@article {pmid41218490,
year = {2025},
author = {Qingrui, L and Hongyang, L and Guijun, W and Yiqiao, Z and Yue, C and Changqun, D and Chang'e, L},
title = {Synergistic ecotoxicity of nanoscale zero-valent iron and cadmium in soil: Insights from Eisenia fetida.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119381},
doi = {10.1016/j.ecoenv.2025.119381},
pmid = {41218490},
issn = {1090-2414},
abstract = {Nano-zero-valent iron (nZVI) has been extensively applied as a soil conditioner in remediation practices. However, studies have suggested that excessive doses of nZVI can adversely affect soil organisms and even exacerbate the toxicity of contaminants such as cadmium (Cd) in earthworms. This study investigated whether nZVI induces stress and exacerbates Cd toxicity in Eisenia fetida under controlled laboratory conditions. Four treatments were established: control (no nZVI or Cd), nZVI (10 g∙kg[-1]), Cd (30 mg∙kg[-1]), and Cd-nZVI (30 mg∙kg[-1] Cd + 10 g∙kg[-1] nZVI). Survival rate, biomass, Cd bioaccumulation, enzyme activity, and other indicators were measured. On day 7 of exposure, reactive oxygen species (ROS) levels in the nZVI, Cd, and Cd-nZVI groups were 1.4-, 1.5-, and 1.6-fold higher than those in the control group, respectively (P < 0.05). Over time, both survival rate and biomass declined, with the lowest survival rate and greatest biomass loss observed in the Cd-nZVI group on day 28. Histological staining revealed that under Cd or nZVI stress, the circular muscle layer of the earthworms was loosened, intestinal tissue was partially detached, and the number of villi decreased. Metagenomic sequencing indicated significant alterations in the community structure of the earthworm intestinal microbiota under different treatments. Both 30 mg∙kg[-1] Cd and 10 g∙kg[-1] nZVI disrupted gut microbial balance, which was further exacerbated by combined exposure.},
}

@article {pmid41218435,
year = {2025},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}

@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
doi = {10.1371/journal.pone.0336700},
pmid = {41218045},
issn = {1932-6203},
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}

@article {pmid41217732,
year = {2025},
author = {Boutin, S and Klein, S and Untergasser, G and Loka, TP and Jakob, S and Caf, Y and Khatamzas, E and Knabl, L and Wrettos, G and Knobloch, H and Nurjadi, D},
title = {Evaluating Seqstant LiveGene Analysis in real-time assessment of metagenomic next-generation sequencing (mNGS) data from respiratory samples.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41217732},
issn = {1439-0973},
abstract = {BACKGROUND: The detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples.

METHOD: We used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results.

RESULTS: We observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant (δ = 10, α = 0.05, 1 - β = 0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable, timely results, as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%.

CONCLUSION: Overall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detecting Aspergillus spp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.},
}

@article {pmid41217690,
year = {2025},
author = {Nguyen, HN and Kim, OTP and Tran, TT},
title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {11},
pages = {445},
pmid = {41217690},
issn = {1573-0972},
support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; },
abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.},
}

@article {pmid41217278,
year = {2025},
author = {Zhang, C and Chang, N and Yin, G and Shen, W and Lu, L and Bao, M and Guan, D and Zhang, S and Wang, R and Zhang, H},
title = {Drivers of Metal Resistance-Virulence Co-Selection in Landfill Leachates.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf275},
pmid = {41217278},
issn = {1365-2672},
abstract = {AIMS: Metal resistance genes (MRGs) and virulence factor genes (VFGs) are driven by environmental factors and host immunity, respectively, and they are traditionally considered to evolve independently. However, their co-selection dynamics in landfill leachates remain poorly characterized. In this study, a multi-regional metagenomic assessment integrating environmental gradients was first presented to reveal how heavy metals shape MRG-VFG interactions and associated ecological risks in landfill leachates.

METHODS AND RESULTS: Landfill leachates were collected from 13 landfills spanning six regions in China. Multi-regional metagenomic sequencing combined with co-occurrence network analysis was applied to examine pathogen-gene relationships. The results revealed pronounced regional disparities in pathogen, MRG, and VFG distribution, alongside shared features. Staphylococcus aureus and Pseudomonas aeruginosa were identified as dominant pathogens. tufA and gyrA emerged as conserved VFGs, whereas arsB and copA represented dominant MRGs. Network analysis revealed Escherichia coli, Salmonella enterica, and Acinetobacter baumannii as central nodes carrying overlapping functional genes, forming a "metal resistance-virulence" synergy module. Redundancy analysis revealed that specific heavy metals (Cu, Zn, Cr, and As) were crucial for the formation and stability of "pathogen-MRG-VFG" functional assemblies.

CONCLUSIONS: This study addresses a critical knowledge gap by integrating multi-regional metagenomic evidence with environmental selection pressures. MRGs conferred survival advantages and synergized with VFGs to enhance pathogen infectivity. These findings provide insight into MRG-VFG co-selection mechanisms in landfill leachates and guide targeted monitoring to mitigate environmental and health risks.},
}

@article {pmid41217198,
year = {2025},
author = {Valade, M and Le Bideau, M and Grimaldier, C and Boschi, C and Colson, P and La Scola, B},
title = {Development of cell combos micromethod to isolate respiratory viruses not detected by molecular techniques.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0257125},
doi = {10.1128/spectrum.02571-25},
pmid = {41217198},
issn = {2165-0497},
abstract = {Virological diagnosis of respiratory infections relies mainly on molecular methods but can be overlooked in cases of unexpected or unknown emerging viruses. In this case, modern approaches use mainly metagenomics without a priori. The other approach to detecting new viruses is based on their isolation in cell culture using virus-specific cells and culture conditions. Unfortunately, inoculation on several lines and metagenomics requires a large volume of clinical sample, while the initial sample has already been largely used to carry out multiplexed RT-PCR. Herein, we aimed to develop micro-methods to inoculate combos of cell lines to isolate respiratory viruses missed by molecular techniques. Ten cell lines were selected, and then five cell combos of two cell lines each were developed. Strains of 15 respiratory virus species were inoculated, and viral growth was assessed by cytopathic effect detection and RT-PCR assays. Among these, all grew on at least one combo. The Caco-2/MRC5 combo was the most promising. As proof-of-concept, 859 human respiratory samples found negative by multiplex RT-PCR panels were inoculated into these five cell combos and monitored for the appearance of cytopathic effects. The efficiency of this approach was evidenced by isolating 12 herpes simplex or varicella-zoster viruses not detected by respiratory multiplex PCR assays. In conclusion, this updated approach can detect known but, most importantly, likely emerging respiratory viruses. It could be used to investigate undiagnosed respiratory infection outbreaks especially if optimized with an approach allowing for the detection of viral multiplications with minor or no cytopathic effects.IMPORTANCEThe detection of respiratory viruses relies on a range of laboratory methods each of which has distinct advantages in terms of speed, practicality, and sensitivity. Current molecular methods for respiratory virus detection, such as multiplex PCR, may fail to identify unexpected, genetically divergent, or emerging viruses. This study presents an innovative approach using micromethods inoculating combinations of cell lines (cell combos) to enhance the isolation of a broad panel of respiratory viruses, including those undetected by standard molecular techniques. This strategy revives and modernizes classical virology techniques for use in contemporary diagnostics, particularly during unexplained respiratory outbreaks. It opens up new possibilities for detecting both known and unknown viruses across different sample types.},
}

@article {pmid41217051,
year = {2025},
author = {Alam, SS and Mehdi, A and Zafar, A and Ali, S and Rehman, AU and Liaqat, I and Peng, L and Kanwal, F and Afzal, S and Haq, IU and Aftab, MN},
title = {Advances in microbial biofuel production by metabolic and enzyme engineering, synthetic biology, metagenomics, and genome editing applications.},
journal = {Emerging topics in life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1042/ETLS20240002},
pmid = {41217051},
issn = {2397-8554},
abstract = {Microorganisms are the primary source of genetic diversity on earth due to their unparalleled metabolic and functional variability. With the depletion of fossil fuels, a sustainable alternative approach is the use of biofuels, where plant biomass as feedstock is essentially degraded to sugars with the aid of microbe-derived enzymes, followed by the conversion of those sugars to biofuels. Several cellulolytic and non-cellulolytic enzymes are involved in biofuel synthesis. Molecular cloning, along with the advancements in genetic and metabolic engineering in microbial cells, plays a significant contribution to biofuel overproduction. Advanced molecular technologies such as metagenomics and synthetic biology approaches are also being used to construct effective microorganisms for biofuel manufacturing. Obtaining novel enzymes from undiscovered microbial consortia and functional gene analysis is possible through a metagenomics approach. While synthetic biology provides engineered biological systems to generate required biofuel productivity, the CRISPR-Cas genome editing tool is another revolutionary tool being utilized for efficient biofuel production. This article provides a brief overview of different methods of biofuel production using microorganisms.},
}

@article {pmid41216332,
year = {2025},
author = {Facciotti, F and Di Stefano, G and Maragno, P and Ferraro, C and Dridi, D and Somigliana, E and Viganò, P and Vercellini, P and Casalechi, M},
title = {Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.},
journal = {Human reproduction open},
volume = {2025},
number = {4},
pages = {hoaf061},
pmid = {41216332},
issn = {2399-3529},
abstract = {STUDY QUESTION: What is the evidence available concerning gut and reproductive tract microbiomes in patients with endometriosis and what are the methodological approaches employed in microbiome studies on endometriosis?

SUMMARY ANSWER: The taxonomic profiles exhibited pronounced heterogeneity within women with and also within women without endometriosis across reviewed studies for all the anatomical districts evaluated.

WHAT IS KNOWN ALREADY: Both human and animal studies support differences in the microbiome composition of individuals with and without endometriosis. Endometriosis onset occurs with variable symptoms and manifestations. The microbiome composition at different sites may contribute to this variability.

STUDY DESIGN SIZE DURATION: We used the scoping review methodology. Systematic searches of studies from the PubMed, EMBASE, and Web of Science databases published between 1 January 2016 and 1 November 2024 addressing endometriosis microbiome characterization in: (i) gut, (ii) vaginal fluid, (iii) cervical fluid, (iv) peritoneal fluid, (v) uterine fluid, (vi) ovarian cyst fluid, (vii) oropharyngeal fluid, and (viii) eutopic and (ix) ectopic tissues were performed using a combination of MeSH terms. References from relevant publications were systematically screened.

Results were reported in accordance with the PRISMA-ScR guidelines. Studies that did not report original data, not written in English or providing a review of the field were excluded. From the 2182 publications retrieved, 36 papers were selected and analyzed, focusing on sample characterization (patients, controls, tissues, and fluids) and methodologies used.

Sound evidence is lacking to support a specific gut dysbiosis profile in women with endometriosis. The largest metagenome study performed using shotgun sequencing and controlling for multiple hypotheses testing did not detect significant differences between women with and without the disease. For eutopic and ectopic tissue microbiomes, the literature is too scant to draw any conclusion. Some data suggest a possible enrichment of Streptococcus sp. in cervical fluid and of Pseudomonas sp. in peritoneal fluid and a depletion of Lachnospira sp. in stool/anal fluid of endometriosis patients. However, these findings may be explained by confounders or by intrinsic patient or population characteristics. We appraised the limitations of the studies and proposed suggestions for optimizing sequencing techniques and experimental designs.

The number of participants per study greatly varied and, with few exceptions, was typically low. Incomplete information on methodological approaches was broadly observed. The impact of participants' menstrual cycle phase, diet, and drug assumption was frequently not considered.

Standardization of research protocols to allow reproducibility is required, as well as collaborations to harmonize data analysis, interpretation, and, more importantly, health outcome prediction or improvement.

The review was funded by the Italian Ministry of Health: RF-2019-12369460, and Current Research IRCCS. P.Vi. serves as co-editor in Chief of Journal of Endometriosis and Uterine Disorders. E.S. serves as Editor in Chief of Human Reproduction Open and discloses research grants from Ferring, Ibsa, Gedeon Richter, and Theramex, and honoraria from Ibsa and Gedeon Richter. P.Ve. serves as Associate Editor for Human Reproduction Open; is a member of the Editorial Board of the Journal of Obstetrics and Gynaecology Canada, of the Italian Journal of Obstetrics and Gynaecology, and of the International Editorial Board of Acta Obstetricia et Gynecologica Scandinavica; has received royalties from Wolters Kluwer for chapters on endometriosis management in the clinical decision support resource UpToDate; and maintains both a public and private gynecological practice. All other authors declare they have no conflict of interest.

