@article {pmid41285136,
year = {2025},
author = {Sujith, S and Vasudevan, S and Sajeevan, A and Solomon, AP},
title = {Genomics to function: integrating rapid metagenomics with quorum-sensing biosensing for precision infectious disease management.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101291},
doi = {10.1016/j.lanmic.2025.101291},
pmid = {41285136},
issn = {2666-5247},
}

@article {pmid41283812,
year = {2025},
author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y},
title = {From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf626},
pmid = {41283812},
issn = {1477-4054},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; 9667256//City University of Hong Kong/ ; 9678241//City University of Hong Kong/ ; 217310019//Open Research Fund of Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Genomics/methods ; *Computational Biology/methods ; Benchmarking ; *Host-Pathogen Interactions ; Genome, Viral ; },
abstract = {Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks-link prediction and multi-class classification-and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.},
}

*Bacteriophages/genetics/physiology
*Genomics/methods
*Computational Biology/methods
Benchmarking
*Host-Pathogen Interactions
Genome, Viral

@article {pmid41283667,
year = {2025},
author = {Zhang, J and Meng, F and Sun, Y and Xu, W and Wu, S and Su, X},
title = {Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145325},
doi = {10.1128/msystems.01453-25},
pmid = {41283667},
issn = {2379-5077},
abstract = {The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning (DL) models, which typically focus on microbial distribution patterns, neglecting the underlying relationships between microbes. As a result, model performance can be significantly affected by data sparsity, misclassified features, or incomplete microbial profiles. To overcome these challenges, we introduce Phylo-Spec, a phylogeny-driven deep learning algorithm that integrates multi-aspect microbial information for improved status recognition. Phylo-Spec fuses convolutional features of microbes within a phylogenetic hierarchy via a bottom-up iteration and significantly alleviates the challenges due to sparse data and inaccurate profiling. Additionally, the model dynamically assigns unclassified species to virtual nodes on the phylogenetic tree based on higher-level taxonomy, minimizing interferences from unclassified species. Phylo-Spec also captures the feature importance via an information gain-based mechanism through the phylogenetic structure propagation, enhancing the interpretability of classification decisions. Phylo-Spec demonstrated superior efficacy in microbiome status classification across two in silico synthetic data sets that simulate the aforementioned cases, outperforming existing ML and DL methods. Validation with real-world metagenomic and amplicon data further confirmed the model's performance in multiple status classification, establishing a powerful framework for microbiome-based health state identification and microbe-disease association. The source code is available at https://github.com/qdu-bioinfo/Phylo-Spec.IMPORTANCEThe human microbiome profoundly influences health and disease, but current computational tools often overlook the evolutionary relationships among microbes, leading to incomplete or inaccurate interpretations of complex microbial data. Phylo-Spec provides a new way to understand the microbiome by combining microbial abundance, taxonomy, and phylogeny within a unified deep learning framework. This model not only improves the accuracy of health status classification but also highlights key microbial contributors linked to disease. By capturing both microbial diversity and evolutionary context, Phylo-Spec bridges the gap between bioinformatics and biological insight, offering a powerful and interpretable approach for advancing microbiome-based diagnostics and precision medicine.},
}

@article {pmid41283171,
year = {2025},
author = {Ping, Y and Zhao, X and Lv, L and Meng, W and Meng, Y and Ruan, G and Cheng, Y and Xiao, Z and Tian, Y and Chen, M and Chen, L and Yi, A and Tang, Z and Li, N and Chen, D and Wei, Y},
title = {Gut microbiota and metabolic signatures of anxiety in ulcerative colitis: a cross-sectional study.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251393419},
pmid = {41283171},
issn = {1756-283X},
abstract = {BACKGROUND: Patients with ulcerative colitis (UC) usually experience anxiety symptoms that seriously affect their quality of life, treatment, and prognosis. Dysbiosis of the gut microbiota plays an important role in UC and mental illness. However, little is known about the role of the gut microbiota in UC patients with anxiety.

