different subgroups. Subgroup 1 was characterized by fermentative metabolism involving formate and ethanol and uniquely exhibited potential for carbon fixation via the Calvin cycle, as indicated by the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene. Notably, WOR-3 RuBisCO is phylogenetically affiliated with archaeal form III, although the carbon fixation pathway follows the canonical bacterial Calvin cycle-a feature of potential evolutionary significance. Subgroup 3 exhibits metabolic versatility, including genes for dissimilatory sulfate reduction, sulfur oxidation, partial denitrification, and fatty acid degradation. In addition, all subgroups harbored key components of hydrogen metabolism, including widespread NiFe hydrogenases, supporting H2-dependent electron transfer and energy conservation. Within the WOR-3 lineage, the coexistence of two respiratory enzyme systems-the Rnf complex and the oxidative phosphorylation respiratory chain-indicates distinct anaerobic and aerobic metabolic lifestyles, respectively. Collectively, this study expands the genomic framework for the WOR-3 phylum and provides novel insights into the metabolic versatility and ecological functions of this previously uncharacterized lineage in biogeochemical cycles of carbon, nitrogen, and sulfur.IMPORTANCEThe WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse various environments. By integrating 181 metagenome-assembled genomes, including 59 newly reconstructed, this study provides the most comprehensive genomic framework to date for WOR-3. Phylogenomic and metabolic reconstruction revealed four distinct subgroups with divergent capacities for carbon, sulfur, and nitrogen metabolism. Notably, subgroup 1 encodes a complete Calvin-Benson-Bassham cycle featuring an archaeal-type form III ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting an unusual evolutionary trajectory for carbon fixation in this lineage. Subgroup 3 exhibits versatile metabolic potential, including dissimilatory sulfur metabolism, partial denitrification, and fatty acid degradation, highlighting its possible roles in multiple biogeochemical processes. These findings not only expand the taxonomic and functional landscape of the WOR-3 phylum but also offer key insights into its ecological roles in global element cycling.},
}
@article {pmid41036698,
year = {2025},
author = {Bulteau, S and Braud, M and Petrier, M and Castain, L and Anani, H and Peltier, C and Mobuchon, L and Bouras, M and Flattres, D and Poschmann, J and Josset, L and Roquilly, A and Bressollette-Bodin, C},
title = {Interferon Gamma Injection and Its Effect on the Respiratory Anelloviridae Population in ICU Ventilated Patients.},
journal = {Journal of medical virology},
volume = {97},
number = {10},
pages = {e70612},
doi = {10.1002/jmv.70612},
pmid = {41036698},
issn = {1096-9071},
support = {//This work was supported by the Horizon 2020 Research and Innovation Framework Programme (grant agreement no. 847782, HAP2 project, https://hap2-project.com). S.B. was also supported by a grant from Region Pays de la Loire./ ; },
mesh = {Humans ; Male ; Female ; Intensive Care Units ; Middle Aged ; *Interferon-gamma/administration &amp; dosage/therapeutic use ; Aged ; *Respiration, Artificial/adverse effects ; Viral Load ; DNA, Viral ; Adult ; Metagenomics ; *Healthcare-Associated Pneumonia/prevention &amp; control/virology ; *Immunologic Factors/administration &amp; dosage ; Critical Illness ; },
abstract = {Immune dysfunctions induced by critical illness are associated with an increased risk of hospital-acquired pneumonia (HAP) in intensive care unit (ICU) patients. The use of immunomodulatory molecules in this setting is under evaluation. The presence of persistent viruses, such as anelloviruses (AVs) or herpesviruses, which are frequently detected in respiratory samples, may indicate immune dysfunction. Herpesvirus infections are associated with increased morbidity in ICU patients, and variations in AV DNA loads are associated with rejection events in immunocompromised patients. We investigated the respiratory viral landscape of 94 patients during the first week under invasive mechanical ventilation using quantitative PCR and targeted metagenomics after capture probe enrichment. The patients were included in a placebo-controlled randomized clinical trial testing IFNγ for the prevention of HAP. We measured AV and herpes simplex virus-1 (HSV-1) DNA loads over time in respiratory samples collected at admission (n = 54), and on Days 3 (n = 73) and 7 (n = 57) after admission. There were no significant differences in mortality, HAP, the development of acute respiratory distress syndrome (ARDS), HSV, or AV DNA detection between patients treated with IFNg and those who received a placebo. Patients who developed HAP had a significantly higher AV DNA load in tracheal aspirates over time (p = 0.011) than those who did not. Target enrichment analysis revealed AV presence in all respiratory samples, with no differences observed in AV composition between IFNg-treated and placebo patients, or between HAP and noHAP patients. Trial Registration: CPP Ouest II 17/02/2021 (avis N°2021/03); ClinicalTrial.gov number: NCT04793568.},
}
@article {pmid41036626,
year = {2025},
author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q},
title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.},
journal = {Nucleic acids research},
volume = {53},
number = {18},
pages = {},
doi = {10.1093/nar/gkaf954},
pmid = {41036626},
issn = {1362-4962},
support = {2022YFA1304100//National Key R&amp;D Program of China/ ; 82&#xa0;270&#xa0;980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82&#xa0;202&#xa0;539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; },
mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; },
abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.},
}
@article {pmid41036540,
year = {2025},
author = {Pei, Y and Cai, S and Xue, Y and Fu, Y and Zhang, J and Shen, Q and Ji, L and Wu, P and Wang, H and Wang, Y and Zhang, W and Yang, S},
title = {First detection of two cycloviruses in cormorant fecal samples in China by high-throughput sequencing technology.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1677378},
pmid = {41036540},
issn = {2297-1769},
abstract = {INTRODUCTION: The Great Cormorant (Phalacrocorax carbo) is widely distributed across China. As an apex predator in aquatic ecosystems, it plays a tripartite ecological role: acting as a natural host, transmission vector, and indicator species for viruses. Current research confirms that cormorants carry diverse viral pathogens from the families including Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Polyomaviridae. Significant knowledge gaps persist regarding their virome diversity.<br><br>METHODS: In this study,46 cormorant fecal swab samples were collected at Xiamen Garden Expo Park, and viralmetagenomics method was conducted to identify two Cycloviruses.<br><br>RESULTS: This study identified two novel cycloviruses, Corcyclo-1 (1,856 bp) and Corcyclo-2 (1,831 bp), from cormorant fecal samples using viral metagenomics. Genomic analyses revealed hallmark features of the genus Cyclovirus, including inversely oriented open reading frames (ORFs) encoding the capsid protein (Cap) and replication-associated protein (Rep), as well as a conserved stem-loop sequence TAATACTAT. The Rep gene of Corcyclo-1 contained a 166-bp intron and shared >96.9% amino acid identity with human-, wild boar-, and chicken-derived cyclovirus strains (HaCV-8) from Vietnam and Madagascar, classifying it as a novel strain of HaCV-8. In contrast, Corcyclo-2 harbored a 98-bp intron in its Rep gene and clustered with unclassified cyclovirus strains from bats and mongooses in China and Saint Kitts and Nevis (>97.4% identity), constituting a putative new species. Phylogenetic and pairwise sequence analyses further supported their taxonomic positions. Epidemiological screening demonstrated a high prevalence of Corcyclo-1 (82.6%, 38/46) and Corcyclo-2 (32.6%, 15/46) in cormorant feces. Cross-species surveillance detected Corcyclo-2 in chickens (25.8%, 16/62) and ducks (11.7%, 9/77), whereas Corcyclo-1 was absent in these hosts.<br><br>CONCLUSION: This study represents the first report of cormorant-associated cycloviruses, highlighting their potential for cross-species transmission and providing new insights into the ecological diversity and evolutionary mechanisms of cyclovirus.},
}
@article {pmid41036230,
year = {2025},
author = {Xin, L and Jiao, X and Gong, X and Yu, J and Zhao, J and Lv, J and Feng, Q and Yuan, Y and Pan, W},
title = {Diagnostic value of metagenomic next generation sequencing of bronchoalveolar lavage fluid in immunocompromised patients with pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1602636},
pmid = {41036230},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Pneumonia/diagnosis/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Adult ; Fungi/genetics/isolation &amp; purification/classification ; Viruses/genetics/isolation &amp; purification/classification ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables simultaneous sequencing of DNA fragments for comprehensive pathogen identification. Pneumonia in immunocompromised patients-characterized by atypical clinical manifestations and rapid progression-poses diagnostic challenges. Conventional microbiological testing (CMT), which relies on pathogen culture and serological assays, is limited by prolonged turnaround times and suboptimal detection rates. This study was performed to evaluate the clinical utility of mNGS through comparative analysis with CMT in detecting pathogens among immunocompromised patients with pneumonia.<br><br>METHODS: We conducted a retrospective cohort study of 146 immunocompromised patients with suspected pneumonia. The mNGS and CMT results were systematically analyzed. Pathogen detection rates and microbial spectrum concordance were visualized using pie and bar charts. Diagnostic performance was compared using McNemar's test and Kappa (&#x3ba;) statistics for inter-method agreement. The sensitivity, specificity, accuracy, and area under the curve were calculated for pathogen-specific evaluations.<br><br>RESULTS: mNGS demonstrated superior detection efficacy, identifying pathogens in 98 cases versus 50 by CMT, with 48 overlapping positives. The microbial spectrum showed substantial differences: mNGS detected 73 bacterial, 46 fungal, and 45 viral pathogens, whereas CMT identified 38 bacterial, 27 fungal, and 21 viral agents. mNGS outperformed CMT across all infection types, including single-pathogen infections (bacterial, fungal, or viral only) and mixed infections (bacterial + fungal, bacterial + viral, fungal + viral, or bacterial + fungal + viral). Bacterial and fungal detections showed low inter-method concordance, while viral detection exhibited moderate agreement (&#x3ba; = 0.510, p < 0.001). Notably, mNGS achieved significantly higher detection rates for Enterococcus faecalis and Pneumocystis jirovecii in intensive care unit (ICU)-admitted patients with severe pneumonia (p < 0.05). Clinical outcomes improved in 45 patients following mNGS-guided therapeutic adjustments.<br><br>CONCLUSIONS: mNGS and CMT demonstrate complementary strengths in bacterial and fungal detection in immunocompromised patients with pneumonia. mNGS provides enhanced diagnostic accuracy for key pathogens such as E. faecalis and P. jirovecii, particularly in severe and ICU-admitted cases. As a high-throughput diagnostic tool, mNGS may improve pathogen detection and clinical management in immunocompromised populations.},
}
@article {pmid41035885,
year = {2025},
author = {Velasco Cardona, DC and Cardona-Acevedo, S and Valencia-Arias, A and Pérez-Delgado, O and Pinella Vega, M},
title = {Bibliometric analysis of the application of artificial intelligence techniques in bacteriology: a PRISMA-guided research agenda.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641967},
pmid = {41035885},
issn = {1664-302X},