REGISTRATION NUMBER: 10.17605/OSF.IO/X6HBT at https://osf.io/registries.},
}

@article {pmid41216322,
year = {2025},
author = {Li, C and Hou, J and Datry, T and Adyel, TM and Zhou, W and Wu, J and You, G and Jin, T and Deng, Y and Miao, L},
title = {How river drying influences greenhouse gas emissions: insights from species and gene shifts.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf187},
pmid = {41216322},
issn = {2730-6151},
abstract = {Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This mesocosm study investigated the greenhouse gas emissions fluxes and underlying mechanisms from benthic habitats prone to 20-100 days of drying. Results show that CO2 and N2O emissions from biofilms did not increase when drying increased, due to the changes in functional communities and genes. Notable is the transformation of biofilm from carbon source to sink following prolonged drying (mean emission fluxes ranged from 804.78 to -305.55 mg m[2] h[2]). This was mainly due to strong increases in the abundance of genes involved in the Calvin-Benson-Bassham cycle (2.82 × 10[-5] to 7.12 × 10[-5]), and functional taxa such as gemmatimonadota and pseudomonadota. These findings reveal a potential mitigation effect of drying on greenhouse gas emissions from rivers and streams, which could be relevant in the face of climate change.},
}

@article {pmid41216321,
year = {2025},
author = {Hawthorne, SEG and Tsola, SL and Carrión, O and Todd, JD and Eyice, Ö},
title = {Active microorganisms and potential metabolic pathways mediating anaerobic degradation of DMSP in anoxic saltmarsh sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf180},
pmid = {41216321},
issn = {2730-6151},
abstract = {Dimethylsulfoniopropionate (DMSP) is a globally abundant organosulfur compound produced by marine organisms, where it plays key physiological roles in stress protection and serves as a major source of carbon, sulfur, and energy for microbial communities. Importantly, DMSP degradation contributes to the formation of the climate-active gas dimethyl sulfide (DMS), which can drive the production of potent greenhouse gases, methane and carbon dioxide, in anoxic environments. While aerobic DMSP degradation is well studied, its fate under anoxic conditions remains poorly understood, and the microbial populations and metabolic pathways underlying these biotransformations are virtually unknown. Here, we present the first detailed investigation of microbial DMSP cycling in anoxic saltmarsh sediments. Our sediment samples had high in situ DMSP concentrations (up to 7.7 μmol/g) and the conversion efficiencies of DMSP to DMS under anoxic conditions (~68%) were comparable to those in oxic environments. Furthermore, using [13]C-labelled DMSP in stable isotope probing (SIP) experiments, combined with 16S rRNA gene sequencing and metagenomics, we identified Amphritea (Oceanospirillales) as a key active DMSP degrader, likely operating via the dddD-encoded lysis pathway. Additional taxa, including Geopsychrobacter, were implicated as potential secondary consumers, while Arcobacteraceae may contribute to sulfur cycling rather than direct DMSP catabolism. This study uncovers a previously overlooked route for DMSP transformation via anaerobic metabolism, expands the known metabolic roles of saltmarsh microorganisms and highlights the potential for DMSP to drive climate-active gas production in anoxic coastal ecosystems.},
}

@article {pmid41216320,
year = {2025},
author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M},
title = {A global deep terrestrial biosphere core microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf176},
pmid = {41216320},
issn = {2730-6151},
abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.},
}

@article {pmid41216181,
year = {2025},
author = {Song, Z and Huang, T and Jiang, X and Hu, M and Wu, H and Wang, J},
title = {A case report of Staphylococcus saccharolyticus bloodstream infection in a non-implanted host diagnosed by mNGS: Mechanism and pathogenesis analysis.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02408},
pmid = {41216181},
issn = {2214-2509},
abstract = {BACKGROUND: Staphylococcus saccharolyticus is an obligate anaerobic skin commensal that is rarely implicated in bloodstream infections, particularly in immunocompetent individuals without implanted medical devices. Due to its low virulence and fastidious growth requirements, it is often overlooked or dismissed as a contaminant. This report describes a rare case of S. saccharolyticus bacteremia and explores the underlying pathogenic mechanism.

CASE PRESENTATION: A 50-year-old immunocompetent female presented with recurrent low-grade fever and oral mucosal ulceration. Pathogen detection was performed using plasma-based metagenomic next-generation sequencing (mNGS), which identified S. saccharolyticus at a relative abundance of 15 % (seven species-specific reads). The result was corroborated by anaerobic blood culture. Laboratory assessment revealed severe vitamin D deficiency (25-hydroxyvitamin D: 11.6 ng/mL). Initial treatment with ceftriaxone was ineffective. Following the initiation of intravenous moxifloxacin and oral vitamin D supplementation (cholecalciferol 2000 IU/day), the patient's fever resolved within five days, and high-sensitivity C-reactive protein (hsCRP) levels decreased markedly from 88.3 mg/L to 12.0 mg/L. Mechanistically, the combination of mucosal barrier disruption due to oral ulceration and vitamin D deficiency may have facilitated translocation of the anaerobic pathogen into the bloodstream.

CONCLUSIONS: This case underscores the diagnostic value of mNGS in detecting low-biomass anaerobic infections and proposes a synergistic "mucosal barrier disruption-pathogen translocation" model. It also highlights the potential role of host-directed adjunctive therapy in managing bloodstream infections not associated with prosthetic material.},
}

@article {pmid41215794,
year = {2025},
author = {Onile-Ere, O and Name, PE and Tibiri, EB and Tiendrébéogo, F and Pita, J and Mohammed, IU and Nkere, CK and Oranusi, S and Eni, A},
title = {Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112204},
pmid = {41215794},
issn = {2352-3409},
abstract = {The dataset presented here was obtained by sequencing selected historic herbarium cassava samples collected across Nigeria. Total DNA was extracted from the samples using the CTAB method, after which the samples were enriched by Rolling Circle Amplification (RCA) and then sequenced on the MinION. The dataset consists of raw sequencing data in FASTQ format reflecting microbial diversity in cassava leaf samples. Taxonomic classification of the samples using the Kraken2 PlusPFP-16 database revealed 12 kingdoms, 36 phyla, 67 classes, 154 orders, 273 families, 524 genera, and 895 species across the dataset, with a substantial proportion (77.9%) of reads remaining unclassified following host removal. The data is beneficial for exploring the microbiome diversity of cassava leaves across Nigeria, as well as serving as a reference for future microbial discovery, given the large number of unidentified reads in the dataset.},
}

@article {pmid41214992,
year = {2025},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Aldehyde metabolism in Maotai-flavor Baijiu: insights from integrated metagenomic and metaproteomic analyses.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117518},
doi = {10.1016/j.foodres.2025.117518},
pmid = {41214992},
issn = {1873-7145},
abstract = {Acetaldehyde and acetal are crucial to the flavor of Maotai-flavor Baijiu, affecting aroma release and sauce-aroma traits. Targeted control of acetaldehyde metabolic flux is critical for stabilizing base liquor quality. However, the diversity of acetaldehyde-metabolizing enzymes and their microbial drivers remain uncharacterized, critically impeding precision control. This study selected the third production round to systematically investigate acetaldehyde accumulation dynamics and metabolic mechanisms. Time-resolved profiling showed that acetaldehyde and acetal concentrations display an initial rise, followed by a decline and stabilization. By integrated metagenomic and metaproteomic analyses, we confirmed that the metabolic network comprised two biosynthetic and three conversion pathways. The dominant biosynthetic pathway featured pyruvate decarboxylase (PDC)-catalyzed decarboxylation, while ethanolamine ammonia-lyase contributed minimally. Among conversion pathways, NADH-dependent alcohol dehydrogenase (NADH-ADH) reduction to ethanol predominated, with lower-flux oxidation to acetate and acetyl-CoA. Dynamic enzyme profiling revealed that PDC activity preceded the activation of NADH-ADH during stacking fermentation, resulting in a temporal mismatch between aldehyde production and consumption, which led to metabolic retention. During pit fermentation, acetaldehyde was more efficiently converted to ethanol through upregulation of NADH-ADH and NADH/NAD[+] ratio. As main contributors of PDC and NADH-ADH, Schizosaccharomyces pombe and Saccharomyces cerevisiae exhibited dual regulatory roles in acetaldehyde metabolism, with their metabolic mode shifts governed by dissolved oxygen and the NADH/NAD[+] ratio. Microbial interaction analysis and simulated fermentation confirmed that Pichia kudriavzevii synergized with Saccharomyces cerevisiae and Schizosaccharomyces pombe, driving rapid acetaldehyde accumulation during the stacking fermentation. These findings establish a theoretical framework for optimizing brewing processes and enhancing base liquor quality.},
}

@article {pmid41214941,
year = {2025},
author = {Kahraman Ilıkkan, Ö and Cerit, ZG and Baloglu, MC and Yılmaz, R},
title = {Microbial monitoring and Resistome analysis in white cheese production at a dairy plant: MALDI-TOF MS and shotgun metagenomics approaches.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117432},
doi = {10.1016/j.foodres.2025.117432},
pmid = {41214941},
issn = {1873-7145},
abstract = {This study presents a comprehensive microbiological evaluation of white cheese production in a small-scale dairy facility in northern Türkiye, integrating culture-dependent and culture-independent methods. Ten samples, including raw milk, milk with starter culture added, curd, clot, final cheese product, and environmental samples such as milk truck, cheese vessel, stirrer, cutting wire, and cheesecloth, were analyzed. Pathogenic bacteria were identified using MALDI-TOF MS, while shotgun metagenomics enabled a detailed investigation of microbial communities, antibiotic resistance genes (ARGs), and functional properties. The analysis using MALDI-TOF MS revealed ten pathogenic species, among which Staphylococcus aureus and Escherichia coli were the most dominant. Shotgun metagenomics corroborated the prevalence of S. aureus in dairy samples and Salmonella spp. on equipment surfaces, particularly the cheese vessel, stirrer, and cutting wire. The highest E. coli contamination was detected on cheesecloth, underscoring a critical point of concern. Across 15 antibiotic classes, 974 ARGs were identified, with equipment samples harboring significantly higher ARG loads than dairy products. Resistance mechanisms included β-lactamase enzymes, RND efflux pumps, and ribosomal protection proteins. Equipment samples showed an enrichment of carbohydrate-active enzymes (CAZymes), notably glycoside hydrolases and glycosyl transferases, suggesting microbial biofilm development and increased spoilage potential. Functional gene profiling revealed distinct metabolic signatures between dairy and equipment samples, with enriched pathways related to virulence and antimicrobial resistance in environmental samples. These findings underscore the limitations of conventional thermal treatment and the necessity of stringent sanitation practices, particularly for reusable equipment such as cheesecloth. The combined use of MALDI-TOF MS and shotgun metagenomics offers an effective strategy for microbial risk assessment in traditional cheese production systems.},
}

@article {pmid41214546,
year = {2025},
author = {Su, YS and Tsai, WH and Wu, HC and Chiu, YT and Jiang, NR and Lee, CY and Cheng, SH and Huang, CT and Chi, CY and Lin, EJ and Kuo, YP and Tsai, WT and Tien, CF and Liao, YC and Lee, KL and Chen, FJ and Yu, GY},
title = {Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1531},
pmid = {41214546},
issn = {1471-2334},
abstract = {BACKGROUND: Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are constrained by predefined targets, limiting their ability to detect novel or unexpected viral strains.

METHODS: We applied Oxford Nanopore Technology sequencing (ONT-Seq), a long-read, real-time, and multiplex metagenomic platform, to 85 clinical specimens using a sequence-independent, single-primer amplification (SISPA) workflow. Sequencing results were compared with routine clinical diagnostics for concordance and for identification of co-infections RESULTS: ONT-Seq achieved 80% concordance with clinical diagnostics and identified co-infections in 7% of cases missed by routine testing, including influenza C virus (ICV), and Sapporovirus. Among 58 adenovirus-positive cases, 31 samples with over 80% genome coverage at 20× depth were used for phylogenetic analysis, revealing adenovirus B3 as the predominant circulating strain.

CONCLUSIONS: ONT-based metagenomic sequencing enhances the detection of both known and emerging viruses in clinical specimens. Its ability to provide real-time, unbiased data supports its utility in improving diagnostic accuracy and viral surveillance.