OBJECTIVES: To identify the gut-microbiome and fecal metabolome profiles uniquely associated with comorbid anxiety in UC patients and to explore potential biomarkers for diagnosis.

DESIGN: A cross-sectional, two-group comparative study.

METHODS: To study the underlying association between them, we recruited 126 UC patients in this study, including 78 with anxiety and 48 without anxiety. A total of 102 fecal samples were collected for metagenomic sequencing and metabolome sequencing. Microbial diversity, differential gut microbiota, functional pathways, and metabolites were analyzed. Multivariable logistic regression was used to identify independent risk factors associated with anxiety in UC patients, while Spearman correlation was employed to explore microbe-metabolite interactions and the performance of potential biomarkers.

RESULTS: We found that disease severity, steroid usage, and abdominal pain may promote the occurrence of anxiety. Compared to UC patients without anxiety, UC patients with anxiety had low fecal microbial community diversity, with an increase in the species Haemophilus sp. HMSC71H05 and Corynebacterium durum, and a decrease in the species Roseburia intestinalis (RI), Bifidobacterium longum (BL), and Enterococcus hirae. The metabolic pathways driven by the gut microbiota were disrupted. Moreover, the levels of most metabolites (such as L-kynurenine) were increased in the feces, while the levels of a few metabolites decreased, including indole-2-carboxylic acid, N-demethylmirtazapine, and tauroursodeoxycholic acid.

CONCLUSION: Our research further revealed that these gut microbiota and metabolites are highly correlated. This study provides a new perspective for understanding the occurrence and development of anxiety in UC patients, suggesting that RI and BL may serve as potential candidate biomarkers to diagnose UC patients with anxiety.},
}

@article {pmid41282996,
year = {2025},
author = {Wang, JM and Pan, YY and Hong, JC and Jiang, ZJ and Zhang, SY and Fan, RJ and Yang, BH and Wang, ZQ and Zhu, JT and Yao, XP},
title = {Exploring the Spectrum of Microbiota in Central Nervous System Infections Through Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6019-6033},
pmid = {41282996},
issn = {1178-6973},
abstract = {PURPOSE: This study leveraged CSF metagenomic next-generation sequencing (mNGS) to bridge this knowledge gap and elucidate the microbiota spectrum of CNS infections.

PATIENTS AND METHODS: We retrospectively analyzed CSF mNGS reports and clinical data from 264 patients with suspected CNS infections, who were enrolled from September 2019 to November 2023.

RESULTS: According to diagnostic criteria, 145 patients were diagnosed with CNS infections, including bacterial (27 cases, 18.6%), Mycobacterium tuberculosis (30, 20.7%), fungal (23, 15.9%), and viral (65, 44.8%) infections. The mNGS positive detection rate was 46.2% (67/145), with significant differences among groups (p < 0.001). A total of 22 pathogens were identified, most commonly Cryptococcus neoformans (16, 23.9%), Mycobacterium tuberculosis (10, 14.9%), and Epstein-Barr virus (9, 13.4%). The most frequent background microorganisms detected by mNGS were Cutibacterium acnes (58.6%), Moraxella osloensis (29.0%), and Malassezia restricta (26.2%).

CONCLUSION: High-throughput sequencing using mNGS revealed the microbial compositions in CSF samples from patients with CNS infections. This approach may enhance our understanding of pathogens and assist clinicians in making effective therapeutic decisions.},
}

@article {pmid41282988,
year = {2025},
author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y},
title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20199},
pmid = {41282988},
issn = {2167-8359},
mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Archaea/genetics/isolation & purification ; },
abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.

METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.

RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.

CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.},
}

*Sewage/microbiology/virology
China
*Metagenomics
*Rain
Bacteria/genetics/classification/isolation & purification
*Microbiota
Archaea/genetics/isolation & purification

@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}

*Soil Microbiology
*Metagenome
China
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Metagenomics

@article {pmid41282900,
year = {2025},
author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, D and Teixeira, M and Earl, AM and Worby, C and Kong, HH and Huang, SS and Segre, J},
title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.25339587},
pmid = {41282900},
abstract = {Antimicrobial resistance (AMR) is a global public health threat that disproportionately affects vulnerable populations, including nursing home (NH) residents. Surveillance and control in NHs are resource-limited and typically restricted to perirectal cultures, overlooking both skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here we show, within the cluster-randomized Project PROTECT trial (NCT03118232), that residents' skin serves as a major reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using shotgun metagenomics, selective culturing, and isolate genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ST131/ST648 in 4 (10.5%) and methicillin-resistant Staphylococcus aureus in 7 (18.4%). In contrast, metagenome-assembled genomes identified broader MDRO colonization, including multidrug-resistant E. coli ST93 in 27 residents (71.1%), methicillin-resistant Staphylococcus epidermidis ST2 in 14 (36.8%), Proteus mirabilis in 16 (42.1%), Providencia stuartii in 7 (18.4%), Enterococcus faecalis in 7 (18.4%), and Pseudomonas aeruginosa in 5 (13.2%). Colonization persisted after bathing. Clonal E. coli ST93 (<=30 SNPs) was shared by 27 residents across 9 facilities, and 5 resident pairs (13.2%) carried clonally related strains of >=2 MDRO species, consistent with polymicrobial transmission. Our findings demonstrated the skin as a persistent reservoir of MDROs and the importance of metagenomic surveillance to uncover hidden colonization and transmission pathways, underscoring the need to expand AMR monitoring in long-term care.},
}

@article {pmid41282695,
year = {2025},
author = {Lande, SJ and Stephney, LM and Ramirez, LGA and Nesbeth, PC and Hartman, TJ and Jones, DP and Valvi, D and Hechenbleikner, EM and Lin, E and McConnell, RS and Chatzi, VL and Alvarez, JA and Ziegler, TR},
title = {Dietary Macronutrient Intake and the Gut Microbiome in Adults Undergoing Bariatric Surgery for Obesity.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.25338397},
pmid = {41282695},
abstract = {Limited information linking dietary intake to gut metagenomic data in bariatric surgery patients is available. We examined whether there were correlations between macronutrient intake and the gut microbiome and related gene pathways prior to and following bariatric surgery. Participants were 29 adults living with obesity undergoing bariatric surgery (93% females). Three-day food records were analyzed prior to and after surgery to estimate mean daily intakes of macronutrients to derive measures of diet quality [glycemic index, added sugar intake, and the Healthy Eating Index 2015 (HEI-2015)]. Pre- and post-operative stool samples were sequenced using whole-genome shotgun sequencing to identify changes in microbial composition. Diversity indices and differential abundance were calculated, and correlations between dietary intake and outcomes were assessed using linear regression and machine learning models. At the phylum level, pre-operative Synergistetes abundance was positively correlated with soluble fiber intake, and Proteobacteria was inversely linked with HEI-2015 scores. Post-operatively, Lentisphaerae was inversely correlated with dietary glycemic index. The change in Verrucomicrobia abundance was inversely correlated with the change in glycemic index, and the change in Fusobacteria abundance was positively correlated with the change in glycemic index. The changes in several functional gene pathways were positively linked to the change in HEI-2015 scores, the change in soluble fiber intake, and the change in insoluble fiber intake. In adults undergoing bariatric surgery, intakes of specific macronutrients pre-operatively and as a function of the change after surgery were correlated with several microbial phyla, genera, and nutrient-related functional gene pathways.},
}