abstract = {INTRODUCTION: The integration of artificial intelligence (AI) into bacteriology has marked a pivotal advancement by enabling the analysis of large-scale microbiological datasets. Despite growing adoption, significant research gaps persist, hindering the full exploitation of AI's potential in bacterial research and diagnostics.<br><br>OBJECTIVE: To analyze global scientific production on the application of AI techniques in bacteriology and propose a future research agenda based on bibliometric trends.<br><br>METHODS: This study conducts a bibliometric analysis of artificial intelligence (AI) applications in bacteriology, explicitly guided by the PRISMA 2020 framework. Unlike traditional reviews, this approach combines PRISMA's methodological rigor with bibliometric techniques to map scientific production. Metadata were retrieved from Scopus and Web of Science using predefined search strategies. Quantitative indicators, co-occurrence networks, and thematic mapping were applied to examine the field's temporal evolution and conceptual structure. The findings provide an evidence-based overview of research trends and gaps, supporting the design of a future research agenda on AI integration in bacteriology.<br><br>RESULTS: The findings reveal exponential growth in scientific output, especially between 2022 and 2024. Leading authors include Singh and Waegeman, with high-impact journals such as Frontiers in Microbiology and MSystems. The United States and China are the most productive countries. Thematic evolution shows a shift from early topics like microbial spoilage toward advanced applications including bacterial classification and diagnostic modeling. Key conceptual clusters were identified around microbiomes, classification, and bioinformatics. Emerging terms such as "diagnosis," "metagenomics," and "transfer learning" indicate future research directions.<br><br>CONCLUSION: AI applications in bacteriology are expanding rapidly yet still rely heavily on traditional machine learning methods. There is a need to incorporate advanced approaches such as deep learning and transformer-based models. The findings support a strategic agenda for promoting interdisciplinary collaboration and technological innovation in bacteriological research.},
}
@article {pmid41035876,
year = {2025},
author = {Jiang, W and Zhai, J and Li, B and Ma, J and Zhang, S},
title = {Pulmonary Rhizopus arrhizus infection treated with high-dose liposomal amphotericin B in a heart transplant recipient under ECMO: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1631873},
pmid = {41035876},
issn = {2296-858X},
abstract = {Pulmonary mucormycosis caused by Rhizopus arrhizus is an emergent, fulminant threat in immunocompromised hosts, yet therapeutic success remains elusive when extracorporeal membrane oxygenation (ECMO) is required. While liposomal amphotericin B (L-AMB) is endorsed as first-line therapy, its pharmacokinetics are profoundly altered by ECMO-dilution, circuit sequestration, and impaired lung penetration all conspire to sub-therapeutic exposure. We report the first documented case in which these challenges were systematically overcome. A 52-year-old cardiac-transplant recipient, supported on veno-venous ECMO for refractory hypoxaemia, developed rapidly progressive pneumonia. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid returned a definitive Rhizopus arrhizus signature within 24 h, prompting immediate escalation to high-dose L-AMB (10 mg/kg/day). Therapeutic drug monitoring confirmed sustained trough levels above 7 μg/mL despite a 3.5-fold increase in volume of distribution. Serial mNGS quantification demonstrated a logarithmic decline in fungal reads to undetectable levels by day 10, accompanied by radiological resolution and preserved renal function. After 28 days of intravenous therapy, the patient was discharged on oral isavuconazole with no relapse at 6 months. This case establishes that early pathogen identification by mNGS, coupled with aggressive L-AMB dose optimisation under rigorous pharmacokinetic guidance, can achieve cure of pulmonary mucormycosis even in the most pharmacologically hostile environment of ECMO support.},
}
@article {pmid41035666,
year = {2025},
author = {Liu, H and Ding, Z and Xu, L and Guo, T},
title = {Severe Legionella pneumonia mimicking immune-related pneumonitis after chemoimmunotherapy for lung cancer: a case report.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1663978},
pmid = {41035666},
issn = {2234-943X},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have significantly improved survival outcomes and quality of life in patients with various malignancies. Nevertheless, their associated toxicities must not be overlooked. Although not the most common immune-related adverse event (irAE), CIP is recognized as one of the most serious. In particular, grade 3-4 CIP that is not promptly treated may compromise subsequent immunotherapy and can result in respiratory failure or even death. Legionnaires' disease, caused by Legionella pneumophila, is an uncommon but potentially life-threatening form of atypical pneumonia. With the expanding use of ICIs, especially in combination with chemotherapy, early stage CIP and Legionella pneumonia may share similar radiological features, such as ground-glass opacities, which makes early differential diagnosis difficult. However, timely differentiation is critical because the management strategies differ substantially: CIP requires systemic corticosteroids, whereas Legionella pneumonia necessitates quinolone antibiotics. Traditional diagnostic methods for Legionella infection, including culture on specialized media and urine antigen testing, are limited by low sensitivity and the risk of false-negative results. In recent years, targeted next-generation sequencing (tNGS) has emerged as a valuable diagnostic tool. Compared with metagenomic next-generation sequencing (mNGS), tNGS offers a shorter turnaround time, higher sensitivity and specificity, and greater cost-effectiveness. As such, it is becoming increasingly important in the accurate identification of atypical pathogens in pulmonary infections.<br><br>CASE SUMMARY: We report the case of a patient with squamous cell lung cancer who developed severe pneumonia following combined chemotherapy and immunotherapy. The initial working diagnosis was immune checkpoint inhibitor-related pneumonia (ICI-P) complicated by bacterial infection. However, sputum-targeted next-generation sequencing (tNGS) subsequently identified Legionella pneumophila infection. Following the administration of quinolone-sensitive antibiotics, the patient's clinical condition improved markedly, and he was discharged in a stable state. A 70-year-old male farmer with a history of lung cancer, type 2 diabetes, and chronic obstructive pulmonary disease (COPD) was admitted on February 4, 2025,with fever, cough, and dyspnea following chemoimmunotherapy. He had received paclitaxel, cisplatin, and tislelizumab on January 24.Initial tests revealed leukopenia, neutropenia, and chemotherapy-induced myelosuppression. On admission, the patient exhibited hypoxemia, hyponatremia, and elevated inflammatory markers, raising suspicion for ICI-P complicated by bacterial infection. Despite empirical broad-spectrum antibiotics and corticosteroids, his condition deteriorated, requiring transfer to the Respiratory Intensive Care Unit (RICU). On February 13, tNGS of sputum identified Legionella pneumophila, Enterococcus faecium, Epstein-Barr virus (EBV),and Herpesvirus-1 (HSV-1). The high relative abundance of Legionella pneumophila indicated it was the primary pathogen; EBV and HSV-1 were presumed latent. Antimicrobial therapy was adjusted to moxifloxacin, cefepime, and ganciclovir, leading to clinical improvement and resolution of hypoxemia. Follow-up chest CT showed partial resolution of pulmonary infiltrates. The patient was discharged with home oxygen and outpatient follow-up.The patient is currently undergoing regular anti-tumor treatment.<br><br>CONCLUSIONS: In the era of chemoimmunotherapy, the presence of pulmonary ground-glass interstitial lesions should prompt consideration not only of immune checkpoint inhibitor-related pneumonia (ICI-P) but also of infections caused by uncommon pathogens such as Legionella, particularly when there is no significant improvement after corticosteroid therapy. It is necessary to consider applying advanced molecular diagnostic techniques such as targeted next-generation sequencing (tNGS) as early as possible to make a clear diagnosis of the pathogen and guide individualized treatment.},
}
@article {pmid41035224,
year = {2025},
author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y},
title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {5},
pages = {e70054},
doi = {10.1002/jcsm.70054},
pmid = {41035224},
issn = {2190-6009},
support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; },
mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.<br><br>METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.<br><br>RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p&#x2009;=&#x2009;0.0486 and p&#x2009;=&#x2009;0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p&#x2009;=&#x2009;0.0449). JAM-A was significantly upregulated (p&#x2009;<&#x2009;0.0001). Colonic CD206+ M2 macrophages increased, while CD68&#x2009;+&#x2009;M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p&#x2009;=&#x2009;0.0022; PSMB9: p&#x2009;=&#x2009;0.0186) as well as FOXO-1 (p&#x2009;=&#x2009;0.0380) and TNF-&#x3b1; (p&#x2009;=&#x2009;0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p&#x2009;<&#x2009;0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p&#x2009;=&#x2009;0.0338; Complex IV, p&#x2009;=&#x2009;0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p&#x2009;=&#x2009;0.0258; FH p&#x2009;=&#x2009;0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p&#x2009;<&#x2009;0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p&#x2009;=&#x2009;0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGF&#x3b2;: mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0248; mdx vs. FTMmdx+ONX, p&#x2009;=&#x2009;0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0024; mdx vs. FTMmdx+ONX, p&#x2009;<&#x2009;0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p&#x2009;=&#x2009;0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p&#x2009;=&#x2009;0.0327, vcam-1p&#x2009;=&#x2009;0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.<br><br>CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.},
}
@article {pmid41035142,
year = {2025},
author = {Wang, B and Fu, Y and Xu, D and Liu, J and Tian, T and Xie, W},
title = {Successful Management of a Rare Keratitis Caused by Mycobacterium Immunogenum After a Series of Misdiagnoses.},
journal = {Eye &amp; contact lens},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICL.0000000000001228},
pmid = {41035142},
issn = {1542-233X},
abstract = {This case report presents the successful diagnosis and management of a rare case of Mycobacterium immunogenum keratitis. A 34-year-old immunocompetent female presented with a 6-month history of recurrent right eye redness and blurred vision. Previous treatment at other hospitals with oral antivirals, topical corticosteroids, and ganciclovir ointment for presumed herpetic keratitis had failed, with progressive vision decline from 20/20 to 20/50. The causative pathogen identification revealed Mycobacterium immunogenum through comprehensive diagnostic workup including microbiological culture, acid-fast staining, and metagenomic next-generation sequencing (mNGS). Initial therapy with topical amikacin proved ineffective and caused significant ocular toxicity, whereas adjunctive oral azithromycin showed no clinical benefit. Subsequent treatment with 0.3% gatifloxacin eye gel resulted in dramatic improvement. During the healing phase, 0.02% fluorometholone was added to control scarring. Complete resolution was achieved within 4 months, with only mild residual scarring and final uncorrected visual acuity of 20/30. The patient remained recurrence-free throughout 4 years of follow-up. This case demonstrates that Mycobacterium immunogenum keratitis does not necessarily occur in immunocompromised individuals or those with a history of trauma or surgery. It is easily misdiagnosed in the early stages, whereas mNGS can aid in pathogen identification. Treatment with 0.3% gatifloxacin eye gel suggests potentially superior efficacy and safety in such condition.},
}
@article {pmid41034963,
year = {2025},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {199},
pmid = {41034963},
issn = {2049-2618},
support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.<br><br>RESULTS: In relation to urine sample volume,&#x2009;&#x2265;&#x2009;3.0&#xa0;mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.<br><br>CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.},
}
@article {pmid41034825,
year = {2025},
author = {Chen, Y and Bai, Y and Li, M and Gan, X and Wang, Y and Zhou, Y and Niu, T},
title = {Machine learning model for differentiating Pneumocystis jirovecii pneumonia from colonization and analyzing mortality risk in non-HIV patients using BALF metagenomic sequencing.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1222},
pmid = {41034825},
issn = {1471-2334},
support = {No. ZYJC21007//1.3.5 Project for Disciplines of Excellence/ ; No. GYYX24003//1.3.5 Project of High Altitude Medicine/ ; No. ZYAI24039//1.3.5 Project for Artificial Intelligence/ ; No. 2023YFS0031//West China Hospital, Sichuan University , Key Research and Development Program of Sichuan Province/ ; No. 82370192, U24A20680//National Natural Science Foundation of China/ ; No. 2022YFC2502600, 2022YFC2502603//West China Hospital, Sichuan University, National Key Research and Development Program of China/ ; },