CLINICAL TRIAL: Not applicable.},
}

@article {pmid41212644,
year = {2025},
author = {Acosta, DJ and Barth, DR and Bondy, J and Appler, KE and De Anda, V and Ngo, PHT and Alper, HS and Baker, BJ and Marcotte, EM and Ellington, AD},
title = {Plastic degradation by enzymes from uncultured deep sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41212644},
issn = {1751-7370},
abstract = {Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are commonly identified in bacteria; however, pipelines for discovery are often biased to recover highly similar enzymes. Here, we searched metagenomic data from hydrothermally impacted deep sea sediments in the Guaymas Basin (Gulf of California) for PETases. A broad diversity of potential proteins were identified and 22 were selected based on their potential thermal stability and phylogenetic novelty. Heterologous expression and functional analysis of these candidate PETases revealed three candidates capable of depolymerizing PET or its byproducts. One is a PETase from a Bathyarchaeia archaeon (dubbed GuaPA, for Guaymas PETase Archaeal) and two bishydroxyethylene terephthalate-hydrolyzing enzymes (BHETases) from uncultured bacteria, Poribacteria, and Thermotogota. GuaPA is the first archaeal PETase discovered that is able to depolymerize PET films and originates from a specific enzyme class which has endowed it with predicted novel structural features. Within 48 h, GuaPA released ~3-5 mM of terephthalic acid and mono-(2-hydroxyethyl) terephthalate from low crystallinity PET. PET co-hydrolysis containing GuaPA and one of the newly discovered BHETases further improves the hydrolysis of untreated PET film by 68%. Genomic analysis of the PETase- and BHETase-encoding microorganisms reveals that they likely metabolize the products of enzymatic PET depolymerization, suggesting an ecological role in utilizing anthropogenic carbon sources. Our analysis reveals a previously uncharacterized ability of these uncultured microorganisms to catabolize PET, suggesting that the deep ocean is a potential reservoir of biocatalysts for the depolymerization of plastic waste.},
}

@article {pmid41212311,
year = {2025},
author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY},
title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {42},
pmid = {41212311},
issn = {1433-4909},
abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.},
}

@article {pmid41211992,
year = {2025},
author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y},
title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0163724},
doi = {10.1128/jvi.01637-24},
pmid = {41211992},
issn = {1098-5514},
abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.},
}

@article {pmid41211985,
year = {2025},
author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O},
title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/msystems.01247-25},
pmid = {41211985},
issn = {2379-5077},
abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.},
}

@article {pmid41211947,
year = {2025},
author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A},
title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054325},
doi = {10.1128/msphere.00543-25},
pmid = {41211947},
issn = {2379-5042},
abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.},
}

@article {pmid41211940,
year = {2025},
author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ},
title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70101},
pmid = {41211940},
issn = {1529-8817},
support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; },
abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.},
}

@article {pmid41211921,
year = {2025},
author = {Wang, Q and Bao, H},
title = {Integrated metagenomics and metabolomics reveal the dynamic mechanism in the rhizosphere soil of Morus alba L. and Fraxinus mandshurica Rupr. with Inonotus hispidus.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0125125},
doi = {10.1128/aem.01251-25},
pmid = {41211921},
issn = {1098-5336},
abstract = {Inonotus hispidus is a medicinal fungus that grows on Morus alba L., Fraxinus mandshurica Rupr., and Ziziphus jujuba Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in the rhizosphere soil of different tree species, specifically M. alba and F. mandshurica, growing with I. hispidus. Therefore, this study conducts a multi-omics joint analysis utilizing metagenomics and metabolomics to explore the differences in the synergistic mechanisms between different hosts of I. hispidus. Using metagenomics technology, a total of 177 phyla and 2,651 genera were identified as significantly different. At both the phylum and genus levels, Actinomycetota and Pseudomonadota as well as Solirubrobacter and Bradyrhizobium emerged as the predominant phyla and genera, respectively. In the Kyoto Encyclopedia of Genes and Genomes database, carbohydrate and amino acid metabolisms were identified as the primary metabolic pathways. Differential analysis of these metabolic pathways revealed that glucokinase and pyruvate kinase were downregulated. Additionally, metabolomics analysis identified 558 differential metabolites, with tyrosine metabolism being the foremost metabolic pathway involved. This pathway included five differential metabolites, among which salidroside, 3,4-dihydroxyphenylpropanoate, rosmarinate, and homovanillate were significantly upregulated in M. alba in association with I. hispidus. Furthermore, correlation analysis indicated that Enhydrobacter was positively correlated with 10 differential metabolites, while Gaiella, Haladaptatus, Jiangella, and Prauserella showed negative correlations. This study lays a solid foundation for elucidating the interactions between I. hispidus and its hosts, as well as for the effective utilization of I. hispidus resources across different tree species.IMPORTANCEInonotus hispidus, which is traditionally recognized as the authentic source of the medicinal fungus, primarily grows on Morus alba L. It is commonly found in ancient regions along the Yellow River, including Linqing, Xiajin, and Wudi in Shandong, as well as Chengde in Hebei Province and Aksu in Xinjiang. In traditional Chinese medicine, it is known as "Sanghuang" and has a long history of medicinal use. In addition to M. alba, I. hispidus also grows on other broad-leaved species, such as Ulmus macrocarpa, Acer truncatum, and Fraxinus mandshurica. The lack of fundamental research on its multi-host and -source diversity has hindered its industrial development and medicinal value. Consequently, this study employs metagenomics and metabolomics to investigate the rhizosphere soil microbial diversity and differential metabolites associated with the different host plants of I. hispidus, specifically M. alba and F. mandshurica, with the aim of providing a reference for its resource conservation and development.},
}

@article {pmid41211880,
year = {2025},
author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ},
title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf592},
pmid = {41211880},
issn = {1477-4054},
support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China/ ; WU2022A009//National Natural Science Foundation of China/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //InnoHK program and Ant Group through CAAI-Ant Research Fund/ ; },
abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.},
}

@article {pmid41211879,
year = {2025},
author = {},
title = {Retraction and replacement of: FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf591},
pmid = {41211879},
issn = {1477-4054},
}

@article {pmid41210936,
year = {2025},
author = {Xu, Y and Miao, J and Chen, J and Ye, L and Yang, K and Wang, H},
title = {Metagenomic next-generation sequencing facilitates precision treatment and prognostic improvement in pulmonary cryptococcosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638215},
pmid = {41210936},
issn = {2235-2988},
abstract = {BACKGROUND: The early diagnosis of pulmonary cryptococcosis (PC) remains challenging due to the low sensitivity and prolonged turnaround time of conventional diagnostic methods. Despite the broad-spectrum pathogen detection capability of metagenomic next-generation sequencing (mNGS), its clinical utility in the diagnosis and therapeutic management of pulmonary cryptococcosis remains underexplored.

METHODS: In this retrospective study, 31 patients diagnosed with Cryptococcus infection through mNGS at The First Affiliated Hospital of Zhengzhou University between July 2023 to March 2025 were included. data on clinical characteristics, treatment regimens, and patient prognosis were systematically collected.

RESULTS: Compared to conventional pathogen detection methods, mNGS demonstrated superior sensitivity, shorter turnaround time (1.00 d vs. 4.50 d, p = 0.002), and significantly reduced interval from admission to clinical decision-making (3.50 d vs. 9.00 d, p = 0.002). Among 31 patients with mNGS-identified cryptococcal infection, only 12 underwent fungal culture, with merely 1 case yielding positive results (positivity rate: 8.33%). Antimicrobial therapy was optimized for all patients based on mNGS findings. During post-discharge follow-up of 27 cases, 1 patient experienced disease recurrence, 1 died from tumor metastasis, and 1 was lost to follow-up.

CONCLUSION: Our retrospective analysis revealed that mNGS facilitated treatment optimization, improved clinical outcomes, and provided crucial evidence supporting the precision management of pulmonary cryptococcosis.},
}

@article {pmid41210414,
year = {2025},
author = {Hu, L and Li, S and Gao, F and Diao, S and Liu, X and Qiu, J},
title = {Silent Threat: Multi-Organ Failure in Neonatal Scrub Typhus Without Traditional Markers.},
journal = {Clinical case reports},
volume = {13},
number = {11},
pages = {e71352},
pmid = {41210414},
issn = {2050-0904},
abstract = {Scrub typhus, an acute zoonotic disease from Orientia tsutsugamushi, is uncommon in newborns and presents atypical symptoms. Untimely diagnosis and treatment can lead to a prolonged and potentially fatal course. Early diagnosis and treatment are essential for better patient outcomes. Metagenomic next-generation sequencing can rapidly and accurately diagnose pathogens, aiding precise treatment.},
}

@article {pmid41210074,
year = {2025},
author = {Lin, L and You, W and Liao, Y and Wu, B and Lin, H and Huang, Z and Zeng, J and Zhang, Z and Huang, C and Li, W and Fang, X},
title = {Impact of Antibiotic Exposure Duration on Pathogen Detection in Periprosthetic Joint Infection.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5661-5670},
pmid = {41210074},
issn = {1178-6973},
abstract = {OBJECTIVE: Antibiotic exposure affects pathogen detection in periprosthetic joint infection (PJI). This study evaluated the impact of antibiotic duration before sampling on the diagnostic performance of microbiological cultures and metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective analysis of 153 patients with PJI treated at our center between January 2013 and March 2024. Patients who had discontinued antibiotics for at least 7 days before sampling and those with no history of antibiotic use were classified into the antibiotic-withdrawal group (AWD group). Based on the duration of antibiotic exposure, those who received antibiotics for ≤7 days before sampling was assigned to the short-term antibiotic group (STA group), while those with >7 days of continuous antibiotic use were included in the long-term antibiotic group (LTA group). By comparing microbiological culture and mNGS results across these groups, we analyzed how antibiotic duration before sampling affects etiological diagnosis in PJI patients.

RESULTS: In the AWD group, microbial culture positivity (86.3%, 44/51) was comparable to mNGS (92.2%, 47/51; P=0.338). However, mNGS demonstrated superior positivity rates in both the STA (86.7% vs 70.0%, P=0.027) and LTA groups (76.2% vs 54.8%, P=0.039). Prolonged antibiotic use (>7 days) markedly reduced culture positivity (86.3% to 54.8%, P=0.001), whereas the decline in mNGS sensitivity was smaller (92.2% to 76.2%, P=0.032), indicating its greater resistance to antibiotic effects. Among culture-negative PJI cases, mNGS maintained robust diagnostic performance across all groups (CN-AWD: 57.1%; CN-STA: 66.7%; CN-LTA: 57.9%), with no significant differences observed.

CONCLUSION: Antibiotic use before sampling significantly impacts PJI pathogen detection. We recommend either: (1) sampling after ≥7 days without antibiotics, or (2) for patients on prolonged antibiotics (>7 days), combining microbial culture with routine mNGS to improve diagnostic accuracy.},
}

@article {pmid41209715,
year = {2025},
author = {Yadav, P and Kumar, A and Ram, K and Kumar, A and Gupta, RK and Dufossé, L},
title = {Microbial degradation of microplastics: Effectiveness, challenges, and sustainable solutions.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100495},
pmid = {41209715},
issn = {2666-5174},
abstract = {Microplastics (MPs), defined as plastic particles ranging from 1 µm to 5 mm, have emerged as pervasive contaminants in both terrestrial and aquatic environments, posing significant ecological and human health risks. Their sources are broadly categorized as primary, such as microbeads, microfibres, paints and pharmaceutical additives, and secondary, which result from the degradation of larger plastic products. This growing concern of MPs led to development of different mitigation techniques but the recent advancements in microbial biodegradation present a promising approach to mitigating MPs pollution. Thus, microbial biodegradation could play a crucial role in developing sustainable solutions to tackle global MPs pollution. This review explores the potential of various microorganisms, including bacteria, fungi, and algae, in degrading MPs through enzymatic processes, thereby shortening the half-life of these pollutants. A detailed examination of the degradation mechanisms of commonly used polymers such as polyethylene, polystyrene, and polyvinyl chloride highlights the efficacy and limitations of microbial biodegradation. Despite the promising capabilities of certain strains, the overall weight loss rate of MPs remains quite low, typically ranging from 0 to 15%, necessitating further investigation into optimizing enzymatic activity and environmental conditions. Advancements in metagenomics and enzyme engineering offer pathways to enhance degradation efficiency, potentially achieving up to 90% degradation within 10 hrs under optimized conditions. This review underscores the need for comprehensive research to identify key microbial strains and enzymes involved, understand their degradation pathways, and investigate the influence of different environmental matrices on biodegradation processes.},
}

@article {pmid41208101,
year = {2025},
author = {Paul, JK and Akter, A and Jewel, NA and Rolin, MH and Karim, D and Niloy, RK and Mondal, SI},
title = {Exploration of Human Skin Phageome to Reveal Endolysins and Novel Antimicrobial Peptides for Therapeutic Applications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70115},
doi = {10.1002/mbo3.70115},
pmid = {41208101},
issn = {2045-8827},
support = {//The study was supported by the SUST Research Center (Grant number: LS/2023/1/05)./ ; },
abstract = {The global rise of antibiotic-resistant pathogens has intensified the search for alternative therapeutics. Bacteriophage-derived endolysins are emerging as promising candidates. They exhibit strong potential due to their target specificity, rapid bactericidal action, and low tendency to induce bacterial resistance. This study presents a comprehensive metagenomic analysis of the human skin phageome using 1564 samples from 10 metagenomic projects. Our analysis led to the classification of 696 phage genomes into clusters and singletons. These genomes displayed considerable variation in size, GC content (average 56%), and coding efficiency (72%). A total of 968 endolysins were identified, including 75 SAR variants, with diverse domain architectures such as CHAP, Amidase, and SH3, suggesting host-specific adaptations. Notably, we identified 37 previously unreported endolysin-derived antimicrobial peptides (AMPs), several of which exhibited nontoxic, antifungal, and antiviral properties. Molecular dynamics and docking studies revealed strong binding affinity and stability of peptides EP-464 and EP-519 to key virulence factors, including Staphylococcus epidermidis autolysin (PDB: 4EPC), beta-lactamase VIM-2 (PDB: 5O7N), and AHL synthase LasI (PDB: 1RO5). These interactions suggest potential for disrupting bacterial virulence, resistance mechanisms, and quorum sensing. This study provides the first large-scale functional characterization of the human skin phageome focused on therapeutic endolysins and their novel AMP derivatives, offering promising candidates for the development of next-generation antimicrobial agents. However, further experimental validation is essential to assess their clinical efficacy in treating skin-related infections.},
}

@article {pmid41207803,
year = {2025},
author = {You, TY and Chen, YW and Chen, SY and Jan, HE and Lee, NY and Ko, WC},
title = {Etiological identification of Rickettsia typhi and Coxiella burnetii by metagenomic next-generation sequencing among adults with acute febrile illness in southern Taiwan.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2025.11.012},
pmid = {41207803},
issn = {0929-6646},
}