@article {pmid41282688,
year = {2025},
author = {Zhang, H and Dominguez, EG and Junak, M and Murtaza, M and Pepperell, CS and Kisat, MT},
title = {Fragment end motif analysis to distinguish pathogens from contaminants in enriched plasma microbial DNA.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.25339688},
pmid = {41282688},
abstract = {INTRODUCTION: Despite its promise, accuracy of microbial cell-free DNA (mDNA) in plasma as a diagnostic tool is hindered by its low abundance and process contaminants. We have previously shown that combining size selection with single-stranded DNA (ssDNA) library preparation increased mDNA yield by 200-fold but also decreased sensitivity for pathogen detection due to higher background noise. A recent study showed that pathogen-derived DNA was enriched for CC dinucleotide at 5' ends compared to contaminants. Since ssDNA libraries preserve sequence motifs at both ends (5' and 3'), we hypothesized that analysis of nucleotide motifs at microbial fragment ends in size-selected ssDNA libraries could help differentiate pathogen DNA from background noise.

METHODS: We performed deep sequencing on size-selected ssDNA libraries (<110 bp) generated from longitudinal plasma samples of 11 critically-ill patients (5 with culture-proven infections, 20 samples; 6 without infections, 18 samples) and 6 no-template controls (NTCs). For each 2-mer and 1-mer motif, we calculated the ratio between its frequency observed at 5' and 3' fragment ends in sequencing data and its expected frequency in the corresponding reference genome (O/E ratio). We compared enrichment of motifs in pathogen DNA and contaminant DNA fragments.

RESULTS: Pathogen-derived mDNA fragments were more biased in O/E end motif ratios compared to contaminants across all 3 groups (NTCs, no-infections and culture-proven infections), at both 5' and 3' fragment ends. Notably, the GG dinucleotide was enriched at the 3' end in pathogens compared to contaminants (P < 0.0001). Combining O/E ratios for C and G nucleotides at the 3' end achieved areas under the receiver operating characteristic curve of >0.98 for distinguishing common contaminants from culture-proven pathogens.

CONCLUSIONS: Pathogen-derived mDNA in size-selected ssDNA libraries is biased at 5' and 3' fragment end compared to contaminants. Incorporating microbial fragment end motif analysis can enhance signal-to-noise ratio and improve pathogen detection and identification in plasma metagenomic sequencing.},
}

@article {pmid41282530,
year = {2025},
author = {Shoji, F and Kawabata, T and Kosai, K and Fujishita, T and Toyozawa, R and Shimamatsu, S and Ito, K and Taguchi, K and Yamaguchi, M},
title = {Intratumoral microbiome is associated with the response to cancer immunotherapy in lung cancer patients with high PD-L1 expression.},
journal = {Immuno-oncology technology},
volume = {28},
number = {},
pages = {101066},
pmid = {41282530},
issn = {2590-0188},
abstract = {BACKGROUND: High expression of tumoral programmed death-ligand 1 (PD-L1) [high PD-L1 tumor proportion score (TPS)] is a predictive biomarker of response to cancer immunotherapy in lung cancer; however, its predictiveness is insufficient. Recently, resident microbiomes in several organs including the lung have been demonstrated to control host immunity but their role in the response to cancer immunotherapy is still unknown.

MATERIALS AND METHODS: This single-center, retrospective study analyzed 32 high PD-L1-TPS lung cancer patients treated with immune checkpoint inhibitors (ICI). We carried out shotgun metagenome sequencing using frozen tumor tissues, then analyzed the correlation between the intratumoral microbiota and response to ICI therapy.

RESULTS: In this study, only 56.3% of patients with high PD-L1-TPS showed response to ICI therapy. Among 11 significant compositional differences in intratumoral microbiota observed in ICI responders, there was significantly longer progression-free survival (PFS) in patients with abundant Tetrasphaera and Mesorhizobium. Of patients with these abundant microbiota, 83.3% showed response to ICI therapy and all patients without these microbiota were ICI nonresponders (P = 0.0050). There were significant differences among three groups classified by the abundance of g_Tetrasphaera and g_Mesorhizobium (PFS, P = 0.0016 and overall survival, P = 0.0013). Twenty pathway modules were enriched in ICI responders and eight were enriched in ICI nonresponders.