}
@article {pmid41034705,
year = {2025},
author = {Bruscadin, JJ and Cardoso, TF and Conteville, LC and da Silva, JV and Ibelli, AMG and Pena, GAC and Porto, T and de Oliveira, PSN and Andrade, BGN and Zerlotini, A and Regitano, LCA},
title = {HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {236},
pmid = {41034705},
issn = {1471-2105},
support = {2022/06281-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/04089-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/04089-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 456191/2014-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*MicroRNAs/metabolism/genetics ; Binding Sites ; *Software ; Humans ; Animals ; *Computational Biology/methods ; Cattle ; *Genome, Microbial ; *Genome, Bacterial ; },
abstract = {BACKGROUND: Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software.<br><br>RESULTS: In this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species.<br><br>CONCLUSIONS: HolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA .},
}
@article {pmid41029837,
year = {2025},
author = {Cabrera, C and Carrión, N and Mateo, D and Vicens, P and Pinzón, A and Heredia, L and Forcadell-Ferreres, E and Pino, M and Yerga, B and Zaragoza, J and Vicente-Pascual, M and Moral, A and Arco, T and Arjó, M and Martínez, E and Galvez, S and Lozano, MJ and Torrente, M},
title = {Gut microbiota characterization in ageing, mild cognitive impairment, and Alzheimer's disease in the context of mediterranean lifestyle in a Spanish population.},
journal = {Alzheimer's research &amp; therapy},
volume = {17},
number = {1},
pages = {211},
pmid = {41029837},
issn = {1758-9193},
support = {PID2019-103888RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-103888RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; },
abstract = {BACKGROUND: Alzheimer’s disease (AD) is a neurodegenerative disorder often preceded by a prodromal stage of Mild Cognitive Impairment (MCI). Previous research suggests that gut microbiota (GMB) dysbiosis may contribute to cognitive decline via the microbiota-gut-brain axis (MGBA). Notably, GMB composition patterns can vary across populations and stages of dementia. This study aimed to characterize the GMB in a cohort of older adults from Tarragona (Spain) diagnosed with AD or MCI, or presenting a healthy cognitive status (HC), all of whom follow a Mediterranean lifestyle (ML).<br><br>METHODS: The present cross-sectional, multicenter case&#x2013;control study analyzed fecal samples from 99 individuals,including 31 with AD, 30 with MCI, and 38 HC,aged 60&#x2013;85 years, recruited from seven hospitals and specialized cognitive centers in the province of Tarragona, Spain. Shotgun metagenomic sequencing was conducted with taxonomic profiling using Kraken2. APOE genotyping was performed from fecal DNA using TaqMan assays. Richness, alpha and beta diversity, differential abundance, multivariate linear modeling, and Jonckheere&#x2013;Terpstra trend tests were conducted to identify GMB species signatures associated with MCI and AD.<br><br>RESULTS: Richness, alpha and beta diversity did not differ across groups. Differential abundance analysis identified 109 taxa, of which ten microbial species were shared across comparisons. Notably, several species, including Coprococcus comes and Odoribacter splanchnicus, emerged as replicable candidates, showing both discriminatory value and severity-related declines, alongside taxa with context-dependent or adverse associations.<br><br>CONCLUSIONS: Overall GMB diversity did not differ across cognitive groups, but specific taxa, particularly short-chain fatty acid producers, showed consistent associations with cognitive decline in this ML cohort. These findings support a role for the GMB in AD pathology and suggest that targeting key microbial species may provide novel avenues for prevention and intervention.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01862-z.},
}
@article {pmid41001489,
year = {2025},
author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Cregeen, SJJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW},
title = {Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41001489},
abstract = {BACKGROUND: Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exists in the realm of wastewater-based viral epidemiology (WBE) of cancer-causing viruses, with existing studies using targeted approaches (i.e PCR-based approaches) which lack scalability. Our study aims to carry out WBE with hybrid-capture probes to detect and track multiple oncogenic viruses simultaneously in wastewater across Texas, USA, overcoming the drawbacks associated with targeted approaches.<br><br>METHODS: Here, we used a hybrid-capture approach to detect, filter and sequence oncogenic virus signals from wastewater samples collected over a duration of three years, from May 2022 to May 2025. Once viral reads were sequenced, we utilized established computational tools to characterize reads into their respective virus of origin. Next, viral abundances of each characterized oncogenic virus were tracked over time and read coverage across their genomes was measured using read mapping techniques.<br><br>FINDINGS: We detected six known oncogenic viruses, along with three suspected oncogenic viruses across all sampling locations within Texas. Over three years, viral abundance gradually increased, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as HPV and EBV rose sharply, with increases in abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using a hybrid-capture technique for almost all oncogenic viruses and their types.<br><br>INTERPRETATIONS: Our study shows that a hybrid-capture method can efficiently overcome the challenges faced with using targeted approaches for WBE. Using this method, we get broader read coverage, coupled with concurrent and consistent real-time tracking dynamics of multiple oncogenic viruses. Our findings also emphasize the persistent circulation and rising prevalence of high-risk cancer-causing viruses, underscoring the need for sustained public health interventions to protect communities and assess viral prevalence in high-risk populations.<br><br>FUNDING: This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), the Baylor College of Medicine and the Alkek Foundation Seed Funds.},
}
@article {pmid41000896,
year = {2025},
author = {Dillard, BA and Sanders, JG and Husain, AP and Yule, KM and Moeller, AH},
title = {Isolation by distance promotes strain diversification in the wild mouse gut microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000896},
issn = {2692-8205},
abstract = {Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.},
}
@article {pmid41033729,
year = {2025},
author = {Chan, CSY and Georgakopoulos-Soares, I},
title = {From nonexistence to novel applications: Nullomers and related k-mer based concepts in bioinformatics.},
journal = {Advances in clinical chemistry},
volume = {129},
number = {},
pages = {191-206},
doi = {10.1016/bs.acc.2025.06.009},
pmid = {41033729},
issn = {2162-9471},
mesh = {*Computational Biology/methods ; Humans ; Genomics ; Proteomics ; Neoplasms/diagnosis/genetics ; },
abstract = {Underrepresented k-mer sequences, provide insights into evolutionary constraints, molecular mechanisms, and organismal fitness. Analysis of these sequences have broad applications across genomics and proteomics, such as in biomarker development, cancer diagnostics, phylogenetic analysis, synthetic biology and novel drug discovery. Absent sequences (nullomers and neomers) show promise for cancer detection and tissue-of-origin identification using nucleic acids derived from liquid biopsies, while quasi-primes serve as genomic fingerprints that offer potential for evolutionary studies for understanding trait evolution, and in metagenomics, as biomarkers of organismal presence. The chapter also discusses computational challenges associated with analyzing absent sequences and highlights available k-mer based resources and databases. With the continuous expansion of genomic and proteomic data, absent sequences present an innovative framework for addressing fundamental biological questions and advancing applications in basic and translational research.},
}
@article {pmid41033716,
year = {2025},
author = {Garima, and Dhanawat, M and Wilson, K and Chaubey, P},
title = {High-throughput sequencing technologies for cancer genomics.},
journal = {Methods in cell biology},
volume = {198},
number = {},
pages = {103-133},
doi = {10.1016/bs.mcb.2025.02.018},
pmid = {41033716},
issn = {0091-679X},
mesh = {Humans ; *Neoplasms/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Genome, Human ; Transcriptome ; },
abstract = {In investigations about transcriptomics, epigenomics, and genomics, high-throughput sequencing technologies have become indispensable. Several hundred million of DNA molecules may be sequenced at once thanks to high throughput sequencing (HTS) technologies, which can simultaneously analyze many DNA molecules. Traditionally, sequencing information has been clarified utilizing a low throughput technique known as Sanger sequencing. This added value makes it feasible to employ HTS to generate tremendous amounts of data, which enhances the comprehension of the transcriptome and genetic fingerprints of cells during various stages of evolution and pathology. By identifying somatic changes, morphological deviations, and repetitive changes across the human genome, techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) provide information about cancer formation as well as prospective therapies. Identifying tumor biology and discovering biomarkers rely on the examination of aberrant networks and variations in gene expression that RNA DNA sequencing, or RNA-Seq, offers. By identifying rare cell kinds and their function in carcinogenesis, the sequencing of one cell offers illumination on the wide range of cells observed across tumors. Metagenomics and chromatin immunoprecipitation sequencing (ChIP-Seq) delivers essential knowledge by discovering alterations that affect the epigenetic configuration and the microenvironment that accompanies tumors. Integrating these recent developments will allow the development of personalized treatments that use unique genetic traits to determine every cancer patient, offering more individualized treatments. The revolutionary implications of high-throughput genome sequencing for cancer research and treatment are addressed in this book chapter, particularly concerning cancer precision as well as effective treatment outcomes.},
}
@article {pmid41033677,
year = {2025},
author = {Ilbağı, H and Kanakala, S and Masonbrink, R and Lozier, Z and Miller, WA},
title = {Metagenomic Sequencing of Maize Reveals Abundant Genomic RNA of a Comovirus, a Genus Previously Known to Infect Only Dicots.},
journal = {The plant pathology journal},
volume = {41},
number = {5},
pages = {656-670},
doi = {10.5423/PPJ.OA.06.2025.0077},
pmid = {41033677},
issn = {1598-2254},
support = {//The Scientific and Technological Research Council of Turkey/ ; NKUBAP.03.GA.21.289//Tekirda&#x11f; Nam&#x131;k Kemal University/ ; 4308//The Iowa Agriculture and Home Economics Experiment Station, Ames, IA/ ; //The Iowa State University Plant Sciences Institute/ ; //DARPA Insect Allies Program/ ; },
abstract = {To better understand the diversity of viral pathogens in Türkiye, a major exporter of cereals in Europe, we performed high-throughput sequencing of total RNA from maize plants collected in the Trakya region. Certain maize plants exhibiting mosaic and mottle symptoms, gathered from Tekirdağ province in Trakya, yielded large numbers of reads corresponding to the genome of a divergent strain of a comovirus, which corresponds to turnip ringspot virus (TuRSV), a recognized species of the genus Comovirus. This finding is unexpected because all known comoviruses infect only dicotyledonous species, and the known host range of TuRSV has been limited to plants in the Brassicaceae family. The nearly complete and partial nucleotide sequences of the bipartite genome of the maize isolate, as named TuRSVTR59, consist of 6,027 nt TuRSV-TR59 RNA1 and 3,920 nt TuRSV-TR59 RNA2, excluding poly (A) tails. RNA1 and RNA2 each encode a single ORF of 1,860 and 1,096 codons, respectively. Phylogenetic analysis demonstrated that TuRSV-TR59 from Türkiye clustered with other TuRSV isolates from diverse hosts and regions, showing highest identity to isolates from Germany, Czech Republic, and Croatia (80.56-77.77% and 92.09-90.50% nucleotide and amino acid sequence identities, respectively). The ability of TuRSV-TR59 isolate to infect maize was confirmed by reverse transcription polymerase chain reaction. Surveys in the Tekirdağ province of Türkiye, done in 2022-2025, revealed that 2 out of 145 maize samples (1.38%) and 8 out of 116 canola samples (6.89%) were found infected with TuRSV. This is the first report of a comovirus in maize from a monocotyledonous plant species.},