@article {pmid41207298,
year = {2025},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1152},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

@article {pmid41207243,
year = {2025},
author = {Kumalo, PC and Amoah, ID and Pierneef, RE and Ismail, A and Bux, F and Kumari, S},
title = {Unveiling the role of aeration systems in the bioaerosol emission rate, particle size and microbial composition from wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140394},
doi = {10.1016/j.jhazmat.2025.140394},
pmid = {41207243},
issn = {1873-3336},
abstract = {Wastewater treatment plants (WWTPs) are important sources of bioaerosols; however, the influence of aeration on emission characteristics, particle size distribution, and microbial composition remains poorly studied. This study investigates how surface aeration (SA) and diffused aeration (DA) systems affect bioaerosol emission rates, particle size distribution, and microbial diversity using an 8-stage Andersen cascade impactor and shotgun metagenomics. Bioaerosol emission rates were estimated by combining measured particle concentrations with system-specific airflow rates. Abiotic factors were analysed through redundancy analysis to determine their influence on community structure. SA consistently generated higher emission rates, particularly in respirable particles (0.43-2.1 µm), which are capable of deep respiratory deposition. Dominant taxa included Rhodococcus, Pseudomonas, Bacillus, Meyerozyma, and Siphoviridae, with SA showing higher relative abundance of opportunistic pathogens even in smaller particle sizes. In contrast, DA systems exhibited a lower emission rate but broader microbial diversity, reflecting more stable aeration conditions. The study indicated that activated sludge was the main source of microbial populations, with a larger bioaerosol -activated sludge overlap in SA than DA. Redundancy analysis revealed that wind speed (WS) and relative humidity (RH) significantly influenced bacterial and viral populations, while WS and air temperature (AT) affected eukaryotes. Notably, SA emissions decreased with distance (100 m), while DA emissions increased. By quantifying emission rates rather than concentrations and integrating high-throughput metagenomics, this study provides a comprehensive framework for characterising bioaerosol hazards in WWTPs. These findings highlight the need for mitigation strategies in WWTPs, especially near SA systems.},
}

@article {pmid41207031,
year = {2025},
author = {Ren, Y and Li, Y and Lei, Y and He, R and Fu, J and Ma, D and Zhong, G},
title = {Deciphering microbial and metabolite dynamics in rice noodle fermentation: A metagenomic and untargeted metabolomic approach.},
journal = {Food chemistry},
volume = {497},
number = {},
pages = {147011},
doi = {10.1016/j.foodchem.2025.147011},
pmid = {41207031},
issn = {1873-7072},
abstract = {Inoculated fermentation accelerates rice noodle production and improves quality, but the underlying microbe-metabolite dynamics remain unclear. This study employed metagenomic and non-targeted metabolomic profiling to investigate microbial succession and metabolic transformations during fermentation. Lacticaseibacillus rhamnosus, Lactococcus cremoris, and Saccharomyces cerevisiae were identified as dominant strains, with Lacticaseibacillus rhamnosus rapidly outcompeting other microbes and suppressing Klebsiella pneumoniae and Salmonella enterica by over 70 %. At 6 h, rice noodle hardness and springiness improved markedly, driven by microbial shifts and metabolic outputs. Metabolomic analysis identified 1405 metabolites, of which 57 showed significant changes: aspartic and citric acid levels declined by 14.99 % and 33.16 %, while citrulline, γ-aminobutyric acid, lactate, and Cinnamic acid increased by 16.38 %, 8.96 %, 70.69 %, and 63.90 %, respectively. Enzyme annotation indicated α-amylase and glycogen synthase regulate starch degradation and amylose synthesis. These findings provide insights into the microbial and metabolic mechanisms that enhance the quality of fermented rice noodles.},
}

@article {pmid41206939,
year = {2025},
author = {Yu, H and Xu, Y and Chen, D and Gong, M and Sun, W and Liu, M and Zhang, T and Xue, J},
title = {The application of mNGS of bronchoalveolar lavage fluid in dissecting pulmonary infections in patients with CTD-ILD.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf571},
pmid = {41206939},
issn = {1462-0332},
abstract = {OBJECTIVES: To evaluate the application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of pulmonary infection in patients with connective tissue disease-associated interstitial lung disease (CTD-ILD).

METHODS: Patients with CTD-ILD who had been evaluated for suspected pulmonary infection by mNGS of BALF were identified, and were then categorized either as pulmonary infection or non-infectious disease progression of CTD-ILD based on clinical composite assessment. The performance of mNGS in the diagnosis of pulmonary infection was compared with that of conventional microbiological tests (CMTs).

RESULTS: In the 48 patients with CTD-ILD who had been evaluated for pulmonary infection by mNGS of BALF, the majority (66.67%) were patients with idopathic inflammatory myopathy-associated ILD (IIM-ILD). According to the clinical composite assessment, 36 patients were classified as pulmonary infection and 12 as non-infectious disease progression. Cytomegalovirus (CMV), pneumocystis jirovecii, and aspergillus were among the most common causative pathogens. While mNGS was superior in identifying bacteria, viruses, and pneumocystis jirovecii, CMTs identified more aspergillus and cryptococcus. Decreased albumin, reduced immunoglobulin M, and increased lactate dehydrogenase (LDH) were predictors for pulmonary infections in CTD-ILD. Short disease duration, decreased lymphocytes, and reduced immunoglobulins were predictive of infection with pneumocystis jirovecii. Older age and increased serum ferritin were more common in patients with aspergillus infection.

CONCLUSION: Pulmonary infections are common in patients with CTD-ILD. mNGS has the advantages of rapidly detecting more bacteria, viruses, and pneumocystis jirovecii. However, infection with aspergillus should be more rigorously evaluated in combination with CMTs.},
}

@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}

@article {pmid41206740,
year = {2025},
author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP},
title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf056},
pmid = {41206740},
issn = {1574-6976},
abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.},
}

@article {pmid41206659,
year = {2025},
author = {Siddiqui, R and Maciver, SK and Khan, NA},
title = {Beyond Predation: Potential Metabolic Roles of Intracellular Bacteria in Acanthamoeba Ecology.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf124},
pmid = {41206659},
issn = {1574-6968},
abstract = {Although Acanthamoeba is well known as a reservoir and "Trojan horse" for other microbes, its relationship with intracellular organisms may extend beyond protection. Here, we discuss that certain bacteria contribute metabolically to the host, breaking down complex substrates and providing nutrients that expand its ecological adaptability. The proposed model reframes amoebae not only as predators and shelters, but also as metabolic consortia, with implications for environmental microbiology, protist ecology, and the evolution of opportunistic pathogens. Further studies using integrated multi-omics and co-culture approaches, combining metagenomic and metabolomic profiling of Acanthamoeba-bacteria interactions and transcriptomic analyses will help identify bidirectional metabolic exchange and functional gene expression within the symbiosis.},
}

@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}

@article {pmid41205488,
year = {2025},
author = {Lv, AP and Ying-Han, and Fang, BZ and Wang, GZ and Liu, MC and Bian, BR and Zheng, ZH and Li, K and Li, BY and Jiao, JY and Liu, L and Dong, L and Chen, LQ and Yang, F and Li, WJ},
title = {Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {6},
pages = {126667},
doi = {10.1016/j.syapm.2025.126667},
pmid = {41205488},
issn = {1618-0984},
abstract = {Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus Pseudogracilibacillus. Phylogenomic analysis demonstrated that three MAGs (A3-12A_bin_9[TS], M2-6-2A_bin_27 and M2-7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus Pseudogracilibacillus. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name Pseudogracilibacillus amylolyticus sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family Bacillaceae in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.},
}

@article {pmid41205408,
year = {2025},
author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J},
title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.},
journal = {Journal of neuroradiology = Journal de neuroradiologie},
volume = {53},
number = {1},
pages = {101402},
doi = {10.1016/j.neurad.2025.101402},
pmid = {41205408},
issn = {0150-9861},
abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.

MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.

RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (β =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (β =-0.003), CRP (β =-0.035), SII (β =-0.062), INFLA (β =-0.010), and SIRI (β =-0.058). We also observed significant correlations between DKI ALPS index and ESR (β =-0.006), CRP (β =-0.051), SII (β =-0.130), INFLA (β =-0.017), SIRI (β =-0.095), IL-6 (β =-0.081) and NLR (β =-0.108).

CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.},
}

@article {pmid41205292,
year = {2025},
author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA},
title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118904},
doi = {10.1016/j.marpolbul.2025.118904},
pmid = {41205292},
issn = {1879-3363},
abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.},
}

@article {pmid41205042,
year = {2025},
author = {Zolkefli, N and Shui, X and Ma, K and Mustapha, NA and Maeda, T},
title = {Unveiling the Impact of Indole Derivatives on Methanogenic Archaea and Microbial Functions in Anaerobic Digestion of Waste Sewage Sludge.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41205042},
issn = {1559-0291},
abstract = {As an interspecies-signaling molecule, indole that is also regulating the microbial community quorum sensing (QS) can be an indispensable factor in influencing the performance of an anaerobic digestion process. Mainly released by Gram-negative bacteria, the impact of indole regulation on methane production in such a system is hardly exposed. This research intends to analyze the methane production affected by the microbial community fluctuations in the waste sewage sludge (WSS) in response to QS repression by indole and its analogs: 4-fluoroindole (4-FI), 5-fluoroindole (5-FI), 6-fluoroindole (6-FI), 3-indoleacetic acid (3-IAA), and 3-indoleacrylic acid (3-IARA). Illumina MiSeq platform was utilized to delve into the active microbes, with ribonucleic acid (RNA) used as the template to generate the 16S metagenomic library. As results, all of them inhibit methane generation even with substrates (acetic acid) availability, and this phenomenon can be led by the slight imbalance of Gram-positive/negative bacterial composition and the inactivation of the viable core fermenters: Firmicutes, Proteobacteria, and Chloroflexi. Plus, the following compounds, indole, 3-IAA, and 6-FI directly disrupted methane production by both acetoclastic and hydrogenotrophic methanogenic archaea. Methanosarcina acetivorans C2A, as a prominent methane synthesizer, was also characterized in terms of its viability and methane synthesis activity against them. Notably, Methanosarcina acetivorans C2A was non-viable in the presence of indole and 6-FI, thus lowering methane production. From here, the affirmation of the direct and indirect inhibitions of methanogenic archaea by indole and its derivatives will pave the way for a valuable future exploration of QS mechanism mapping in archaea during methanogenesis.},
}

@article {pmid41204634,
year = {2025},
author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q},
title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.},
journal = {Journal of food science},
volume = {90},
number = {11},
pages = {e70654},
doi = {10.1111/1750-3841.70654},
pmid = {41204634},
issn = {1750-3841},
support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; },
abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.},
}

Animals
*Gastrointestinal Microbiome
*Probiotics/pharmacology
Rats, Inbred SHR
*Antihypertensive Agents/pharmacology
Rats
*Hypertension/diet therapy
Male
Blood Pressure/drug effects
*Cultured Milk Products/microbiology
Fermentation
Lactobacillus plantarum/metabolism
Renin-Angiotensin System/drug effects
Metabolomics
Multiomics

@article {pmid41204581,
year = {2025},
author = {Zhuang, Q and Xu, R and Sun, X and Pan, X and Wan, L and Li, S and Chen, H and Yu, X and Zheng, L and Yu, Y and Deng, Z and Zheng, X and Chen, Z},
title = {Performance of metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen detection in patients with acute exacerbations of bronchiectasis.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45606},
doi = {10.1097/MD.0000000000045606},
pmid = {41204581},
issn = {1536-5964},
support = {FYQM-LC-202003//The Affiliated Hospital of Medical School of Ningbo University Youth Talent Cultivation Program/ ; 2021Y13//Ningbo Medical Science and Technology Program/ ; 2015C50012//Ningbo Social and Scientific Development Fund/ ; 2020SWSQNGG-05//Ningbo Health Youth Technical Key Talents Training Special Project/ ; 2018A610271ã€2017A610250//the Natural Science Foundation of Ningbo/ ; 2022ZYC-Z31//Clinical Medicine Special Fund Project of Zhejiang Medical Association/ ; Normal project No.6//Special Project on Scientific and Technological Research of COVID-19 Infection Diseases/ ; 2016KYB268//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; },
mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Pseudomonas aeruginosa/isolation & purification ; Sensitivity and Specificity ; },
abstract = {This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in detecting pathogens among bronchiectasis patients with acute exacerbations. A retrospective analysis was conducted on 89 bronchiectasis patients who were treated for acute exacerbations at the First Affiliated Hospital of Ningbo University from April 1, 2021, to September 30, 2023. Among the 89 patients, 88 were diagnosed with pulmonary infection, of which 15.9% (14/88) were cases of mixed infections. The sensitivity of BALF-mNGS for detecting pathogens in bronchiectasis patients during acute exacerbations was significantly higher than that of BALF culture (93.2% vs 28.4%; P < .001). All cases of mixed infection were fully identified by BALF-mNGS. The most common pathogens in patients with bronchiectasis were Pseudomonas aeruginosa, nontuberculous mycobacteria, Haemophilus influenzae, and Aspergillus. In conclusion, compared with the traditional microbial culture method, BALF-mNGS significantly improves the accuracy of diagnosis for detecting pathogens associated with bronchiectasis infections.},
}

Humans
*Bronchiectasis/microbiology
*Bronchoalveolar Lavage Fluid/microbiology
Male
Retrospective Studies
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Aged
*Metagenomics/methods
Pseudomonas aeruginosa/isolation & purification
Sensitivity and Specificity

@article {pmid41204496,
year = {2025},
author = {Tian, J and Dong, J and Yu, G and Guan, W},
title = {Bronchoscopy-associated dissemination of pulmonary nocardiosis caused by Nocardia terpenica in an immunocompetent patient with bronchiectasis: A case report.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45875},
doi = {10.1097/MD.0000000000045875},
pmid = {41204496},
issn = {1536-5964},
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/etiology/microbiology ; Middle Aged ; *Bronchoscopy/adverse effects ; *Bronchiectasis/complications ; *Nocardia/isolation & purification ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Bronchoalveolar Lavage/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration & dosage ; Bronchoalveolar Lavage Fluid/microbiology ; Immunocompetence ; },
abstract = {RATIONALE: Bronchoscopy with bronchoalveolar lavage (BAL) is essential for diagnosing pulmonary infections; however, its potential to iatrogenically disseminate a localized Nocardia infection represents a severe and unreported risk. This case aims to alert clinicians to this danger and underscore essential therapeutic lessons for disseminated disease.