CONCLUSIONS: This study revealed the specific compositions of intratumoral microbiota as demonstrating relevance to response to ICI therapy in high PD-L1-TPS lung cancer patients. The intratumoral microbiota components Tetrasphaera and Mesorhizobium may have a key role in determining the response to cancer immunotherapy for lung cancer.},
}

@article {pmid41282313,
year = {2025},
author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Tahir, M and Zhong, J},
title = {Multi-omics profiling reveals microbial regulation of a key aromatic ester phenethyl acetate formation in fermented alfalfa and its impact on sheep feed preference.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103249},
pmid = {41282313},
issn = {2590-1575},
abstract = {This study utilized headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) to identify the key volatile flavor compounds in fermented alfalfa. The contribution of core microbiota to forming these key flavor compounds was investigated using a combination of absolute quantification of 16S rRNA gene copy number and metagenomic technology. Additionally, the critical roles of core fermentation microorganisms were quantitatively detected and validated through liquid chromatography mass spectrometry (LC-MS). Results revealed that Lactiplantibacillus plantarum B90 treated group achieved superior fermentation quality, with esters and aldehydes being the dominant volatile flavor compounds. Phenethyl acetate was the only aromatic ester that was significantly up-regulated after fermentation. The aryl alcohol dehydrogenase from L. plantarum facilitated the conversion of phenylacetaldehyde into phenylethyl alcohol, which serves as the precursor for phenethyl acetate. Furthermore, fermented alfalfa sprayed with phenethyl acetate was associated with increased feed intake in sheep. These findings propose new insights for microbial modulation of fermented flavor in fermented forage to enhance sheep feed intake.},
}

@article {pmid41282134,
year = {2025},
author = {Zitvogel, L and Carrier, A and Manghi, P and Silva, CAC and Lahmar, I and Birebent, R and Suissa, D and Laheurte, C and Schreibelt, G and Lemant, L and Fahrner, JE and de Sousa, E and Berthier, F and Villemonteix, J and Chevalier, M and Piccinno, G and Hocquet, D and Lebhar, I and Maeurer, M and Caillat-Zucman, S and Kroemer, G and Derosa, L and Launay, O and Golden, E and Bol, K and De Vries, IJM and Adotévi, O and Segata, N and Formenti, S and Kobold, S and Pieper, D and Vital, M and Santos-Peral, A and Zaucha, M and García-Bengoa, M and Thorn-Seshold, J and Stirling, H and Rothenfusser, S and Iebba, V and Almonte, A and Ajami, N and White, M and Sahasrabhojane, P and Hoballah, Y and Losh, J and DePinho, C and Dondossola, E and Wargo, J},
title = {Gut microbiota: a new factor modulating the immunizing potential of viral and cancer vaccines.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4294379/v1},
pmid = {41282134},
issn = {2693-5015},
abstract = {Vaccines represent a major public health intervention against infectious diseases and potentially cancer. Surrogate markers of vaccine efficacy usually rely on neutralizing antibody titers afflicted by high interindividual variabilities. Automated multiplexed T cell assays currently allow to test the clinical relevance of T lymphocyte responses during vaccine rollout. We examined cellular and/or humoral immune responses in five independent cohorts of health care workers, young healthy individuals and patients with cancer (melanoma or lung cancer) receiving various immunizing formulations (non-replicating, viral/tumoral, mRNA/peptides/cellular/viral particles). Here we show that about 20% of vaccinees to non-replicating formulations fail to mount protective antibody and Th1/Tc1 responses while 9% receiving a live vaccine were hyperresponders. Vaccine outliers could at least in part be attributed to gut dysbiosis at baseline, evaluated by shotgun metagenomics-based machine learning or the TOPOSCORE. These findings highlight the requirement of diagnostic tools to identify intestinal dysbiosis, as well as microbiota-centered interventions to optimize the efficiency of mass vaccinations.},
}