}
@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}
@article {pmid41033498,
year = {2025},
author = {Saejung, C and Akkahat, S},
title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133411},
doi = {10.1016/j.biortech.2025.133411},
pmid = {41033498},
issn = {1873-2976},
abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.},
}
@article {pmid41033373,
year = {2025},
author = {Yarim, D and Abay, S},
title = {First Comprehensive Genome Analysis and Antimicrobial Resistance Profile of Clostridium innocuum from a Domestic Cat.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108076},
doi = {10.1016/j.micpath.2025.108076},
pmid = {41033373},
issn = {1096-1208},
abstract = {This study aimed to investigate the molecular and phenotypic properties of a C. innocuum isolate from a healthy cat, which was previously misidentified as C. difficile by molecular testing (tpi-PCR). To resolve the misidentification and obtain more information on the isolate at the genetic level, whole genome sequencing (WGS) on the long-read sequencing platform Oxford Nanopore PromethION was performed. WGS data were analysed to identify virulence factors, antibiotic resistance, and hypothetical prophage genes. The isolate was identified as C. innocuum as a result of WGS. While several virulence genes, including pilM, yabQ, HrcA, and CptIN family toxins, were detected, toxin-coding genes in other Clostridium species were not detected. Four prophage regions were detected; three appeared as intact phage sites, while one was incomplete. The isolate was susceptible to ampicillin, clindamycin, vancomycin, and metronidazole but was resistant to meropenem using the E-test method. The genome also contained resistance genes such as tet(M), aph(2'')-Ia, and VanT, VanW, VanY, VanG, and VanZ. Genetic similarities between our isolate and those obtained from global human-derived metagenome-associated genomes (MAGs) and non-MAG genomes from healthy humans and animals were illustrated through WGS-SNP-based phylogenetic analyses. This study provides insights into the phenotypic and genotypic characteristics of C. innocuum, an emerging pathogen. Taken together, the isolation of this agent-possessing intrinsic resistance mechanisms and emerging after the treatment of C. difficile infections from a domestic cat highlights its potential threat to public health. Nevertheless, many clinical questions remain unanswered, underscoring the need for further research to deepen our understanding of this pathogen and to develop effective control and treatment strategies.},
}
@article {pmid41033148,
year = {2025},
author = {Luo, L and Wong, JWC and Yan, B and Xu, S and Rabaey, K},
title = {Mechanistic insights into fermentative pathway control during solid-state food waste acidogenesis under autogenic pressure.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124679},
doi = {10.1016/j.watres.2025.124679},
pmid = {41033148},
issn = {1879-2448},
abstract = {The efficiency of two-phase anaerobic digestion hinges on the acidogenic phase, where acidogenic off-gas generates autogenic pressure that alters the physicochemical environment and may affect microbial activity, pathways, and intermediates. However, its mechanistic role under solid-state conditions remains unclear. To address this knowledge gaps, we investigated the effects of autogenic pressure on solid-state food waste acidogenesis, focusing on soluble microbial product (SMP) formation and the associated metabolic responses at the molecular level. Autogenic pressure enhanced acidogenic decomposition, increasing SMP yields from 365.3 ± 10.5 g COD/kg VSadded to 407.1 ± 7.3 g COD/kg VSadded. It initially promoted lactate production, followed by enhanced conversion of lactate to butyrate and acetate functioning by Megasphaera. Metagenomic and metabolite analyses revealed that autogenic pressure increased the abundance of functional genes associated with homoacetogenesis and butyrate synthesis. Incubation experiments further confirmed that acetate, stimulated by autogenic pressure, played a key role in driving the reverse β-oxidation pathway while suppressing the acrylate pathway during lactate conversion. As a result, butyrate production increased by 25 %, while propionate decreased by 43 %. These findings provide new insights into how SMP-producing microbial communities respond to autogenic pressure and demonstrate the potential of self-regulation to enhance product yield and process controllability. This strategy advances sustainable solid waste management and promotes the development of circular bioeconomy.},
}
@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}
@article {pmid41032855,
year = {2025},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M},
title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01564},
pmid = {41032855},
issn = {1520-5851},
abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.},
}
@article {pmid41032194,
year = {2025},
author = {Naderian, R and Alibabaei, F and Paraandavaji, E and Dehghan, P and Eslami, M},
title = {Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41032194},
issn = {1867-1314},
abstract = {The diversified ecology of microorganisms, including bacteria, archaea, fungi, protozoa, and viruses known collectively as the gut microbiota, which includes bacteriophages, is crucial to human health because it affects functions like immune system regulation, vitamin production, and pathogen protection. Bacteriophages are viruses that infect bacteria and are increasingly recognized as a viable treatment option for antibiotic-resistant strains, owing to their high host specificity, which enables precise targeting of drug-resistant bacteria while sparing commensal microbiota. The complex relationships between bacteriophages and gut microbiota are examined, with emphasis on their roles in maintaining health and contributing to disease. Gut microbiota homeostasis is influenced by a number of factors, including age, nutrition, and drugs. Bacteriophages, via lytic cycles and lysogenic conversion, influence the gut microbiota composition and microbial community structure. Gaining an understanding of these processes is crucial to appreciating their contribution to the stability and variety of microbes. Recent research highlights the gut phageome's potential for therapeutic interventions by demonstrating its substantial influence on immunological responses and metabolic problems. The study of phage-microbiota interactions has been transformed by cutting-edge technologies, including high-throughput sequencing, CRISPR-Cas systems, and viral metagenomics, which allow for thorough research and the creation of new therapeutics. Even though tailored medicine and pathogen management hold great potential, obstacles such as regulatory difficulties and bacterial resistance call for additional investigation. Phage-based therapeutic strategies are rapidly advancing, ranging from genetically engineered phages and phages with modified capsid proteins designed to enhance efficacy to phage cocktails that target multiple bacterial strains.},
}
@article {pmid41031628,
year = {2025},
author = {Yu, D and Kang, Y and Lu, W and Chen, B},
title = {Progress in diagnosis and treatment of primary spondylodiscitis: a systematic literature review.},
journal = {EFORT open reviews},
volume = {10},
number = {10},
pages = {815-828},
doi = {10.1530/EOR-2025-0041},
pmid = {41031628},
issn = {2058-5241},
abstract = {OBJECTIVE: Primary spondylodiscitis poses significant diagnostic and therapeutic challenges, with delayed diagnosis or improper treatment potentially resulting in severe complications. This systematic review aimed to summarize the latest diagnostic and therapeutic approaches for primary spondylodiscitis.<br><br>METHODS: Adhering to PRISMA 2020 guidelines, we conducted a systematic literature review. PubMed was comprehensively searched for English-language original studies from January 1, 1990, to October 31, 2024. Structured queries combined keywords and MeSH terms relevant to spondylodiscitis, vertebral osteomyelitis, spinal infection, and associated treatments. Two reviewers independently screened titles, abstracts, and full texts, with manual bibliography searches as a supplement. A total of 147 articles were finally included.<br><br>RESULTS: The literature indicates that diagnosis can be based on clinical suspicion, using serological, radiological, and microbiological tests. Newer methods such as metagenomics next-generation sequencing (mNGS) and positron emission tomography-computed tomography (PET-CT) can enhance diagnostic sensitivity and specificity. For confirmed cases, appropriate antibiotic therapy is crucial. Surgical treatment can benefit patients with neurological deficits, sepsis, spinal instability/deformity, epidural abscesses, or failed conservative treatment, accelerating recovery and reducing complications. Minimally invasive surgical approaches may also serve as an alternative to open surgery for select patients.<br><br>CONCLUSION: Although new technologies have improved diagnostic accuracy and treatment success rates for primary spondylodiscitis, establishing a robust staging system is vital to ensure patients receive effective, evidence-based treatment options.},
}
@article {pmid41031110,
year = {2025},
author = {Slunečko, J and Kogoj, R and Zakotnik, S and Suljič, A and Knap, N and Bosilj, M and Strle, F and Avšič-Županc, T and Bogovič, P and Korva, M},
title = {Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1667422},
pmid = {41031110},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Fever ; *Bacteria/genetics/isolation &amp; purification/classification ; *Blood/microbiology/virology ; Computational Biology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Female ; Male ; },
abstract = {INTRODUCTION: Blood culture is the cornerstone of microbiological diagnostics for patients with acute undifferentiated fever and no obvious localization of infection; however, up to 50% of cases remain undiagnosed. Infections caused by arboviruses, fastidious or even uncultivable bacteria, or parasites often go undiagnosed without the use of target-specific molecular methods. These are typically performed in a stepwise manner, increasing cost and delaying results. Metagenomic next-generation sequencing (mNGS) has recently gained recognition as a potential universal pathogen detection tool for such cases. Our study aimed to develop a streamlined mNGS workflow for simultaneous detection of intracellular and cell-free pathogens within a single sequencing library.<br><br>METHODS: Total nucleic acid was isolated separately from 200 EDTA blood samples. The plasma isolate was processed with DNase, followed by the depletion of host ribosomal and messenger RNA, reverse transcription, and sequence-independent single primer amplification (SISPA). The whole blood isolate was only reverse transcribed, with no other pre-processing manipulation. Finally, the two fractions were combined prior to library preparation and sequencing using either Oxford Nanopore Technologies or Illumina. Following established bioinformatics analysis, we developed a mathematical ranking approach (ClinSeq score) that enabled quick identification of relevant pathogens in approximately one hour.<br><br>RESULTS: The mNGS workflow reached 79.5% (159/200) overall sensitivity. For bacteria the sensitivity was 88.6% (70/79), DNA viruses, 66.7% (10/15) and for RNA viruses 73.8% (76/103). Pathogen detections by individual sequencing methods showed overall sensitivity of Illumina and ONT to be 80.0% (76/95) and 79.1% (83/105) respectively. The ClinSeq score correctly highlighted the pathogen in 126/200 (63.0%) samples effectively with a Cohen's kappa (&#x3ba;) agreement of 0.61 with manual analysis.<br><br>CONCLUSION: Developed comprehensive mNGS workflow detects a wide range of pathogens in patients with acute undifferentiated fever. The unified workflow improves sensitivity for intracellular bacteria and RNA viruses, reduces time, cost and complexity by eliminating the need for separate library preparations, enabling faster turnaround suitable for clinical settings. The ClinSeq score effectively differentiates true pathogen signals from background noise, reducing false positives and manual interpretation time. Overall, the workflow demonstrates flexible, and efficient pathogen detection, supporting its potential for clinical diagnostics and improved patient management.},
}
@article {pmid41031025,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.23.595633},