PATIENT CONCERNS: A 51-year-old immunocompetent woman with longstanding bronchiectasis presented with 1-day of hemoptysis and a 40-year history of chronic cough and sputum production. These symptoms had worsened over the preceding 2 months despite broad-spectrum antibiotic therapy.

DIAGNOSES: Bronchiectasis was diagnosed based on chronic respiratory symptoms and characteristic computed tomography findings. Nocardia terpenica infection was confirmed by BAL fluid culture and metagenomic next-generation sequencing. Within 24 hours post-BAL, the patient developed fever, respiratory failure, and new bilateral consolidations on computed tomography, indicating procedure-related disseminated nocardiosis.

INTERVENTIONS: Diagnostic bronchoscopy with BAL was performed. Therapeutically, the patient received a total of 24 days of intensive combination therapy with intravenous imipenem/cilastatin and oral trimethoprim-sulfamethoxazole (TMP-SMX), followed by sequential long-term oral TMP-SMX monotherapy.

OUTCOMES: The initial 10-day course of combination therapy led to rapid clinical improvement, with resolution of fever and respiratory failure within 3 days, and normalization of C-reactive protein levels by day 10. Radiographic improvement was also evident. However, relapse (recurrent fever and malaise) occurred promptly within 3 days after de-escalation to TMP-SMX monotherapy. After reinstitution of imipenem/cilastatin plus TMP-SMX for an additional 14 days (totaling 24 days of intensive therapy), the patient achieved sustained clinical and radiographic remission. She was successfully discharged on long-term TMP-SMX monotherapy and remained well at the 2-month follow-up.

LESSONS: This is the first report suggesting that bronchoscopy, particularly BAL, can disseminate a localized airway Nocardia infection, causing acute disseminated pulmonary nocardiosis. Extreme caution is warranted when performing bronchoscopy in bronchiectasis patients with suspected or confirmed nocardiosis. For disseminated pulmonary nocardiosis, intensive combination therapy for at least 3 weeks is mandatory to prevent relapse, regardless of a rapid initial response.},
}

Humans
Female
*Nocardia Infections/drug therapy/diagnosis/etiology/microbiology
Middle Aged
*Bronchoscopy/adverse effects
*Bronchiectasis/complications
*Nocardia/isolation & purification
Anti-Bacterial Agents/therapeutic use/administration & dosage
Bronchoalveolar Lavage/adverse effects
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration & dosage
Bronchoalveolar Lavage Fluid/microbiology
Immunocompetence

@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}

Humans
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Intensive Care Units, Neonatal
Metagenomics
Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Gestational Age
Enteral Nutrition

@article {pmid41203352,
year = {2025},
author = {Tonoli, A and Dalby, PA and Hailes, HC and Jeffries, JWE},
title = {Transketolase enzyme discovery and engineering.},
journal = {Methods in enzymology},
volume = {722},
number = {},
pages = {343-368},
doi = {10.1016/bs.mie.2025.07.002},
pmid = {41203352},
issn = {1557-7988},
mesh = {*Transketolase/genetics/metabolism/chemistry/isolation & purification ; Substrate Specificity ; *Protein Engineering/methods ; Directed Molecular Evolution/methods ; Ribosemonophosphates/metabolism ; Metagenomics/methods ; Pyruvates ; },
abstract = {Transketolases (TKs) are important C-C bond forming enzymes that in vivo transfer a two carbon ketol unit to the acceptors d-ribose-5-phosphate or d-erythrose-4-phosphate. There is significant interest in biocatalytic applications where frequently the donor β-hydroxypyruvic acid is used. In recent years there has been interest in the discovery of new TKs with unique or robust properties that are an excellent starting point for mutagenesis, or that are able to accept new acceptors or donors. Similarly, TK mutagenesis has led to TKs with alternative substrate profiles. In this chapter, firstly an overview of the substrates accepted by TKs is briefly summarized. Then, metagenomic strategies for the discovery of unique TKs and how this approach has developed with an early example, and a more recent study on the discovery of 'split'-TKs, are described with methods. Finally, enzyme evolution methods and approaches to develop a wide range of TKs with modified substrate acceptance and improved stabilities are detailed.},
}

*Transketolase/genetics/metabolism/chemistry/isolation & purification
Substrate Specificity
*Protein Engineering/methods
Directed Molecular Evolution/methods
Ribosemonophosphates/metabolism
Metagenomics/methods
Pyruvates

@article {pmid41203168,
year = {2025},
author = {Vangah, SJ and Kermani, AA and Vali, H and Noghabi, KA and Zahiri, HS},
title = {Engineering Saccharomyces cerevisiae for the secretion of an acidic, halotolerant, and cold-adapted xylanase derived from the camel rumen metagenome: Enzyme characterization and strain assessment.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148805},
doi = {10.1016/j.ijbiomac.2025.148805},
pmid = {41203168},
issn = {1879-0003},
abstract = {This study reports the development of a recombinant Saccharomyces cerevisiae strain engineered to produce and secrete a novel xylanase (rXylM) derived from the camel rumen metagenome. The recombinant enzyme exhibited optimal activity at 35 °C, pH 5.0, and retained 58 % of its activity even at 5 °C. The enzyme activity was not significantly affected by high sodium chloride (NaCl) concentrations up to 5 M. These properties characterize rXylM as an acidic, halotolerant, and cold-adapted xylanase. The combination of these adaptive traits in a single enzyme offers substantial advantages for industrial applications. Enzyme kinetic analysis was performed at 35 °C and pH 5.0 using beechwood xylan, wheat bran, and high-extraction wheat flour as substrates, yielding specific activities of 1190 U/mg, 1029 U/mg, and 383 U/mg respectively. Scanning electron microscopy (SEM) revealed noticeable morphological alterations indicating substantial degradation of the substrates following treatment with rXylM. The engineered strain, CEN.PK-Xyl, was assessed as a leavening agent for baking applications. Rheological analysis of the dough demonstrated a significant reduction in elasticity and viscous resistance, improving dough handling and kneading properties. Correspondingly, the resulting bread exhibited a significant decrease in hardness, gumminess, and chewiness, indicating an improvement in texture and overall quality. Cytotoxicity evaluation using the MTT assay showed that rXylM did not affect the viability of L929 mouse fibroblast cells under the tested conditions. The favorable biochemical properties and non-toxicity of rXylM, together with the established safety of S. cerevisiae, highlight CEN.PK-Xyl as a promising platform for applications in food, feed, bioprocessing, and fermentation.},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202935,
year = {2025},
author = {Wu, B and Cheng, Y and Gu, J and Yuan, H and Murphy, JD},
title = {Toward sustained and efficient n-caproate production: Insights into magnetite-encapsulated biochar mediated microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133617},
doi = {10.1016/j.biortech.2025.133617},
pmid = {41202935},
issn = {1873-2976},
abstract = {Decarbonization of the chemical sector may be facilitated by microbial chain elongation, through conversion of organic waste into chemical products. Challenges in efficient interspecies electron transfer is a barrier to this technology. Here we introduce a magnetite-encapsulated biochar (Fe@biochar) amendment strategically integrated with chain elongation to facilitate sustained and efficient n-caproate production. This strategy increased n-caproate yields to 13.92 g COD/L, 199 % and 71 % higher than the control (4.66 g COD/L) and biochar (8.13 g COD/L) groups, respectively. Most importantly, Fe@biochar consistently enhanced n-caproate production after recycle, a continuity not observed with biochar. This difference may be attributed to the inhibitory effects of high concentrations of undissociated n-caproic acid (up to 9.06 mM or 2.32 g COD/L) on functional microbes in the biochar group. Microbial community analysis identified Clostridium_sensu_stricto as the key genus involved in n-caproate production. Comparative metagenomic and microbial activity analyses revealed the energy metabolism, where Fe@biochar promoted extracellular iron-based electron transfer, and further accelerated intracellular electron sinks. This is substantiated by a 3.6 fold increase in electron transfer system activity and evaluated relative abundances of key genes encoding acetyl-CoA synthetase (15.0 % increase), cytochrome c biosynthesis (28.7 % increase) and NADH dehydrogenase (48.0 % increase). This study offers a new paradigm for sustained n-caproate production.},
}

@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}

@article {pmid41202381,
year = {2025},
author = {Jiang, CH and Zhang, SJ and Li, P and Miao, H and Zhao, YY},
title = {Natural products targeting TGF-β/Smad signaling in renal fibrosis: Multiomics-based novel molecular mechanisms and therapeutic strategies.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157496},
doi = {10.1016/j.phymed.2025.157496},
pmid = {41202381},
issn = {1618-095X},
abstract = {BACKGROUND: Renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) have become one of the major global public health challenges. Regardless of the underlying aetiology, renal fibrosis is a common pathological endpoint in the progression of diverse kidney diseases to end-stage renal disease. Increasing studies have highlighted that emerging multi-omics techniques (metagenomics, transcriptomics, proteomics and metabolomics) have been used for elucidating the pathogenesis of kidney disease and underlying molecular mechanism of renal fibrosis. However, few reviews provide a comprehensive and systematic presentation of multi-omics signaling-mediated TGF-β/Smad pathway in both AKI and CKD as well as therapeutic strategies for targeting signaling cascades by natural products.

PURPOSE AND STUDY DESIGN: This review summarizes multi-omics signaling-mediated TGF-β/Smad pathway and therapeutic strategies of natural products by targeting this signaling axis in patients and animal models with kidney disease.

METHODS: All the available information is searched by several electronic database such as Web of Science, Pubmed, ScienceDirect, Splinker, Google Scholar, etc., that covered approximately 1000 publications from 2015 to 2025.

RESULTS: Ample evidence has indicated that transforming growth factor-β (TGF-β)/suppressor of mothers against decapentaplegic (Smad) signaling pathway plays a central role in renal fibrosis. Based on the multi-omics techniques, a variety of novel mediators are identified and affects kidney diseases by regulating TGF-β/Smad pathway. Therefore, targeting TGF-β/Smad pathway is an important and promising antifibrotic therapy. This review summarizes TGF-β/Smad pathway in both AKI and CKD, elaborate on the multidimensional regulatory mechanisms in renal fibrosis by crosstalk between TGF-β/Smad pathway and novel multi-omics signaling-associated mechanisms including microbial dysbiosis, dysregulating non-coding ribonucleic acids including long non-coding RNAs and microRNAs and metabolite disorder and shed light on the latest therapeutic effects of natural products such as terpenoids, anthraquinones, xanthones and flavonoids as well as natural polysaccharides by targeting multi-omics signaling-mediated TGF-β/Smad pathway.

CONCLUSION: This review presents a multiomics-driven therapeutic strategy for the development of effective and precise antifibrotic therapies.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001541},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}

Animals
Phylogeny
Genome, Viral
*Skates, Fish/virology
*Papillomaviridae/genetics/isolation & purification/classification
*Papillomavirus Infections/virology/veterinary
Sequence Analysis, DNA
DNA, Viral/genetics

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201496,
year = {2025},
author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C},
title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.10.048},
pmid = {41201496},
issn = {2090-1224},
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.

OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.

METHODS: PPE was extracted using 50 % ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.

RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1α/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.

CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1α/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41200800,
year = {2025},
author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Chen, CH and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E},
title = {Metagenomics in the diagnosis of pneumonia: a systematic review.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/23744235.2025.2580954},
pmid = {41200800},
issn = {2374-4243},
abstract = {BACKGROUND: Pneumonia is a major cause of morbidity and mortality, yet causative organisms are rarely identified. Metagenomic next-generation sequencing (mNGS) may improve this, however the impact on outcomes is uncertain and the relative utility in pneumonia subtypes or different clinical samples is unclear.

