@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 & development/microbiology ; Temperature ; Bacteria/genetics ; Triticum/growth & development/microbiology ; Fagopyrum/growth & 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).},
}

*Rhizosphere
Soil Microbiology
*Microbiota
*Microbial Consortia
*Stress, Physiological
*Plant Development
Crops, Agricultural/growth & development/microbiology
Temperature
Bacteria/genetics
Triticum/growth & development/microbiology
Fagopyrum/growth & development/microbiology

@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.

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.

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.

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.},
}

Animals
Cattle/genetics
*Genetic Variation
*Adaptation, Physiological/genetics
Sudan
Selection, Genetic
Breeding
Hot Temperature
*Heat-Shock Response/genetics
Whole Genome Sequencing

@article {pmid41465030,
year = {2025},
author = {Kahraman Ilıkkan, Ö and Bağdat, EŞ and Yılmaz, R and Çetin, B and Çon, AH and Erten, H and Göksungur, MY and Şimşek, Ö},
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.

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.

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.

CONCLUSION: This synthesis highlights the significant technological, nutritional, and cultural value of Türkiye'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, Ł 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 & 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.},
}

*Cellulase/genetics/metabolism/chemistry/isolation & purification
Cloning, Molecular
*Metagenomics
Phylogeny
Enzyme Stability
Hydrogen-Ion Concentration
Escherichia coli/genetics
Metagenome
Recombinant Proteins/genetics/metabolism
Temperature
*Bacterial Proteins/genetics/metabolism/chemistry

@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.

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.

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, Educación 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.

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 ≈1.6 Tbp). Overall, ≈42,000 viral contigs (> 10 kb) were obtained, resulting in ≈12,500 and ≈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 < 1% of all species and genera, including some of the most abundant viruses, were captured by all methods; reaching a value of ≈2% when only viromics excluding SVG were considered. The highest pairwise diversity consensus was observed between PacBio-HiFi and Illumina, with approximately ≈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.

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.},
}

*Methane/metabolism
*Wastewater/chemistry/microbiology
*Ciprofloxacin
Anaerobiosis
*Waste Disposal, Fluid/methods
*Water Pollutants, Chemical/analysis
Anti-Bacterial Agents
Drug Resistance, Microbial/genetics
Carbon

@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 & 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.},
}

*Particulate Matter/analysis
Republic of Korea
Bacteria/genetics
*Air Pollutants/analysis
*Environmental Monitoring
Particle Size
*Fungi/genetics
*Metagenome
*Air Microbiology
Microbiota
Air Pollution/statistics & numerical data

@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.},
}

*Norfloxacin
Sewage/microbiology/chemistry
Zea mays/chemistry
Anaerobiosis
Charcoal/chemistry
*Waste Disposal, Fluid/methods
Anti-Bacterial Agents
*Drug Resistance, Microbial/genetics
Biodegradation, Environmental

@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.},
}

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

@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 & 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.},
}

Animals
*Meat/virology
*Mammals/virology
*Animals, Wild/virology
Democratic Republic of the Congo
*Viruses/genetics/isolation & purification/classification
Zoonoses/virology
Humans
Phylogeny
Belgium
Genetic Variation

@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 & 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.

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.

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).

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.},
}

Humans
*Software
Metagenome
Rhizosphere
Microbiota/genetics
*Metagenomics/methods
Gastrointestinal Microbiome/genetics
Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology
Lung Neoplasms/genetics/pathology

@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.

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.

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.

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.

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.

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.

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.

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).

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 = 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.

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 & 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.

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.

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.

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.},
}

Humans
*Meningitis, Cryptococcal/diagnosis/microbiology/cerebrospinal fluid
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Male
Female
Middle Aged
Adult
*Cryptococcus/genetics/isolation & purification
Sensitivity and Specificity
Aged
Antigens, Fungal/cerebrospinal fluid
Tertiary Care Centers
*Molecular Diagnostic Techniques/methods

@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 & 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.},
}

*Phylogeny
*Circovirus/genetics/classification/isolation & 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

@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.

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.

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.

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.

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 and to explore potential implications for the gut-brain-metabolic axis.

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.

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).

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.},
}

*Cytochrome P-450 Enzyme System/genetics/chemistry
Amino Acid Sequence
Diffusion
Algorithms

@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.

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.

RESULTS: The positive detection rate of pathogens by mNGS was significantly higher than that by conventional methods (p < 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 < 0.01). The sensitivity of mNGS was 66% higher than that of conventional methods (p < 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 < 0.05).

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.

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 Förderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium für 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.

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.

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.

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/m² 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.

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.

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.

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&E and Masson's trichrome staining), immunohistochemistry (α-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.

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.

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.

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.

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/μL, 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.

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.

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.

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.

FINDINGS: Among the eight patients with colorectal cancer, α-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.

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.