pmid = {41031025},
issn = {2692-8205},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.},
}
@article {pmid41030903,
year = {2025},
author = {Li, Y and Jiang, X and Ji, J and Yao, B and Zhao, F and Zhang, J and Yu, Y and Fu, Y},
title = {Case report: Laboratory diagnosis methods on brain abscess pathogens caused by anaerobic species and Streptococci constellatus.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02373},
pmid = {41030903},
issn = {2214-2509},
abstract = {Brain abscess (BA) represents a severe, intracranial infection associated with high morbidity and mortality. Multiple pathogens may contribute to BA development, some of which are difficult to detect using conventional diagnostic methods alone. With the wide utilization of metagenomic next-generation sequencing (mNGS), more experiences are concluded in authenticity practice except for being regarded as a comprehensive method for detecting all pathogens. Here, we report a severe case of BA in a patient diagnosed by CT imaging, who subsequently underwent surgical removal of the abscess. To identify the causative pathogen and support anti-infection treatment, Gram staining, culture, and mNGS were performed on the abscess specimen. Interesting, we found the results were discordant: the Streptococcus constellatus was identified by culture, whereas mNGS predominantly detected anaerobic bacteria. Following additional human DNA removal, sequencing detected S. constellatus in the specimen as well. In conclusion, we highlight that a combined diagnostic strategy, leveraging both conventional culture and mNGS, is critical for comprehensive pathogen identification and informed clinical decision-making in BA.},
}
@article {pmid41030838,
year = {2025},
author = {Maqsood, S and Arshad, MT and Ikram, A and Al-Aoh, HA and Gnedeka, KT},
title = {Foodomics in Diabetes Management: A New Approach.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {10},
pages = {e71021},
pmid = {41030838},
issn = {2048-7177},
abstract = {Critical information regarding the interactions among food components, human metabolism, and disease is contained in foodomics, an interdisciplinary field that bridges food science with contemporary omics technologies (genomics, proteomics, metabolomics, and lipidomics). In order to gain a better understanding of the metabolic dysregulation in type 2 diabetes mellitus (T2DM), foodomics examines bioactive compounds derived from food (e.g., polyphenols, fibers, and lipids) alongside host molecular responses. For the enhancement of glycemic control and the prevention of diabetes-related complications, the current study is concerned with how foodomics enables personalized dietary interventions that are aligned with one's metabolic and genetic characteristics. We investigate deeper into the role of the gut microbiota in T2DM progress and how foodomics-informed methodologies, such as metabolomics and metagenomics, can be functional to discover treatments intended at the microbiota. In addition, we discover the prospective that functional foods enriched with bioactive elements, comprising β-glucans and flavonoids, may influence metabolic processes in diabetes. In addition, foodomics improves food safety by recognizing conceivable diabetes-causing contaminants (endocrine disruptors). Foodomics has incredible potential for improving precision nutrition in the prevention and treatment of T2DM, though experiments in data integration and standardization are present. Through the integration of dietary concepts, molecular biology, and clinical consequences, this method offers revolutionary strategies towards metabolic wellness.},
}
@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}
@article {pmid41030552,
year = {2025},
author = {Zhang, B and Yang, T and Cheng, C and Li, T and Zhang, N and Wang, F and Chen, W and Zhong, Z and Liu, Z and Gu, G and Lin, X and Xie, X},
title = {Multi-omics analysis reveals the alleviating effect of oxidation remediation on tobacco quinclorac stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625585},
pmid = {41030552},
issn = {1664-302X},
abstract = {The extensive use of the herbicide quinclorac has led to significant residues in agricultural soil, posing adverse effects on crop safety and high-quality production. In this study, using the tobacco variety CB-1 as material, we found that oxidizing agent K2S2O8 can significantly reduce quinclorac-induced phytotoxicity symptoms in tobacco. Furthermore, we integrated biochemical methods, metagenomics, metabolomics, and transcriptomics to investigate the effects of K2S2O8 on both quinclorac-contaminated soil and tobacco plants. Soil physicochemical properties analysis showed that the incorporation of K2S2O8-based remediation significantly mitigated the negative effects of quinclorac and largely restored the soil properties affected by quinclorac stress. Metagenomic analysis found that quinclorac significantly reduced soil species diversity, while K2S2O8-based remediation soil exhibited higher richness of microbial communities, with increased abundance of Sphingomonas and Bradyrhizobium, and decreased abundance of Alphaproteobacteria. Differential gene expression analysis showed significant up-regulation and down-regulation of genes under C10H5Cl2NO2 stress, which was partially mitigated by K2S2O8 treatment. Gene Ontology (GO) enrichment analysis indicated that these genes were mainly involved in cellular processes, metabolic pathways, and biological regulation. Metabolomic analysis further confirmed significant changes in metabolite profiles, with K2S2O8 treatment restoring many metabolites to near control levels. Integrated metabolomic-transcriptomic analysis revealed enrichment of differentially expressed genes (DEGs) and metabolites in six key pathways: (1) lysine degradation, (2) stilbenoid diarylheptanoid and gingerol biosynthesis, (3) arginine and proline metabolism, (4) phenylalanine biosynthesis, (5) tyrosine metabolism, and (6) flavonoid biosynthesis. Additionally, the levels of 4-hydroxyphenylacetylglutamic and 5-aminovaleric acid were down-regulated, along with the expression of genes associated with these metabolites, when quinclorac residual soil was treated by K2SO8. The results of this study provide a theoretical basis for the remediation of pesticide residue soil in rice tobacco rotation areas, offering valuable insights for sustainable agricultural practices.},
}
@article {pmid41030387,
year = {2025},
author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X},
title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101200},
pmid = {41030387},
issn = {2665-9271},
abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.},
}
@article {pmid41030376,
year = {2025},
author = {Aldeguer-Riquelme, B and Rodriguez-R, LM and Konstantinidis, KT},
title = {Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf140},
pmid = {41030376},
issn = {2730-6151},
abstract = {The importance of rarefying ecological or amplicon sequencing data to a standardized level of diversity coverage for reliable diversity comparisons across samples is well recognized. However, the importance of diversity coverage, i.e. the fraction of the genomic diversity of a sample sequenced, in comparative shotgun metagenomic studies remains frequently overlooked. Using both in silico and natural metagenomes from a wide range of environments, we demonstrate that uneven metagenome coverage can result in misleading biological conclusions, particularly for identifying differentially abundant features, i.e. groups of genes or genomes assigned to the same protein family or taxonomic rank, respectively, and for comparing diversity between samples. The main underlying cause is that not all members of a feature may be detectable, and thus counted, across such unevenly covered metagenomes depending on the sequencing effort applied and the underlying member-abundance curves. Unfortunately, 99.5% of previous comparative metagenomic studies have overlooked this metric, suggesting that their reported results might be misleading. We show that achieving high Nonpareil coverage (≥0.9), a metric that estimates metagenome diversity coverage, is the most reliable strategy to mitigate this issue. When high Nonpareil coverage is not achievable, such as for highly diverse and complex samples like soils, we show that standardizing (or subsampling) metagenomic datasets to the same Nonpareil coverage, rather than sequencing effort, prior to comparative analysis provides for more accurate results. We provide a set of practical recommendations and the corresponding Python scripts to help researchers to assess and standardize metagenome diversity coverage for their comparative analyses.},
}
@article {pmid41030375,
year = {2025},
author = {Sheridan, PO and Meng, Y and Bodington, D and Coutts, D and Williams, TA and Gubry-Rangin, C},
title = {Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf152},
pmid = {41030375},
issn = {2730-6151},
abstract = {Genome reconstruction from metagenomic samples has dramatically increased our understanding of uncultivated lineages of life. However, untargeted metagenomic sequencing is biased towards the more abundant microbes, neglecting less abundant lineages playing important ecological roles, such as the ammonia-oxidising archaea. Here, we demonstrate that separating soil molecular DNA using a bisbenzimide-CsCl guanine-cytosine (GC)-content-based DNA fractionation approach separates microbial DNA along a GC-content gradient. The fractions from both extremes of the GC-content gradient possess different 16S rRNA gene composition than the original unfractionated DNA. The high diversity in the lower GC-content fractions (< 45%) contrasts with the higher DNA abundance in the higher GC-content fractions (50%-70%), highlighting the low GC fractions as an enriched source of rare microbe DNA. Metagenomic sequencing of specific low- and high-GC fractions enabled the reconstruction of 204 taxonomically diverse metagenome-assembled genomes from 31 microbial phyla, with at least 63 of these originating from rare (< 0.1% relative abundance) or very rare (< 0.01% relative abundance) microbial families. Therefore, this approach facilitates genomic assembly of rare taxa in resulting pseudo-communities. Ultimately, this technique enables a semi-targeted metagenomic approach to recover genomes from low-abundance microbes with GC-contents that differ significantly from the environmental microbial community of interest. As mounting evidence suggests that rare microbes drive critical ecosystem functions, this approach will facilitate a deeper understanding of their metabolic potential in the environment.},
}
@article {pmid41029845,
year = {2025},
author = {Rey-Velasco, X and Auladell, A and Deulofeu-Capo, O and Lundin, D and Pinhassi, J and Ferrera, I and Sánchez, O and Gasol, JM},
title = {Decoding the genetic drivers of marine bacterial blooms through comparative genomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {198},
pmid = {41029845},
issn = {2049-2618},
support = {PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; FPU20/01625//Ministerio de Universidades/ ; },
mesh = {*Bacteria/genetics/classification/growth &amp; development/isolation &amp; purification ; *Genome, Bacterial ; *Seawater/microbiology ; *Genomics/methods ; *Microbiota/genetics ; Phytoplankton ; Metagenome ; Eutrophication ; Metagenomics/methods ; },
abstract = {BACKGROUND: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.<br><br>RESULTS: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.<br><br>CONCLUSIONS: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.},
}
@article {pmid41029787,
year = {2025},
author = {Lemieux, &#xc9; and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, &#xc9; and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.<br><br>RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both &#x3b1;- and &#x3b2;-diversity between sample types (digesta, feces) than between treatments. &#x3b2;-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. &#x3b2;-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}
@article {pmid41029310,
year = {2025},
author = {Huang, J and Dong, T and Yang, C},
title = {Diagnosis of pleural aspergillosis caused by Aspergillus infection via metagenomic next-generation sequencing from a patient with unexplained pleural effusion: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {434},
pmid = {41029310},
issn = {1471-2466},
mesh = {Humans ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; *Pleural Effusion/microbiology ; *Aspergillus fumigatus/genetics/isolation &amp; purification ; Metagenomics ; *Aspergillosis/diagnosis/drug therapy/microbiology/complications ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; },