METHODS: This systematic review compared mNGS with conventional microbiology, assessing pathogen identification, turnaround time and clinical impact. It also reviewed difference related to the pneumonia subtype, or sample used. We searched EMBASE, MEDLINE, Scopus, and the Cochrane Central Register of Controlled Trials (CENTRAL) for studies comparing mNGS with conventional microbiology, in patients with pneumonia. All study types were included (excluding case reports of <10 people). Eligibility assessment and data extraction was performed by two independent reviewers, and risk of bias assessed using the QUADAS-2.

RESULTS: We identified 74 studies including 10,566 people, with all studies having high risk of bias or applicability concerns in at least one domain. Conventional tests identified a pathogen in 43.2% of cases (3559/8229) compared to 78.9% for mNGS (6242/7980). mNGS had faster turnaround times than conventional microbiology (MD -73.6h, CI-111.36 - -35.73 hrs) but meta-analysis was not possible for other outcomes. Most studies did not specify the pneumonia subtype. 92%of studies used exclusively or predominantly bronchoalveolar lavage fluid (BALF), and the utility of other sample types could not be established.

CONCLUSIONS: mNGS may identify possible pathogens with greater frequency than standard techniques although bias in study design limits definite conclusions, and the clinical relevance of this remains unresolved. There is a need for studies assessing clinical outcomes, and the differential impact in pneumonia subtypes and in samples other than BALF.},
}

@article {pmid41200470,
year = {2025},
author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {535},
pmid = {41200470},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).},
}

@article {pmid41200317,
year = {2025},
author = {Kazemzadeh, S and Korneeva, O and Shabunin, S and Syromyatnikov, M},
title = {Antibiotic resistance in mastitis-causing bacteria: Exploring antibiotic-resistance genes, underlying mechanisms, and their implications for dairy animal and public health.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {3980-4006},
pmid = {41200317},
issn = {2218-6050},
mesh = {Animals ; *Mastitis, Bovine/microbiology/drug therapy ; Female ; Cattle ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Public Health ; *Bacteria/drug effects/genetics ; Dairying ; Humans ; Milk/microbiology ; },
abstract = {The development and spread of superbugs, which are bacterial strains resistant to several types of antibiotics, threatening the lives of myriad people and animals worldwide, is one of the most concerning issues facing both global and animal health. Dairy animals are considered to be key reservoirs of antibiotic-resistant bacteria, which are closely correlated with the widespread and inappropriate application of antibiotics in agriculture and veterinary medicine, particularly for mastitis treatment. Although antimicrobial agents are administered in dairy farming for various conditions beyond mastitis, such as respiratory infections and digestive disorders, as well as prophylaxis and growth promotion, the most common reason for antimicrobial use in this industry is mastitis treatment. Since raw milk can be contaminated with opportunistic pathogens carrying antimicrobial resistance genes, these pathogens increase the gene pool from which pathogenic bacteria can acquire resistance traits. Indeed, these resistance genes may be horizontally transferred from livestock to human pathogens through mobile genetic elements through the consumption of raw milk. This phenomenon poses a global health threat, emphasizing the necessity of applying the "One Health" approach in global health and medicine to safeguard animal health and public health. Given the high prevalence and economic impact of mastitis and the evidence supporting mastitis as a major driver of antimicrobial use in dairy farming, this review summarizes recent genomic and metagenomic studies on major mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, Streptococcus spp., and Pseudomonas spp.) in dairy animals, detailing their primary resistance mechanisms. We highlight advanced surveillance tools, such as metagenomics, whole-genome sequencing, and quantitative polymerase chain reaction, for the rapid detection of resistance genes and mobile elements in the dairy chain.},
}

Animals
*Mastitis, Bovine/microbiology/drug therapy
Female
Cattle
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Public Health
*Bacteria/drug effects/genetics
Dairying
Humans
Milk/microbiology

@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.

METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.

RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-α and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.

DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}

@article {pmid41199948,
year = {2025},
author = {Vasanthrao, R and Nidhin, IK and Taj, Z and Chattopadhyay, I},
title = {Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649872},
pmid = {41199948},
issn = {1664-302X},
abstract = {INTRODUCTION: Environmental contamination by heavy metals and hydrocarbons significantly impacts microbial diversity and soil functionality.

METHODS: This study employs whole-genome metagenome sequencing to analyse microbial compositions, antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRs), and virulence genes (VGs) in soil samples from diverse locations, including gardens, poultry farms, cattle sheds, markets, hospitals, thermal power plants, paper industries, and waste disposal sites.

RESULTS: The findings indicate that heavy metal concentrations (Pb, Cr, Cd, and Cu) and hydrocarbons (heptadecane, triacontane, docosane, and heneicosane) were positively correlated with several microbial phyla with relatively high abundances in these contaminated sites, such as Actinobacteria, Proteobacteria, Basidiomycota, Ascomycota, Euryarchaeota, and Apicomplexa. The prevalence of multidrug resistance genes, including MexD, MexC, MexE, MexF, MexT, CmeB, MdtB, MdtC, and OprN, was significant, facilitating antibiotic resistance primarily via efflux pump mechanisms (42%), followed by antibiotic inactivation (23%) and changes in antibiotic targets (18%). Virulence genes such as espR, regX3, sigA/rpoV, bap, and sugB were significantly prevalent in contaminated locations, indicating microbial pathogenic potential in polluted ecosystems. The functional gene analysis revealed significant metabolic pathways related to protein metabolism, carbohydrates, amino acids and their derivatives, metabolism, and DNA metabolism, highlighting the microbial adaptation processes engaged in pollution degradation and resource utilisation.

DISCUSSION: This study establishes a clear link between environmental pollution, microbial adaptations, and functional resilience, emphasizing the ecological significance of microbial bio-remediation in shaping targeted remediation strategies and long-term ecological recovery. Understanding these microbial interactions is essential for developing targeted remediation techniques and assessing long-term ecological recovery in contaminated regions.},
}

@article {pmid41199944,
year = {2025},
author = {Dai, L and Guo, XR and Chen, XR and Ma, MH and Liu, ZH and Lai, J and Lu, J and Feng, M and Liu, XX and Yang, SH},
title = {A review of the mechanism, diagnosis, and treatment of Naegleria fowleri infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1686695},
pmid = {41199944},
issn = {1664-302X},
abstract = {Naegleria fowleri is a rare pathogen responsible for primary amoebic meningoencephalitis (PAM), a fatal central nervous system infection characterized by rapid clinical progression and an extremely high mortality rate. The existing diagnostic methods are insufficiently sensitive, and therapeutic options are minimal, making early recognition and intervention extremely challenging. This review systematically examines the biological characteristics and pathogenic mechanisms of this pathogen, as well as current diagnostic and treatment strategies, with a particular focus on the groundbreaking applications of emerging technologies such as metagenomic next-generation sequencing (mNGS) in the diagnosis of difficult-to-treat infections. The aim is to provide theoretical support and practical guidance for rapid identification, accurate diagnosis, and timely intervention in clinical practice, serving as a reference for the prevention and treatment of N. fowleri infections.},
}

@article {pmid41199943,
year = {2025},
author = {Zhang, M and Di, H and Wang, S and Ning, Z},
title = {Column experiment reveals high natural attenuation potential for toluene in iron-rich aquifers but significant concomitant secondary Fe pollution risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687219},
pmid = {41199943},
issn = {1664-302X},
abstract = {INTRODUCTION: Iron mineral reduction mediated by indigenous microbes represents a crucial natural attenuation mechanism for organic contaminants like toluene in anaerobic aquifers, yet the partitioning of generated Fe(II) species and associated secondary pollution risks remain poorly constrained.

METHODS: This study employed controlled column experiments simulating an iron-rich aquifer (ferrihydrite-amended quartz sand) to track the biogeochemical dynamics of toluene degradation coupled with iron transformation. Over 43 days, we quantified spatiotemporal changes in toluene concentrations, dissolved/solid-phase iron species, and microbial community structure through high-frequency hydrochemical monitoring and metagenomic sequencing.

RESULTS AND DISCUSSION: Results demonstrated that iron-reducing consortia (notably Thiobacillus and Pseudomonas) drove > 99% toluene degradation within 10 cm flow distance, effectively containing plume migration. However, Fe(III) reduction generated Fe(II) predominantly (98%) as immobile solid-phase minerals, with only 1%-2% manifesting as dissolved Fe[2+]. This dissolved fraction accumulated progressively across space and time, exceeding China's groundwater quality threshold (0.3 mg/L) at 90% of monitoring points by experiment termination despite near-complete toluene removal. The study confirms that iron-rich aquifers provide significant natural attenuation capacity for petroleum hydrocarbons but concurrently pose substantial secondary contamination risks through highly mobile Fe[2+] generation. Therefore, it is recommended to include solidphase ferrous iron [Fe(II)] as an indicator in natural attenuation assessments and to take into account biogeochemical by-products such as Fe[2+] in risk assessment efforts.},
}

@article {pmid41199942,
year = {2025},
author = {Zeng, W and Yang, L and Cui, L and Liang, C and Zhu, D and Fang, Y and Zhang, Y and Liu, H},
title = {Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699705},
pmid = {41199942},
issn = {1664-302X},
abstract = {INTRODUCTION: Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.

METHODS: This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species-Haemaphysalis flava, Haemaphysalis longicornis, and Rhipicephalus sanguineus sensu lato-were collected and analyzed through metagenomic sequencing.

RESULTS: The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.

DISCUSSION: These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.},
}

@article {pmid41199613,
year = {2025},
author = {Kagemasa, S and Kuroda, K and Nakai, R and Sato, M and Li, YY and Kubota, K},
title = {Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70231},
doi = {10.1111/1758-2229.70231},
pmid = {41199613},
issn = {1758-2229},
support = {JP18H01564//Japan Society for the Promotion of Science/ ; JP21H01460//Japan Society for the Promotion of Science/ ; JP23H02545//Japan Society for the Promotion of Science/ ; JP23K27236//Japan Society for the Promotion of Science/ ; JP23K19153//Japan Society for the Promotion of Science/ ; JP24H00328//Japan Society for the Promotion of Science/ ; JP21J11654//Japan Society for the Promotion of Science/ ; //Tohou University - AIST matching fund/ ; //MEXT WISE Program for Sustainability in Dynamic Earth (SyDE), Japan/ ; },
mesh = {*Sewage/microbiology ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Wastewater/microbiology ; },
abstract = {Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46-1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.},
}

*Sewage/microbiology
Phylogeny
Genome, Bacterial
Metagenomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Wastewater/microbiology

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid41198952,
year = {2025},
author = {Makarova, KS and Shmakov, SA and Wolf, YI and Mutz, P and Altae-Tran, H and Beisel, CL and Brouns, SJJ and Charpentier, E and Cheng, D and Doudna, J and Haft, DH and Horvath, P and Moineau, S and Mojica, FJM and Pausch, P and Pinilla-Redondo, R and Shah, SA and Siksnys, V and Terns, MP and Tordoff, J and Venclovas, Č and White, MF and Yakunin, AF and Zhang, F and Garrett, RA and Backofen, R and van der Oost, J and Barrangou, R and Koonin, EV},
title = {An updated evolutionary classification of CRISPR-Cas systems including rare variants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41198952},
issn = {2058-5276},
support = {Intramural funds//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.},
}

@article {pmid41198823,
year = {2025},
author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, Ó},
title = {The association of the rumen virome with methane emissions in dairy cattle.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1534},
pmid = {41198823},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; },
abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.},
}

Animals
Cattle
*Methane/metabolism/biosynthesis
*Rumen/virology/microbiology/metabolism
*Virome
Female
Viruses/genetics/classification
Metagenome
Bacteria/metabolism
Metagenomics

@article {pmid41197746,
year = {2025},
author = {Yu, PF and Jiang, DL and Wang, D and Ma, XG and Jun-Li, and Han, LY and Wang, A and Fu, YB and Jin, X},
title = {Manganese cycle-mediated synchronous bacteria-algae/anammox coupled denitrification system under low-temperature conditions: Performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133593},
doi = {10.1016/j.biortech.2025.133593},
pmid = {41197746},
issn = {1873-2976},
abstract = {The treatment of high-nitrogen complex wastewater in an efficient, economical, and environmentally friendly manner has attracted growing attention in recent years. However, slow reaction rates remain a significant obstacle to its broad application. This study investigated the addition of Mn@BC to enhance the low-temperature resistance of an anaerobic ammonia oxidation (anammox) process coupled with denitrification. The results demonstrated that under 17℃ conditions, the average nitrogen removal efficiency increased to 82% with the addition of Mn@BC, representing a 9% improvement compared to the addition of BC alone. Moreover, Mn@BC promoted the secretion of extracellular polymeric substances and diversified the microbial community structure.The incorporation of microalgae created a synergistic microalgal-bacterial system that maintained a phosphorus removal rate of 50% and reduced the reliance on external organic carbon, as confirmed by TOC analysis.The underlying intra- and extracellular metabolic pathways, formed by functional genes including mtrC, nirS/K, and c-Cyts, were elucidated using metagenomic sequencing. Therefore, the development of a high-efficiency nitrogen and phosphorus removal process capable of synchronizing microalgal-bacterial interactions, overcoming low-temperature inhibition, enhancing microbial synergy, and reducing carbon source dependency holds practical application value for treating high-nitrogen and low-temperature wastewater, while also providing theoretical support for constructing microalgal-bacterial synergistic systems to achieve efficient autotrophic nitrogen removal.},
}