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.

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.

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.

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 & 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.},
}

Animals
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
Seasons
Altitude
Feces/microbiology
*Climate Change
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
China

@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.},
}

*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

@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&D Program/ ; 202401AS070025//Yunnan Fundamental Research Projects/ ; },
mesh = {*Fermentation ; *Biogenic Amines/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & 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.},
}

*Fermentation
*Biogenic Amines/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
Putrescine/metabolism
Cadaverine/metabolism
Food Microbiology
Metabolic Networks and Pathways
Metabolomics

@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.

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 < 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 cm chopping length, the Control group exhibited significantly higher levels of ARGs and VFs compared to the 1 cm and 3 cm treatments (P < 0.05).

CONCLUSION: The findings highlight the efficacy of reducing chopping length (to 1 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.

METHODS: Seventy-two community-dwelling individuals aged ≥ 65 years with a BMI between 23 and 32 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.

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.

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 & 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]).

METHOD: This two-year NINDS-funded study collects oral microbiome samples, blood, and CSF annually in a cognitively normal, racially diverse cohort (n = 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.

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.

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.},
}

Humans
*Biomarkers/cerebrospinal fluid
Female
Male
*Alzheimer Disease/cerebrospinal fluid
Middle Aged
*Microbiota
*Periodontal Diseases/microbiology
*Social Determinants of Health
Aged
Inflammation

@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 & 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 & 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.},
}

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

@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.

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.

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 > 50% genome coverage achieved at 10[4] GCE/mL.

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 & 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 & 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.

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.

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.

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.},
}

Humans
*Bile/microbiology
*Biliary Tract/microbiology
Drainage/adverse effects
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Female
Male
Middle Aged
Aged
Metagenomics
Adult

@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.

MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31 ± 9 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 × nitrate intake interaction term.

RESULTS: Mean nitrate intake was 190 ± 171 mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p < 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 = 0.002), but levels were similar in those with high MINES (p = 0.84).

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.

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 mg PO every 12 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.

CONCLUSIONS: This case demonstrates the effectiveness of a sequential approach with a linezolid‒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.

CLINICAL TRIAL NUMBER: Not applicable.

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 & 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.

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.

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 = 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.

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.},
}

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

@article {pmid41447357,
year = {2025},
author = {Worachotsueptrakun, K},
title = {Biomarkers.},
journal = {Alzheimer's & 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.

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.

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 = 40) and age- and sex-matched control participants (n = 40). Microbiome features correlated with plasma phosphorylated tau 181 (p-tau181) and plasma neurofilament light chain (NFL), but not with APOE ε3 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.

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.},
}

Humans
*Biomarkers/blood
*Gastrointestinal Microbiome/physiology
Female
Male
*Alzheimer Disease/blood
Aged
tau Proteins/blood
Amyloid beta-Peptides/blood

@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 & 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.

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.

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.

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).},
}

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

@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).

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.

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.

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.},
}

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

@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 & 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.

METHOD: Stool samples from MCI patients (n =  3) and HC (n =  3) (aged 55-80) were used for FMT in 4-month-old iNOS-KO/3xTg-AD mice (FMT-MCI, n = 4 and FMT-HC, n = 6) for three consecutive days after a 7-day antibiotic treatment. Mice without FMT (CTL, n = 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 = 4/group) using 7T MRI with Continuous Arterial Spin Labelling (CASL) - Echo Planar Imaging (EPI) sequence.

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.

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-β and tau accumulation, or preserving cognitive functions. Our preliminary data shows that iNOS could be a potential target to ameliorate AD risk.},
}

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

@article {pmid41445049,
year = {2025},
author = {Loew, EB},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & 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.

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.

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 = 10 declining vs n = 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.

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.},
}

Humans
*Alzheimer Disease/immunology/metabolism
Aged
Male
Female
*Gastrointestinal Microbiome
Feces/microbiology/chemistry
*Cognitive Dysfunction/immunology/metabolism
Metabolomics
Aged, 80 and over

@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 & 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.

METHODS: This cross-sectional study enrolled 75 T1D participants (disease duration ≥ 10 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.

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.

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.},
}

Humans
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications
Male
Female
Adult
Dysbiosis
*Bacteria/genetics/metabolism/classification/isolation & 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

@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 & 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 & 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.

METHOD: This study examined changes in gut microbiota and SCFA across three groups; Cognitively unimpaired individuals with low amyloid-beta ((CU) Aβ Low (n =  71)), CU Aβ High (n =  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.

RESULT: Firmicutes, Proteobacteria, and Bacteroidetes exhibited significant correlations with SCFAs across all groups. In the CU Aβ 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 Aβ Low group, and a positive correlations between Proteobacteria and Actinobacteria with butyric acid in the CU Aβ 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.

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.},
}

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

@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.

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.

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]).

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.},
}