abstract = {Pleural aspergillosis is a severe pathological condition triggered by Aspergillus species and commonly affects immunocompromised individuals. This case report describes a 63-year-old man with normal immune function who was admitted to the hospital due to a 20-day history of right-sided chest pain and cough. He was diagnosed with an infection-related pleural effusion of unknown origin. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus in the pleural effusion intrapleurally, and pathological examination revealed granulomatous inflammation. The patient received three months of antifungal treatment with voriconazole tablets. A six-month follow-up examination showed complete resolution of both pleural and pulmonary abnormalities. This case highlights the utility of mNGS as a diagnostic tool for detecting clinical fungal pathogens with atypical features, thereby improving diagnostic accuracy and therapeutic strategies for such conditions.},
}
@article {pmid41029068,
year = {2025},
author = {Gao, J and Lao, C and Chen, J},
title = {Chlamydia psittacosis infection complicating cerebral infarction: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {39},
pages = {e44854},
doi = {10.1097/MD.0000000000044854},
pmid = {41029068},
issn = {1536-5964},
support = {No.2024ZL175//Chinese Medical Science and Technology Project of Zhejiang Province/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Cerebral Infarction/etiology/complications/therapy/microbiology ; *Psittacosis/complications/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Chlamydophila psittaci/isolation &amp; purification ; },
abstract = {RATIONALE: Chlamydia psittaci (CP) pneumonia is a rare zoonosis. Severe infection predisposes patients to thrombotic complications; however, only 2 documented cases of delayed cerebral infarction occurring during anticoagulant therapy exist in the literature.<br><br>PATIENT CONCERNS: A 60-year-old female with a history of hypertension and a concealed history of avian exposure presented with fever, chest tightness, and dyspnea. Examination revealed severe hypoxemia (PaO2 46.8&#x2005;mm&#x2005;Hg), systemic inflammation (C-reactive protein 343.65&#x2005;mg/L), and multi-organ dysfunction.<br><br>DIAGNOSES: CP pneumonia; cerebral infarction.<br><br>INTERVENTIONS: Following definitive diagnosis via metagenomic next-generation sequencing of bronchoalveolar lavage fluid, targeted antimicrobial therapy with omadacycline (100&#x2005;mg daily) and moxifloxacin (400&#x2005;mg daily) was initiated immediately. Concurrent interventions included mechanical ventilation and prophylactic anticoagulation with enoxaparin (5000&#x2005;IU daily). Upon development of an acute cerebral infarction, the antithrombotic strategy was modified: anticoagulation was discontinued and dual antiplatelet therapy (aspirin 100&#x2005;mg/d&#x2005;+&#x2005;clopidogrel 75&#x2005;mg/d) was commenced, alongside early rehabilitation in a dedicated stroke unit.<br><br>OUTCOMES: By day 5 of antimicrobial therapy, inflammatory markers decreased significantly and oxygenation improved. Neurological function showed partial recovery by day 14 postinfarction (National Institutes of Health Stroke Scale score reduced from 8 to 3), enabling successful weaning from ventilation and hospital discharge.<br><br>LESSONS: Active screening for avian contact history and early application of metagenomic next-generation sequencing should be considered in patients with severe pneumonia. CP infection can trigger immunothrombosis, warranting vigilance for delayed stroke even during anticoagulation. Multidisciplinary management is crucial for optimizing outcomes in infection-associated cerebral infarction.},
}
@article {pmid41029053,
year = {2025},
author = {Wang, CC and Chen, Y and Li, MJ and Xie, B and Shan, Q and Guo, H and Huang, QC and Guo, BM},
title = {Acute fibrinous and organizing pneumonia presents as right lung upper lobe cavitary lesion: Case report and literature review.},
journal = {Medicine},
volume = {104},
number = {39},
pages = {e44915},
doi = {10.1097/MD.0000000000044915},
pmid = {41029053},
issn = {1536-5964},
mesh = {Humans ; Male ; Middle Aged ; Tomography, X-Ray Computed/methods ; Diagnosis, Differential ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/diagnostic imaging ; *Lung/pathology/diagnostic imaging ; *Pneumonia/diagnosis/drug therapy ; Methylprednisolone/therapeutic use/administration &amp; dosage ; Organizing Pneumonia ; },
abstract = {RATIONALE: The upper lobe of the right lung, due to its unique anatomical structure that is prone to tumor occurrence, poses a challenge for the differential diagnosis of focal cavitary lesions. Cases of acute fibrinous and organizing pneumonia presenting as cavitary lesions in the upper lobe of the right lung are extremely rare in the previous literature.<br><br>PATIENT CONCERNS: This case presents a 59-year-old man who was hospitalized with a cough, phlegm, and low-grade fever after a bout of strenuous exercise and exposure to rain. A chest computed tomography (CT) revealed a cavitary lesion (lesions maximum diameter 9&#x2009;cm, hollow maximum diameter of 3.5&#x2009;cm) in the upper lobe of the right lung.<br><br>DIAGNOSES: Initially, he was incorrectly diagnosed with community-acquired pneumonia, and the empirical anti-infective and antiviral therapies proved ineffective. The flexible bronchoscopy lavage fluid showed negative results in metagenomic Next-Generation Sequencing (mNGS), but the pathological micrograph indicated a suspected diagnosis of acute fibrinous and organizing pneumonia.<br><br>INTERVENTIONS: He was taken off antibiotics, changed to 40&#x2009;mg of methylprednisolone intravenously each day.<br><br>OUTCOMES: Six days after receiving methylprednisolone, the cough disappeared. A reexamination chest CT showed a significant reduction of the lesion. Additionally, the patient did not report any discomfort during the 6 months of follow-up.<br><br>LESSONS: This case highlights the particular characteristics of the focal cavitary lesions in the upper lobe of the right lung and emphasizes the role of liquid-based cytology in the diagnosis of acute fibrinous and organizing pneumonia, rather than mNGS.},
}
@article {pmid41028724,
year = {2025},
author = {Li, Z and Wei, T and He, L and Qian, H and Zhu, YG and Wang, Y},
title = {Genomic potential for mercury biotransformation in marine sediments across marginal slope to hadal zone.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8655},
pmid = {41028724},
issn = {2041-1723},
support = {42376149//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Mercury/metabolism ; Metagenome/genetics ; Biotransformation/genetics ; China ; Seawater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; Phylogeny ; Genomics ; Methyltransferases/genetics/metabolism ; Methylation ; Ecosystem ; },
abstract = {Mercury accumulates in the deep sea, but its ecological impact on deep-sea ecosystems remains poorly understood. We conduct an analysis of 32 sediment cores, comprising 101 layers for the study of metagenomes, and additional 41 global reference sediment metagenomes. These sediment cores are collected from two deep-sea regions: the South China Sea and Mariana Trench, followed by revealing high mercury accumulation in the South China Sea. In these metagenomes, we find that the mercury methylation genes hgcAB are abundant in marginal seas but negligible in open oceans. Genomics result indicates that some Hg-methylating microorganisms affiliated with Desulfobacterota, Spirochaetota, and Zixibacteria in the deep-sea sediments encode MttB, the sole corrinoid-dependent methyltransferase identified in these taxa, which may interact with HgcA to transfer methyl groups from possibly osmolyte-derived trimethylamine for methylation. The demethylation gene merB is widely distributed and exhibits higher abundance in the open ocean. Moreover, we identify a large number of novel Hg demethylating taxa that are associated with horizontal transfer of the merB gene potentially involving methane generation. Our results expand the diversity of Hg-transforming taxa and reveal their unique ecophysiological adaptations in deep-sea sediments.},
}
@article {pmid41028597,
year = {2025},
author = {Maile-Moskowitz, A and Brown, CL and Rumi, MA and Moumi, NA and Majeed, H and Finkielstein, CV and Ceci, A and Gonzalez, R and Xia, K and McDaniel, L and Baffoe-Bonnie, A and Rao, J and Zhang, L and Pruden, A and Vikesland, PJ},
title = {Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {82},
pmid = {41028597},
issn = {2731-8745},
support = {1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; },
abstract = {Minimizing antimicrobial use is a recommended strategy to reduce the evolution and spread of antibiotic resistance; however, efficacy is elusive to measure. Wastewater-based surveillance provides a promising means to relate trends in microbial community antibiotic resistance profiles as a function of interventions and other factors. We examined influent sewage metagenomes for two neighboring wastewater treatment plants (WWTPs) serving a university and a nearby community. We compared antibiotic resistance gene (ARG) profiles as a function of diagnoses of COVID-19 and other illnesses, antibiotic use, antibiotic/antimicrobial and disinfectant/quaternary ammonium compound concentrations, and COVID-19-related behavioral shifts. Diversity and abundances of ARGs unique to the corresponding sewage were consistently higher for the community WWTP, but converged in 2022 when antibiotic prescriptions surged in the university zip code. Decreases in ARG diversity/abundance were not apparent during periods of decreased antibiotic usage, indicating that extended times may be required for wastewater ARG signals to attenuate following interventions.},
}
@article {pmid41028522,
year = {2025},
author = {Moon, SJ and Kim, HJ and Lim, JE and Hong, S and Won, HH and Jeong, BC and Kim, JH},
title = {HSF1-DBC1 axis drives prostate cancer progression by activating a metastatic transcriptional program.},
journal = {Experimental &amp; molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41028522},
issn = {2092-6413},
support = {2023R1A2C1005018//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01064189//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01053377//National Research Foundation of Korea (NRF)/ ; 2021R1A2C1004656//National Research Foundation of Korea (NRF)/ ; },
abstract = {Heat shock factor 1 (HSF1) is a key stress-protective transcription factor that acts as a guardian of proteostasis. HSF1 also plays multifaceted roles in tumor-associated processes including proliferation and metastasis. HSF1 is frequently overexpressed and activated in a wide range of cancers, including prostate cancer, and hijacked by cancer cells to promote their survival in harsh tumor microenvironments and during metastasis. However, mechanisms underlying the persistent activation of HSF1 and its coregulators in malignancies are largely unknown. Here we show that HSF1 is highly activated and required for metastatic spread and growth of metastatic castration-resistant prostate cancer (mCRPC) cells. The HSF1-driven transcriptional program and its genome occupancy in mCRPC cells were distinct from those of castration-resistant prostate cancer cells and massively reprogrammed during the metastatic progression of castration-resistant prostate cancer cells. In addition, we report DBC1 as a key coregulator of HSF1. DBC1 positively regulated HSF1-mediated transcription and genome-wide chromatin binding of HSF1. Moreover, DBC1 was required for super-enhancer formation and activation of super-enhancer-associated HSF1 target genes, including MMP11, involved in metastasis. Mechanistically, DBC1 activated and stabilized HSF1 by enhancing trimerization and DYRK2-mediated phosphorylation of HSF1 and inhibiting CHIP-mediated HSF1 ubiquitination, thereby increasing the transcriptional activity and genome-wide binding of HSF1. Importantly, DBC1 loss suppresses the metastatic growth of mCRPC cells, and HSF1-DBC1 double-high expression correlated with worse outcomes in patients with mCRPC. Our results highlight the critical role of HSF1 as a metastasis-promoting transcription factor and a novel regulatory mechanism of HSF1 activity and stability by DBC1. Thus, targeting the HSF1-DBC1 axis could be a promising therapeutic strategy for metastatic cancers.},
}
@article {pmid41028378,
year = {2026},
author = {Sahil, R and Jain, M},
title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2977},
number = {},
pages = {181-196},
pmid = {41028378},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; },
abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.},
}
@article {pmid41028236,
year = {2025},
author = {Ning, Z and Liu, J and Zhang, J and Zhong, W and Yang, T and Huang, Y and Qin, X and Zhang, X and Xu, X},