@article {pmid41197744,
year = {2025},
author = {Li, Y and Wang, G and Yang, Y and Liu, L and Dang, X and Li, YY and Chen, R},
title = {Operational thresholds and microbial mechanisms in high-solid anaerobic membrane bioreactors treating swine wastewater: from process performance to metabolic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133596},
doi = {10.1016/j.biortech.2025.133596},
pmid = {41197744},
issn = {1873-2976},
abstract = {This study investigated swine wastewater treatment using a high-solid anaerobic membrane bioreactor (HSAnMBR), focusing on microbial adaptive mechanisms and process stability under stepwise-increased organic loading rates (OLRs: 5-26 g COD/L/d). The HSAnMBR achieved high efficiency at OLRs ≤ 17 g COD/L/d, with COD removal > 96 % and optimal methane yield (0.28 L CH4/g CODremoved). However, OLR elevation to 26 g COD/L/d induced volatile fatty acid (VFA) accumulation (5.57 g/L), causing acute methanogenic inhibition that reduced methane yield efficiency by 39 %. System functionality was rapidly restored within 10 days after OLR reduction to 21 g COD/L/d. Microbial analysis revealed divergent diversity dynamics: bacterial alpha diversity peaked at 14 g COD/L/d before declining, while archaeal diversity increased continuously, enhancing functional redundancy. Sludge acclimation enriched key functional taxa (such as Clostridium_sensu_stricto and hydrogenotrophic methanogens), forming a resilient "metabolic complementarity-functional substitution" network that maintained process stability under VFA stress. Metagenomic evidence confirmed metabolic pathway restructuring, including upregulation of hydrogenotrophic methanogenesis genes (e.g., coenzyme F420 biosynthesis) and a decline in acetoclastic dominance. This work deciphers the microbial mechanisms enabling high-load operation of HSAnMBRs, establishing the foundation for energy-efficient swine wastewater valorization.},
}

@article {pmid41197631,
year = {2025},
author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL},
title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.007},
pmid = {41197631},
issn = {1932-7420},
abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.},
}

@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}

@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}

@article {pmid41197513,
year = {2025},
author = {Luo, J and Hou, C and Wang, Z and Gui, N and Wang, YX and Jiang, X and Mu, Y and Shen, J},
title = {Simultaneous removal of nitrate and ammonia at the sulfur/pyrite-microbe interface: A novel insight of pyrite in wastewater polishing treatment for nitrogen metabolism.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140316},
doi = {10.1016/j.jhazmat.2025.140316},
pmid = {41197513},
issn = {1873-3336},
abstract = {The development of advanced nitrogen removal technologies for municipal wastewater effluents is critical to meeting increasingly stringent discharge standards. We present a sulfur/pyrite-microbe interfacial system that optimizes nitrogen-transformation pathways to achieve simultaneous removal of NO3[-]-N and NH4[+]-N with reduced sulfate production. This overcomes the drawbacks of conventional sulfur autotrophy (poor NH4[+] removal and excessive sulfate production) and stand-alone iron systems (low denitration rate and easy passivation), delivering synchronous ammonia and nitrate elimination in a single step. A comprehensive analysis of the microstructure and composition of the bio-abiotic interface was performed to elucidate the regulatory role of pyrite in electron transfer and substance transformation. The formation of secondary minerals, structural alterations in extracellular proteins, and enhanced activity of redox-active proteins collectively activated both intracellular and extracellular electron transfer channels. Pyrite-induced quorum sensing promoted iron transport and stimulated microbial metabolic functions. Driven by Fe(II)/Fe(III) redox cycling, nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) reduced sulfate production and suppressed sulfur disproportionation. Metagenomic analysis further confirmed that Feammox, rather than conventional Anammox, served as the dominant pathway for NH4[+]-N conversion. Pilot-scale validation demonstrated robust nitrogen removal (TN > 90 %) and low sulfate production with a treatment cost 40 % lower than conventional carbon-driven systems. This study offers a sustainable, low-carbon alternative for advanced nitrogen polishing and provides mechanistic insights into bio-abiotic interface engineering for wastewater treatment.},
}

@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}

@article {pmid41197330,
year = {2025},
author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE},
title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.},
journal = {Nutrition research (New York, N.Y.)},
volume = {144},
number = {},
pages = {1-15},
doi = {10.1016/j.nutres.2025.10.004},
pmid = {41197330},
issn = {1879-0739},
abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.},
}

@article {pmid41196658,
year = {2025},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196712},
pmid = {41196658},
issn = {1558-8238},
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.},
}

@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/spectrum.00944-25},
pmid = {41196057},
issn = {2165-0497},
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}

@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173225},
doi = {10.1128/spectrum.01732-25},
pmid = {41196055},
issn = {2165-0497},
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}

@article {pmid41196050,
year = {2025},
author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N},
title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095425},
doi = {10.1128/msystems.00954-25},
pmid = {41196050},
issn = {2379-5077},
abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.},
}

@article {pmid41195400,
year = {2025},
author = {Zhili, G and Jie, L and Peihao, Y},
title = {Macro- and metabolome-based characterization between gut microbiota and metabolites in patients with colorectal adenomas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1628315},
pmid = {41195400},
issn = {1664-302X},
abstract = {OBJECTIVE: The gut microbiota has been recognized as a significant regulator in the development and progression of colorectal adenoma (CRA). However, few studies have investigated the presence and association of resident microbial species and metabolites in patients with CRA. Our aim was to analyze differences in gut microbiome composition and metabolites, as well as to evaluate their diagnostic potential for CRA.

METHODS: We conducted metagenomic and metabolomic analyses on fecal samples from 90 subjects, including 60 patients with CRA (CRA group) and 30 healthy subjects who served as normal controls (NC group). By integrating fecal metagenomic and metabolomic data, we identified gut microbiota-associated metabolites that showed significant abundance changes in CRA patients. Furthermore, we explored whether these metabolites and microbial species could distinguish CRA patients from healthy individuals.

RESULTS: 16S rRNA gene sequencing and untargeted metabolomics analysis revealed microbial changes that distinguished CRA patients from controls. Microbial population analysis showed that the CRA group formed distinct clusters from the controls, with significant β-diversity (PCA and PCoA analyses, p < 0.05). At the phylum level, the dominant taxa in terms of relative abundance included Firmicutes, Ascomycota, Mycobacteria, Actinobacteria, and Clostridia. Differential analysis of the gut flora based on species abundance revealed significant differences in taxonomic composition between healthy individuals and CRA patients. KEGG functional enrichment analysis indicated that the differential flora were primarily involved in metabolic pathways, including metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, amino acid biosynthesis, and cofactor biosynthesis. In this study, three microbial species-Fusobacterium mortiferum, Alistipes, and Bacteroides fragilis-were validated as discriminators between healthy individuals and CRA patients, with Alistipes showing higher classification efficacy. Metabolomic analysis revealed differences in tryptophan metabolism, protein degradation products, amides, and phenolic acid metabolites. KEGG enrichment results indicated that metabolic pathways were the most significantly enriched. Differential metabolites were mainly associated with the biosynthesis of plant secondary metabolites. Procrustes and Venn analyses were performed on functional entries of the two omics datasets, highlighting enriched pathways including Metabolic pathways, Glycerophospholipid metabolism, Sphingolipid metabolism, and Alpha-linolenic acid metabolism. A review of the literature confirmed that the differential flora and metabolites are associated with adenoma growth.

CONCLUSION: In this study, metagenomic and metabolomic analyses were conducted in subjects with CRA. The findings based on fecal metagenomic and metabolomic assays suggest that intestinal microecology is altered in CRA patients, leading to changes in gut cellular structure.},
}

@article {pmid41195399,
year = {2025},
author = {, },
title = {Correction: Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721706},
doi = {10.3389/fmicb.2025.1721706},
pmid = {41195399},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1652229.].},
}

@article {pmid41195309,
year = {2025},
author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F},
title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.},
journal = {Pediatric diabetes},
volume = {2025},
number = {},
pages = {3013063},
pmid = {41195309},
issn = {1399-5448},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; },
abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.

METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included α/β-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.

RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2] = 0.0562, p=0.003 and R [2] = 0.0343, p=0.003). HLA-C [∗] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2] = 0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2] = 0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [∗] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19 ± 0.14 vs. 0.26 ± 0.19 µg/mL, p=0.029).

CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [∗] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.},
}

Humans
*Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology
*Gastrointestinal Microbiome/genetics
Child
Male
Female
Cross-Sectional Studies
Adolescent
Child, Preschool
Age of Onset
Cohort Studies
Infant

@article {pmid41194765,
year = {2025},
author = {Li, J and Zhao, S and Guo, F and Zhang, W and Chen, M and den Haan, R and Xin, F and Jiang, Y and Jiang, M},
title = {Strategies to Improve the Efficiency of Enzymatic Carbon Dioxide Conversion In Vitro.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00760},
pmid = {41194765},
issn = {2161-5063},
abstract = {With the rapid industrial development, massive fossil fuel use has caused excessive carbon dioxide (CO2) emissions, triggering global warming and environmental issues. Thus, CO2 recovery and reuse have become a research focus, among which artificially designed in vitro biocatalytic pathways for converting CO2 into high-value chemicals show promise, with advantages like shorter routes, higher efficiency and lower energy consumption compared to natural pathways. However, challenges remain due to natural enzymes' issues in specificity, affinity, efficiency, stability and oxygen sensitivity. To tackle these problems, extensive research efforts have been undertaken. These include elucidating the mechanisms and catalytic efficiencies of carbon-fixing enzymes from diverse sources, as well as developing and refining novel in vitro carbon fixation pathways. Moreover, significant progress has been made in computer-aided investigations of enzyme structure, function, and engineering optimization, alongside advancements in enzyme immobilization strategies, cofactor regeneration systems, and the development of artificial cofactors. By summarizing the latest research progress in recent years, we can identify the current bottlenecks and challenges in in vitro enzymatic CO2 conversion, propose effective methods to enhance the efficiency of CO2 conversion, and thus promote the development of research in related fields.},
}

@article {pmid41194716,
year = {2025},
author = {Liu, YH and Sheng, SY and Hu, HB and Wang, Y and Zhang, LW and Feng, YF and Feng, YY},
title = {Effects of drought on the thermal adaptation of soil microbial respiration: A review.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {10},
pages = {2965-2977},
doi = {10.13287/j.1001-9332.202510.032},
pmid = {41194716},
issn = {1001-9332},
mesh = {*Droughts ; *Soil Microbiology ; Climate Change ; Soil/chemistry ; *Adaptation, Physiological/physiology ; Ecosystem ; Carbon Cycle ; },
abstract = {Drought induced by global climate change affects the thermal adaptation of soil microbial respiration, which has complex consequences on the carbon (C) cycle. Drought can either enhance C emissions and create a positive feedback loop, or promote C sequestration and generate a negative feedback effect. We reviewed the effects of drought on microbial thermal adaptation, analyzed the underlying mechanisms, and summarized current research findings and related debates. Drought significantly influences microbial thermal adaptation through altering soil aggregate structure, organic carbon molecular composition, and microbial community structure. Due to variations in climatic zones, ecosystem types, and soil conditions, the impacts of drought on microbial thermal adaptation exhibit regional variety and complexity. Future research should focus on experimental designs that simulate natural environments, utilizing diverse organic substrates (e.g., cellulose, oxalic acid and xylan) to generate more accurate data and explore the synergistic effects of drought with other environmental factors (e.g., elevated CO2 concentrations, increased ultraviolet radiation, and nitrogen deposition) to reveal their combined impacts on microbial thermal adaptation. Advanced techniques like metagenomics and DNA-stable isotope probing should be warranted to further reveal the microbial mechanisms involved in the regulation of drought on microbial thermal adaptation.},
}

*Droughts
*Soil Microbiology
Climate Change
Soil/chemistry
*Adaptation, Physiological/physiology
Ecosystem
Carbon Cycle

@article {pmid41194562,
year = {2025},
author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A},
title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70199},
doi = {10.1111/1462-2920.70199},
pmid = {41194562},
issn = {1462-2920},
support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnología/ ; },
mesh = {*Archaea/genetics/metabolism/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.},
}

*Archaea/genetics/metabolism/classification/isolation & purification
*Bacteria/metabolism/genetics/classification/isolation & purification
*Genome, Bacterial
Metagenome
*Microbiota
Sulfur/metabolism
*Geologic Sediments/microbiology
Salinity
Genome, Archaeal
Carbon/metabolism
Nitrogen/metabolism
Phylogeny

@article {pmid41194295,
year = {2025},
author = {Breukers, E and Kim, H and Banihashem, F and Andersson, K and Leijon, M and Westin, R and Sjölund, M and Zohari, S},
title = {The first detection of swine orthopneumovirus in a pig farm in Sweden: a case report.},
journal = {Porcine health management},
volume = {11},
number = {1},
pages = {56},
pmid = {41194295},
issn = {2055-5660},
abstract = {BACKGROUND: Respiratory diseases are globally a major challenge in today's pig production. Despite the efforts to manage the disease, the number of pigs affected is still increasing, indicating gaps in the current knowledge. In 2016, a novel pneumovirus, swine orthopneumovirus, was detected in the USA. Since then, the virus has been detected in a few European countries and in South Korea. However, the wider distribution of the virus is still greatly unknown, as well as its clinical relevance.