title = {Enhancement of short-chain fatty acids production by biochar-supported zero-valent iron in anaerobic fermentation: focusing on metabolic reactions and electron transport.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41028236},
issn = {1615-7605},
abstract = {Carbon-based and iron-based materials have been widely reported as effective promoters in biogas fermentation due to the promotion of electron transport. However, the effect of these materials, especially in combination, on short-chain fatty acids (SCFAs) production has been scarcely reported. In this study, the production of short-chain fatty acids (SCFAs) from green cabbage waste was promoted by adding biochar (BC) and biochar-supported zero-valent iron (BC@ZVI). The underlying mechanisms, focusing on metabolic pathways and electron transport, were subsequently investigated through metagenomic analysis. The optimal SCFAs yields were achieved with BC (5 g·L[-]1) and BC@ZVI (15 g·L[-]1). While BC notably enhanced n-butyrate production (89.4-fold), BC@ZVI balancedly promoted acetate and n-butyrate. Metagenomics revealed that BC@ZVI's superiority stemmed from its enhanced ability to enrich functional microbes and facilitate electron transfer. Metagenomic analysis revealed that BC@ZVI enriched Sphaerochaeta and Herbinix, which could participate in the direct interspecies electron transfer process. The abundance of almost all functional enzymes involved in carbohydrate hydrolysis and the synthesis of acetate and n-butyrate were remarkably increased by BC@ZVI. BC and BC@ZVI lead to a notable enrichment of conductive pili genes, including pilB, pilC, and pilM. BC@ZVI enriched both conductive pili and c-type cytochromes, which could be considered a more effective selection than BC. Notably, BC@ZVI was more effective than BC in stimulating n-butyrate-type fermentation, significantly shortening the lag phase and the overall fermentation cycle, thereby exhibiting better comprehensive performance, enhancing pH buffering capacity, and strengthening electron transfer and substrate hydrolysis. The results proved the potential of BC@ZVI in SCFAs fermentation and deciphered the underlying mechanisms, which provided a new perspective to promote resource recovery of organic waste by anaerobic system.},
}
@article {pmid41028186,
year = {2025},
author = {Chen, J and Lou, H and Yao, Y and Chen, Q and Liu, C and Zhou, H},
title = {Metagenomic next-generation sequencing for concurrent diagnosis of infections and malignancies in patients with lung lesions: a single-center prospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33721},
pmid = {41028186},
issn = {2045-2322},
support = {2022YFC2504502//the Key R&amp;D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//the Research and Development Program of Zhejiang Province/ ; 82272338//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lung Neoplasms/diagnosis/genetics ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Prospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; DNA Copy Number Variations ; Adult ; Sensitivity and Specificity ; Diagnosis, Differential ; },
abstract = {Metagenomic next-generation sequencing (mNGS) offers sensitive and rapid pathogen detection and has the added advantage of analyzing chromosomal copy number variations (CNVs) of the host in the same test. This study aimed to evaluate the dual diagnostic performance of mNGS in clinical cases where pulmonary infections and malignancies are difficult to be distinguished. A single-center prospective study was conducted at the First Affiliated Hospital, Zhejiang University School of Medicine. The study recruited patients with lung lesions from October 2021 to October 2022 that required differential diagnosis of infection, malignancy, or other pulmonary diseases. The mNGS was used to detect both pathogens and potential CNVs of the host chromosomes to inform presence of neoplasm, and the results were compared to conventional microbiological tests (CMTs), bronchoalveolar lavage fluid (BALF) cytology, histology, and clinical composite diagnoses. The mNGS demonstrated a significantly higher sensitivity of infection diagnosis (56.5% vs.39.1% for CMTs, P < 0.05). The CNVs analysis showed moderate sensitivity (38.9%) and high specificity (100%) for diagnosing malignancy, which helped determine lung cancer in 4 cases who were initially considered as pneumonia. Combining CNVs analysis with BALF cytology has increased the sensitivity for detecting malignancy from 38.9% to 55.6%. Furthermore, the sensitivity of CNVs analysis was higher (50%) when bronchoscopy directly found positive signs, such as neoplasm or bronchial mucosal infiltration. This study highlights the dual capacity of mNGS to simultaneously detect infections and malignancies. The integration of both pathogen and tumor detection could significantly enhance clinical decision-making, particularly for patients with overlapping symptoms of infection and cancer.},
}
@article {pmid41028005,
year = {2025},
author = {Xu, H and Ba, W and Yu, R and He, Z and Wang, P and Gou, X and Zhang, X and Wang, F},
title = {Fructophilic Apilactobacillus kunkeei alleviates high-fructose diet-induced lipid accumulation by modulating gut microbiota and intestinal barrier function in mice.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {201},
pmid = {41028005},
issn = {2396-8370},
support = {32402039//National Natural Science Foundation of China/ ; },
abstract = {Excessive fructose consumption is strongly linked to metabolic syndrome, with gut microbiota playing a pivotal role in mediating fructose metabolism and associated metabolic disturbances. In this study, we aimed to characterize Apilactobacillus (A.) kunkeei, a fructophilic lactic acid bacterium from honey, and evaluate its probiotic function in male C57BL/6 J mice fed a high-fructose diet (HFD). Transcriptome analysis was carried out to analyze the activation of pathways under various culture conditions. Pathway inhibitors were used in cell culture and a hepatectomy mouse model to study the function of different pathways in hepatocyte growth and liver regeneration. Our results showed that A. kunkeei FM01 exhibited strong tolerance to simulated gastrointestinal stress in vitro, indicating good probiotic potential. Administration of A. kunkeei FM01 significantly reduced body weight gain, improved glucose tolerance, and attenuated hepatic and visceral (perirenal and epididymal) lipid accumulation in HFD-fed mice. Serum lipid profiling and targeted lipidomic analysis revealed that A. kunkeei FM01 lowered triglycerides, phosphatidylcholine, and lysophosphatidylcholine levels while increasing beneficial phospholipids such as phosphatidylethanolamine. Metagenomic analysis demonstrated that A. kunkeei FM01 modulated gut microbiota composition by reducing pro-inflammatory and fructose-metabolizing taxa, including Alistipes, Oscillibacter, Desulfovibrio, Lawsonibacter, and Enterococcus, while enriching beneficial species, including Kineothrix alysoides and Faecalibaculum rodentium. These microbial shifts were associated with increased abundances in genes encoding carbohydrate-active enzymes and amino acid biosynthesis pathways. Furthermore, A. kunkeei FM01 restored intestinal barrier integrity by upregulating tight junction proteins (Zonula Occludens-1 and occludin) and reduced serum lipopolysaccharide and diamine oxidase levels. Collectively, these findings suggest that A. kunkeei FM01 exerts protective effects against HFD-induced metabolic dysfunction through multi-targeted mechanisms involving lipid metabolism, gut microbiota modulation, and intestinal barrier restoration. This study identifies A. kunkeei FM01 as a promising probiotic candidate for preventing and managing fructose-associated metabolic disorders.},
}
@article {pmid41027803,
year = {2025},
author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU},
title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2025.08.029},
pmid = {41027803},
issn = {1468-2060},
abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.<br><br>METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.<br><br>RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.<br><br>CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.},
}
@article {pmid41027356,
year = {2025},
author = {Kahwage, S and Lanzarini, NM and de Paula, BB and Saggioro, EM and Motta, ATF and Mannarino, CF and Miagostovich, MP},
title = {Viral genetic diversity in surface and groundwater at a non-operational dumpsite and its surrounding neighborhood.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180604},
doi = {10.1016/j.scitotenv.2025.180604},
pmid = {41027356},
issn = {1879-1026},
abstract = {Inappropriate municipal solid waste disposal areas lack waterproof base liners, drainage systems, treatment of waste degradation by-products, mass coverages, and vector control. Leachate is a by-product derived from water percolation through solid waste disposal sites, comprising an environmental and health contamination source when not adequately collected and treated. This study aimed to describe surface and groundwater viral diversity in a dumpsite area non-operational for over a decade and its surrounding neighborhood in the metropolitan Rio de Janeiro region employing shotgun metagenomic analysis. Between May 2021 and March 2023, 100 leachate samples (2 L each) were collected from 21 sampling points and subsequently organized into five pooled samples. Nucleic acids were extracted employing the Biopur Nucleo-mag Virus kit, followed by purification with AMpure XP beads and quantification via Qubit 4.0, Next-Generation Sequencing was performed on a NextSeq 2000 sequencer (Illumina, USA). Sequencing analysis identified 578 operational taxonomic units, of which 312 (54 %) were classified into 46 viral families, while 266 (46 %) remained unclassified, the Microviridae family was the most abundant. Viral sequences linked to pathogenic hosts were detected, including canine circovirus. Comparable viral family profiles were observed between the dumpsite and the residential area suggesting that some of the shared viral families may be influenced by groundwater flow originating from the closed dumpsite. Although irregular land use hinders precise attribution of contamination sources, the detection of potentially pathogenic viruses in waters intended for human use raises significant public health concerns. These findings support long-term virome-based surveillance of groundwater near closed dumpsite.},
}
@article {pmid41027219,
year = {2025},
author = {Li, X and Zhu, S and Wang, H and Zhen, Q and She, D},
title = {Silicon-modified lignin biochar outperforms hydrochar in heavy metal remediation: stochastic microbial assembly and functional gene reprogramming drive soil multifunctionality.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139966},
doi = {10.1016/j.jhazmat.2025.139966},
pmid = {41027219},
issn = {1873-3336},
abstract = {Heavy metal contamination severely threatened soil health, microbial stability, and food safety worldwide. While lignin-based biochar had shown potential in mitigating metal toxicity, its regulatory effects on soil microbiomes and ecosystem functions remained inadequately understood, especially across different carbonization strategies. A cross-scale remediation framework using silicon-modified lignin-based hydrochar (Si-LHB) and pyrochar (Si-LPB) was developed to restore cadmium (Cd)/zinc (Zn)-contaminated soil ecosystems. In a pot experiment combined with metagenomics and biochemical assays, metal speciation, microbial dynamics, nitrogen cycling, and soil multifunctionality were evaluated. Results showed that both Si-LHB and Si-LPB effectively enhanced metal stabilization and plant growth, yet Si-LPB outperformed Si-LHB by significantly reducing acid-soluble Cd and Zn (by 16.22 % and 48.43 %) and increasing residual fractions up to 72.70 %, primarily via silicate precipitation and microenvironment modulation. Compared to Si-LHB, Si-LPB more effectively restructured bacterial communities, enriching Pseudomonadota and increasing community stochasticity (NST＞50 %). It also selectively upregulated nitrogen transport genes (e.g., narK, nrtP) and suppressed denitrification genes (e.g., nirK, nosZ), enhancing nitrogen retention and carbon fixation. Consequently, Si-LPB improved soil multifunctionality by 72.13 % and reduced Cd/Zn accumulation in plants by up to 99.66 %. This study demonstrates that silicon-enhanced lignin biochars, particularly Si-LPB, restore soil ecological functions through functional redundancy and enrichment of keystone taxa rather than by increasing diversity, offering a promising carbon-silicon-microbe strategy for sustainable remediation.},
}
@article {pmid41027192,
year = {2025},
author = {Xu, H and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H},