CASE PRESENTATION: This report describes the first detection of swine orthopneumovirus in a Swedish pig herd. The virus was detected as the result of an investigation conducted between September 2023 to June 2024, where all clinical samples (n = 682) sent to the Swedish Veterinary Agency for diagnostic purposes from 112 Swedish pig farms exhibiting clinical signs of respiratory disease were screened for the presence of swine orthopneumovirus. The virus was detected in one piglet producing farm that had a respiratory disease outbreak in autumn 2023, which presented with cough and nasal discharge. In November 2023, 11 nasal swabs were collected, of which 9 were PCR-positive for swine orthopneumovirus. In addition, each sample was also PCR-positive for Mesomycoplasma hyorhinis and Pasteurella multocida, and 2 samples were PCR-positive for Actinobacillus pleuropneumoniae, indicating a polymicrobial respiratory infection.

CONCLUSIONS: This report emphasises the importance of ongoing efforts to identify emerging pathogens and determine their clinical significance. Therefore, further research is needed to assess the distribution and potential clinical relevance of swine orthopneumovirus.},
}

@article {pmid41194257,
year = {2025},
author = {Parsons, C and Fournier, GP},
title = {Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.},
journal = {Biology direct},
volume = {20},
number = {1},
pages = {107},
pmid = {41194257},
issn = {1745-6150},
support = {EAR-1615426//National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Bacteria/genetics/enzymology ; Phylogeny ; *Matrix Metalloproteinases/genetics ; *Evolution, Molecular ; Archaea/genetics/enzymology ; *Biological Evolution ; Metagenome ; },
abstract = {BACKGROUND: The early evolution of animals is characterized by the emergence of complex tissues, organs, and integument, made possible in part by the diversification of groups of structural proteins. The abundance of this new kind of organic material in the environment would have provided novel nutrient opportunities for microbes, as part of the beginnings of animal-microbial coevolution. Indeed, a diverse ensemble of extant microbial groups appear to possess the enzymatic ability to cleave collagen, the most abundant animal-specific protein, through the use of matrix metalloproteinases (MMPs). In animals, MMPs serve to reshape the extracellular matrix in the course of development, but their prevalence in the microbial world has been largely overlooked.

RESULTS: MMPs have extensive diversity in Bacteria, Eumetazoa, and Streptophyta. We show that in marine metagenomes, MMP abundance is highly correlated with chitinase abundance, implying that even microbial MMPs are associated with animal-derived substrates. Reconstructing the phylogeny of MMP proteins reveals a history of rapid diversification, as well as multiple interkingdom and interdomain horizontal gene transfers. Included among these is a transfer to the ancestral lineage of the archaeal family Methanosarcinaceae, constraining this group to postdate the evolution of collagen, and therefore animal diversification.

CONCLUSIONS: MMPs have an unusual genetic history, marked by multiple instances of gene transfer between bacteria and multicellular eukaryotes, a smoking gun for some of the earliest coevolution between prokaryotes and metazoans. By calculating an end-Permian divergence of Methanosarcina, we demonstrate that the phylogenies of substrate-specific enzymes can provide valuable older-bound age calibrations for improving molecular clock age estimates across the Tree of Life.},
}

*Gene Transfer, Horizontal
Animals
*Bacteria/genetics/enzymology
Phylogeny
*Matrix Metalloproteinases/genetics
*Evolution, Molecular
Archaea/genetics/enzymology
*Biological Evolution
Metagenome

@article {pmid41194238,
year = {2025},
author = {Ellis, VA and Theodosopoulos, A and Sharma, I and Bardil, A and Stjernman, M and Hellgren, O},
title = {Simultaneous population genomics of hosts and their parasites with selective whole genome amplification.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {448},
pmid = {41194238},
issn = {1756-3305},
support = {NIH/NIGMS P20 GM103446, S10 OD028725/GF/NIH HHS/United States ; DEL00854, NE1943, NE2443//USDA Hatch/ ; VR 2021-03663//Swedish Research Council/ ; },
mesh = {Animals ; *Haemosporida/genetics ; *Host-Parasite Interactions/genetics ; *Protozoan Infections, Animal/parasitology ; *Bird Diseases/parasitology ; *Genome, Protozoan ; DNA, Protozoan/genetics ; Genomics ; *Passeriformes/parasitology/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: Generating parasite genomes is challenging when little of the DNA in infected host tissue is from the parasite. We used selective whole genome amplification (SWGA) to generate genomic data from wildlife samples of the avian haemosporidian Haemoproteus majoris (lineage PARUS1) and its host, the blue tit (Cyanistes caeruleus).

METHODS: We used SWGA to amplify the parasite DNA in nine avian blood samples collected between 1996 and 2021, and subsequently performed short-read sequencing and bioinformatically separated the host and parasite reads in each sample.

RESULTS: SWGA increased the percentage of parasite reads significantly. Sequencing to a depth of about 56 million reads (forward and reverse) per sample resulted on average (± standard error [SE]) in 11.3X ± 1.85 for the host genome and 1.17X ± 0.446 mean depth of coverage for the host and parasite, respectively, after SWGA. Furthermore, about 74% of the host genome (genome size approx. 1.2 Gb) and 33% of the parasite genome (approx. 23.9 Mb) had at least 1X coverage on average; two samples had 1X coverage of approximately 60% of the parasite genome. Parasite sequencing success was positively correlated with parasitemia. When comparing the parasite sequences in the four best samples, we identified 9895 sites (minimum 5X coverage) that varied among the infections. When filtering the full dataset to at least six samples per variant, we identified 14,512,339 and 7068 sites that varied among samples in the host and parasite populations, respectively, revealing variation among samples and years.

CONCLUSIONS: SWGA facilitates dual host-parasite population genomics in this system and will greatly expand our understanding of host-parasite interactions over space and time.},
}

Animals
*Haemosporida/genetics
*Host-Parasite Interactions/genetics
*Protozoan Infections, Animal/parasitology
*Bird Diseases/parasitology
*Genome, Protozoan
DNA, Protozoan/genetics
Genomics
*Passeriformes/parasitology/genetics
Metagenomics/methods

@article {pmid41194219,
year = {2025},
author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH},
title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {136},
pmid = {41194219},
issn = {2524-6372},
support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; },
abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.},
}

@article {pmid41194006,
year = {2025},
author = {Ivanova, A and Buzova, V},
title = {A novel enzymatic approach for a targeted fungal growth inhibition.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {719},
pmid = {41194006},
issn = {1471-2180},
support = {03-ZP23-087//SkyLab AG/ ; 03-ZP23-087//SkyLab AG/ ; },
abstract = {BACKGROUND: Dandruff represents a complex, multifactorial disorder characterized by impaired barrier function, altered lipid composition, and microbial imbalance. The principal pathogenic mechanism, however, involves excessive colonization by Malassezia species, notably M. furfur, M. restricta and M. globosa, on the scalp. Standard antifungal options often lead to undesirable effects, including itching and irritation, and may negatively impact the scalp microbiome. This study evaluates combination of chitinase and chitosanase, targeting fungal cell wall chitin and chitosan, as a promising targeted approach for scalp Malassezia spp.

METHODS: The in vitro antifungal activities of chitinase (100 U/g) and chitosanase (200 U/g) were evaluated against Malassezia furfur, Malassezia restricta, and Malassezia globosa at concentrations ranging from 0.125% to 5% w/w. Their efficacy was compared to that of conventional antifungal agents, including climbazole, piroctone olamine, selenium sulfide, zinc pyrithione, and propanediol caprylate. Cytotoxicity was assessed using fibroblast cell lines via MTT assay and fluorescence microscopy. A clinical study (n = 18) evaluated the impact of a solution containing 0.25% chitinase and 0.25% chitosanase on scalp M. furfur and M. restricta DNA and RNA levels using quantitative PCR (qPCR). A metagenomic analysis was conducted to assess the impact of enzymatic treatment on bacterial composition and diversity.

RESULTS: Individually, 0.25% chitinase and 0.25% chitosanase inhibited Malassezia spp. growth by 23.85% and 26.15%, respectively (p < 0.05). When combined at 0.25%, they achieved 98.38% inhibition (p < 0.05), with complete suppression observed at 0.5%. In a clinical study, a 3-hour scalp treatment with a solution containing 0.25% chitinase and 0.25% chitosanase followed by quantitative PCR of post-treatment samples demonstrated significant reductions in DNA and RNA levels of M. furfur and M. restricta. DNA content decreased 2.4- and 1.9-fold, and RNA levels declined 2.4- and 4.6-fold, respectively. Cytotoxicity was detected only at concentrations ≥ 7.6%, well above the effective antifungal doses. The metagenomic analysis demonstrated that a three-hour scalp treatment with chitinase - chitosanase solution increased alpha diversity (Chao1 index) and doubled the number of identifiable operational taxonomic units (OTUs).

CONCLUSIONS: The chitinase-chitosanase combination offers a promising targeted approach for scalp Malassezia spp. control without broad antimicrobial effects.},
}

@article {pmid41193697,
year = {2025},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41193697},
issn = {1759-5053},
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}

@article {pmid41193636,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {Author Correction: A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-025-02212-3},
pmid = {41193636},
issn = {2058-5276},
}

@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}

@article {pmid41192565,
year = {2025},
author = {Tóth, GE and Petersen, M and Chevenet, F and Sikora, M and Tomazatos, A and Bialonski, A and Baum, H and Horváth, B and Siriyasatien, P and Heitmann, A and Jansen, S and Offergeld, R and Lachmann, R and Schmidt, M and Schmidt-Chanasit, J and Cadar, D},
title = {Blood donors as sentinels for genomic surveillance of West Nile virus in Germany using a sensitive amplicon-based sequencing approach.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106647},
doi = {10.1016/j.jinf.2025.106647},
pmid = {41192565},
issn = {1532-2742},
abstract = {BACKGROUND: West Nile virus (WNV) has emerged as a public health concern in Germany since its first detection in 2018, with evidence of expanding geographic spread. Genomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. However, genome recovery from low-viremia samples such as those obtained through blood donor screening remains technically challenging.

AIM: To develop and validate a sensitive amplicon-based sequencing protocol optimized for WNV lineage 2 and apply it to low-titer samples to support genomic surveillance in Germany.

METHODS: A novel primer scheme was designed for WNV lineage 2 and applied to 43 nucleic acid testing (NAT)-positive blood donor samples collected between 2020 and 2024. Amplicon-based sequencing performance was benchmarked against metagenomic next-generation sequencing (mNGS). Recovered genomes were subjected to phylogenomic analysis to assess viral diversity and transmission dynamics.

RESULTS: The amplicon protocol enabled genome recovery (>70% coverage) from samples with viral loads as low as ~10¹ RNA copies/µL, outperforming metagenomic NGS (mNGS). Of the 43 samples, 30 yielded complete or near-complete genomes. Six distinct WNV subclades (2A-2F), including German strains, were identified, indicating multiple introductions into Germany from Central Europe. Subclade 2F emerged as the dominant and widely distributed group. Berlin, Brandenburg, Saxony, and Saxony-Anhalt were identified as persistent transmission hubs.

CONCLUSION: This study highlights blood donors as valuable sentinels for WNV genomic surveillance. The validated amplicon-based sequencing approach enables sensitive, scalable genome recovery from low-viremia samples, and when integrated with routine blood donor screening, provides a robust framework for early detection, transmission dynamics, and public health preparedness.},
}

@article {pmid41192489,
year = {2025},
author = {Meng, F and Wang, L and Xu, J and Li, X and Hao, J},
title = {Enhanced electron transfer mediated by surface functional groups of targetedly modified sludge-based biochar for sustainable microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133600},
doi = {10.1016/j.biortech.2025.133600},
pmid = {41192489},
issn = {1873-2976},
abstract = {While unmodified sludge-based biochar (SBBC) exhibits limited electron transfer capacity in chain elongation (CE), its surface functional groups are recognized as critical factor influencing direct interspecies electron transfer (DIET). This study employed three modification methods, i.e., H2O2, HNO3, and anthraquinone sulfonate (AQS), to explore the effects of modified SBBC on CE process. Results indicated that the AQS-modified SBBC (SBBC-AQS) exhibited optimal electron transfer properties and electrochemical activity. Thus, SBBC-AQS greatly promoted DIET-mediated CE, leading to 62% higher caproate production compared to no biochar. Further recycling experiments confirmed the reusability of SBBC-AQS, along with the biofilm formation. Lastly, metagenomic analysis revealed that modified SBBC improved the abundance of CE bacteria such as Clostridium kluyveri, and introduced electron-transferring bacteria such as Petrimonas, so as to reinforce ethanol oxidation and medium-chain fatty acids production. This study offers novel insights into the sustainable material and microbes synergistic regulation to achieve an efficient CE system.},
}

@article {pmid41192488,
year = {2025},
author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y},
title = {Microbial necromass analogues reshape composting humification pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133583},
doi = {10.1016/j.biortech.2025.133583},
pmid = {41192488},
issn = {1873-2976},
abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.},
}