title = {Effects of microplastics and excessive nitrogen pollution on oat growth and soil nitrogen cycling.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119119},
doi = {10.1016/j.ecoenv.2025.119119},
pmid = {41027192},
issn = {1090-2414},
abstract = {Both excessive nitrogen (N) and microplastic (MPs) pollution pose global change challenges to ecosystems and human health. The effects of MPs coexisting with excessive N on plant growth and N cycling are still largely unknown. This study employed a pot experiment to assess how polypropylene (PP) MPs influence oat (Avena sativa L.) growth and soil N cycling under conditions of excessive N fertilization. In the treatments of excessive N treatment, 2 % PP MPs significantly increased underground biomass (54.5 %). [15]N stable isotope results showed that 2 % PP MPs treatment significantly reduced the percentage of N from fertilizer in oat by 10.4 %. Compared to without N treatment, excessive N treatment reduces the Shannon index of the rhizosphere soil bacterial community. Only at the 0.5 % PP MPs level, excessive N treatment significantly reduced the diversity of bacterial communities in the bulk soil compared to the without N treatment. The Shannon index of fungal community was not affected by N treatment and MPs. Microbial biomass nitrogen (MBN) and pH were significant related to sensitive species in microbial communities. The coexistence of excess N and 2 % PP MPs significantly reduced the abundance of genes (norB, nosZ and nirB) related to denitrification process. Structural equation modeling showed that MPs could promote underground biomass, reduce soil pH, inorganic N content, and reduce N uptake efficiency, thus resisting growth damage caused by high N. In the future, the effects of different concentrations and types of MPs and different nitrogen forms on soil and crops should be further investigated.},
}
@article {pmid41027153,
year = {2025},
author = {Zhang, S and Gao, W and Gao, X and Xu, W and Liu, Y and Guo, Z and Liu, G and Zhang, P and Shi, H and Chang, X},
title = {Astragaloside VI attenuates mechanical stress-induced cardiac remodeling through piezo1-VDAC1 dependent endoplasmic reticulum unfolded protein response.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157288},
doi = {10.1016/j.phymed.2025.157288},
pmid = {41027153},
issn = {1618-095X},
abstract = {BACKGROUND: The dysregulation of protein homeostasis is a condition associated with mechanical stress-induced cardiac remodeling (CR) due to endoplasmic reticulum (ER) dysfunction and stress.<br><br>PURPOSE: This research explores the effect of Piezo1 on the ER unfolded protein response (UPR) in cardiomyocytes following hypoxic stress, specifically through its interaction with VDAC1. In addition, the study evaluates the therapeutic potential that this mechanism holds for treating CR and cardiomyocyte hypertrophy.<br><br>STUDY DESIGN: Considering the relative limitation of potential therapeutic drugs for CR, our goal is to utilize a multi-omics approach to confirm the process by which Astragaloside IV (AS) alleviates CR through the Piezo1-VDAC1 dependent UPR.<br><br>METHODS: We utilized multiple omics studies, such as single-cell sequencing, network pharmacology, and metagenomics, for the validation of AS's targets and phenotypic mechanisms. Following this, we created Piezo1/VDAC1 transgenic mice (Piezo1[TG]/VDAC1[TG]) and wild-type mice, which were then subjected to transverse aortic constriction (TAC) to induce myocardial damage. We performed assessments of cardiac function, myocardial injury staining, and cardiomyocyte hypertrophy on these animal models both before and after the drug intervention. The analysis into the interaction between Piezo1-VDAC1 and the structural integrity of cytoskeletal proteins and the ER was conducted utilizing laser confocal microscopy, immunofluorescence, and molecular biology experiments.<br><br>RESULTS: The regulation of mechanical stress-induced cardiac remodeling crucially involves Piezo1-VDAC1. Data from single-cell sequencing and network pharmacology suggest that ER damage, mitochondrial energy metabolism dysfunction, and the dysregulation of subcellular organelles are important phenotypes that mediate this process. Our animal experiments demonstrated that AS is capable of improving cardiac function after TAC, inhibiting myocardial injury and the associated inflammatory reaction, and suppressing excessive UPR stress. The therapeutic effect of the drug was eliminated by the transgenic treatment of Piezo1. In vitro experiments also offered confirmation that AS can ameliorate cardiomyocyte damage through the ER pathway. This is achieved by regulating the Piezo1-VDAC1 interaction mechanism, which restores ER structural collapse after hypoxic injury, enhances energy metabolism levels, and inhibits excessive UPR stress.<br><br>CONCLUSION: The abnormal activation of the UPR, which is mediated by Piezo1-VDAC1, constitutes the pathological mechanism behind mechanical stress-induced cardiac remodeling. By regulating the Piezo1-VDAC1 interaction, AS inhibits excessive UPR stress and improves the breakdown of ER structure and functional abnormalities. These actions further normalize ER function and ameliorate cardiac function and myocarditis-related injury. This work offers a promising strategy for utilizing natural medicine to treat mechanical stress-induced cardiac remodeling.},
}
@article {pmid41026933,
year = {2025},
author = {Greco, M and Coculo, D and Conti, A and Agresti, S and Pontiggia, D and Mélida, H and Favaro, L and Lionetti, V},
title = {Biorefining of Anaerobic Digestates for the Recovery of Biostimulants and Bioelicitors for Immune Priming and Plant Protection.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03321},
pmid = {41026933},
issn = {1520-5851},
abstract = {Olive oil production is a major global agricultural industry that generates significant waste, particularly olive pomace, which poses environmental and economic challenges. Anaerobic digestion emerges as a promising solution for its valorization into biogas. However, the resulting digestate remains underutilized and its long-term environmental impact is uncertain. Traditional disposal methods are costly and inefficient, underscoring the need for more sustainable approaches. In this study, olive pomace digestate was biorefined, and its components were upcycled into soil amendments and plant immunostimulants. Metagenomic analysis revealed a diverse microbial community in the liquid fraction. A microbial-enriched protein extract (MIPE) was obtained, containing precursors of microbe- and damage-associated molecular patterns, including Flagellin, Elongation Factor Tu, and the plant phytocytokine Golven. Plant treatment with MIPE triggered a rapid immune response, characterized by oxidative burst, mitogen-activated protein kinase activation, and the upregulation of defense-related genes such as CYP81F2, FRK1, and WRKY53. MIPE-induced priming enhanced Arabidopsis and tomato resistance to Botrytis cinerea and Pseudomonas syringae. Our findings highlight olive pomace digestate as a valuable growth biostimulant, with its liquid fraction also representing a promising resource of immunity bioelicitors. This refinement valorizes olive mill waste, providing a sustainable alternative to chemical fertilizers and pesticides and supporting sustainable agriculture.},
}
@article {pmid41026643,
year = {2025},
author = {Wu, D and Van Goethem, MW and Graham, DW and Zhang, X and Li, Z and Shi, G},
title = {Antarctic Environmental Resistomes Closely Associated with Human and Animal Waste Releases.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06023},
pmid = {41026643},
issn = {1520-5851},
abstract = {Antarctica harbors a diverse spectrum of antibiotic resistance genes (ARGs) across lake, soil, and seawater environments. However, linkages between resistomes in waste-impacted and pristine settings are not well understood in polar settings, especially how phage, plasmids, and microbial community assembly influence the spatial distribution of ARGs. Metagenomic sequencing of 85 Antarctic samples showed 10-fold greater ARG abundances near animal and human waste-impacted sites compared with more remote settings, including glacial, lake, soil, and offshore seawater sites (-1.9 to -0.1 log10(ARGs/cell), P < 0.01), although (except for glaciers) resistome compositions were broadly similar. Based on metagenomic data, plasmids appear to be more associated with ARGs than phages in the Antarctic samples, with Pseudomonas, Staphylococcus, Bacillus, and Mycobacterium being primarily associated with ARG prevalence because they dominate local microbial assemblages. These primary taxa exhibit wide cross-setting prevalence and are not significantly impacted by local environmental selection (P > 0.05, SNPs-RDA). As such, human- and animal-waste-impacted locations, which have higher microbial migration rates (m = 10.8, NCM), are primary sources of ARG-containing and assembly predominant bacteria in Antarctic settings. Thus, better management of waste releases from human settlements must be central to retaining "pristine" Antarctic environments against the globally expanding resistomes.},
}
@article {pmid41026231,
year = {2025},
author = {Qian, M and Zhou, J and Chen, P and Jiang, N and Wang, T and Chen, X and Xu, H and Zhou, F and Yang, Y and Lin, X and Yang, Q and Shao, L and Ruan, Q and Zhang, W},
title = {A Novel Compound Heterozygous Mutation in the IL12RB1 Gene Causes Susceptibility To Mycobacterium Tilburgii Infection.},
journal = {Journal of clinical immunology},
volume = {45},
number = {1},
pages = {133},
pmid = {41026231},
issn = {1573-2592},
support = {82271794//National Natural Science Foundation of China/ ; KY2024-664//Clinical Research Project of Huashan Hospital, Fudan University./ ; },
mesh = {Humans ; Female ; *Receptors, Interleukin-12/genetics ; *Genetic Predisposition to Disease ; Adult ; Heterozygote ; *Mycobacterium Infections/genetics/diagnosis/drug therapy/immunology ; *Mutation ; *Mycobacterium ; Interferon-gamma ; },
abstract = {Mendelian susceptibility to mycobacterial disease (MSMD) is a rare clinical syndrome that is characterized by selective vulnerability to intracellular pathogens. Deficiency in IL12RB1 is the most common type of MSMD but the heterogeneity of its clinical Manifestation Makes precise diagnosis difficult. Here, we report a previously healthy 29 year-old woman who had suffered from disseminated infection with Mycobacterium tilburgii, which is a rare, unculturable environmental mycobacteria, for over 2 years. We used whole exome sequencing to detect a novel compound heterozygous variant in the IL12RB1 gene. Immunological analysis of the patient's peripheral lymphocytes showed a barely detectable level of IL-12Rβ1, a reduced population of follicular helper T (Tfh) cells and impaired production of IFN-γ in response to IL-12/IL-23 stimulation. Metagenomic next-generation sequencing was used to identify the causative pathogen and to analyze drug susceptibility. The infection was contained by a combination of anti-mycobacterial drugs and IFN-γ supplementary treatment. An RNA-seq analysis, using follow-up blood samples, revealed the limited success of these treatments over 6 months. Our findings support the screening for inherited immunological problems in patients with difficult-to-treat mycobacterial infections. The suboptimal response to prolonged anti-mycobacterial drugs and IFN-γ supplementation warrants the development of novel therapeutic strategies for MSMD patients.},
}
@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}
@article {pmid41026152,
year = {2025},
author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA},
title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.},
journal = {Journal of medical microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002079},
pmid = {41026152},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; },
abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.},
}
@article {pmid41026097,
year = {2025},
author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S},
title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf097},
pmid = {41026097},
issn = {1574-6941},
abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in above-ground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.},
}
@article {pmid41025937,
year = {2025},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).<br><br>METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.<br><br>RESULTS: Eighty participants (54% female; age: 50.3&#x2009;&#xb1;&#x2009;10.1&#x2009;years) were randomized to BV379 (n&#x2009;=&#x2009;39) or placebo (n&#x2009;=&#x2009;41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p&#x2009;=&#x2009;0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9%