@article {pmid41282078,
year = {2025},
author = {Rumi, MA and Nguyen, L and Davis, BC and Brown, CL and Pruden, A and Zhang, L},
title = {Mapping the underlying drivers of resistome risk across diverse environments.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7085902/v1},
pmid = {41282078},
issn = {2693-5015},
abstract = {Background Understanding the drivers of antimicrobial resistance (AMR) across the One Health spectrum is crucial for controlling its spread. The MetaCompare framework, which assesses "resistome risk" based on antibiotic resistance gene (ARG) co-occurrence patterns on metagenomic contigs, has been expanded to distinguish between "ecological resistome risk" (ERR) and "human health resistome risk" (HHRR) scores across anthropogenic gradients. However, comprehensive surveys are still needed to untangle the biological (e.g., ARG relative abundance), ecological (e.g., taxonomic diversity), and technical (e.g., coverage) factors influencing these risk scores. Here, we analyzed 1,326 metagenomes from 12 key environments using the MetaCompare 2.0 pipeline to map global ERR and HHRR landscapes, identifying significant factors modulating risk scores through network analysis, machine learning, and multivariate regression models. Results ERR and HHRR scores varied significantly across environments and were highly correlated (ρ = 0.73, p < 2e-16), indicating shared underlying drivers. Transient environments closely linked to human activity, such as wastewaters and the human gut, produced the highest ERR and HHRR scores, while stable environments like sediments, soils, and activated sludge yielded the lowest. These patterns corresponded directly with taxonomic diversity, where more diverse ecosystems exhibited lower risk scores, supporting the hypothesis that niche occupation may act as an ecological barrier to ARG invasion. In contrast, scores were positively correlated with sul1 and crAssphage, further confirming that transient, low-diversity environments have higher resistome risks, although they did not fully account for risk variability across all environments. ARG relative abundance correlated with risk scores, but only in high-diversity, low-coverage environments due to poor assembly quality and an inability to resolve ARG flanking regions. The ARGs contributing to ERR and HHRR scores were largely aligned with existing ARG risk ranking frameworks. Conclusions This study demonstrated how the MetaCompare 2.0 pipeline can effectively disentangle complex relationships between ARG abundance, composition, and environmental context. Although robust across diverse environments, the framework's ability to detect ARGs and their co-occurrences may be limited in high-diversity, low-coverage samples, such as soils and sediments. Finally, we provide a series of recommendations for appropriate use cases for MetaCompare 2.0.},
}

@article {pmid41282070,
year = {2025},
author = {Bowie, K and Luhung, I and Burke, T and Roberts, S and Martinello, R and Gerstein, M and Peccia, J and Healy, H},
title = {Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7888495/v1},
pmid = {41282070},
issn = {2693-5015},
abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas . Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.},
}

@article {pmid41281954,
year = {2025},
author = {Johnston, PI and Chizani, K and Chirwa, E and Dale, H and Patel, P and Silungwe, N and Mkwangwanya, C and Kachala, T and Mhango, C and Nyirenda, G and Diness, Y and Mpesi, S and Wachepa, R and Shumba, F and Mwakiseghile, F and Rashid, V and Misiri, T and Ashton, PM and Chunga, A and Cocker, D and Cunningham-Oakes, E and Jewell, C and Feasey, N and Gordon, MA and Nyirenda, T},
title = {Transmission dynamics for invasive Non-Typhoidal S almonella serovars (TiNTS): protocol for a household study of transmission and immune response to non-typhoidal Salmonella in Malawi.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {581},
pmid = {41281954},
issn = {2398-502X},
abstract = {BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) disease is a leading cause of community-onset bloodstream infection in Africa, driving high morbidity in young children. The World Health Organization has published preferred product characteristics for an iNTS vaccine, but lack of transmission data is an impediment to vaccine licensure. Enteric NTS (eNTS) is the asymptomatic carriage of NTS in stool that precedes invasive disease. We do not know how long eNTS shedding lasts, how often infection spreads in endemic settings, or how an eNTS episode shapes immunity against later invasion. These gaps make it difficult to define trial sites, select cohorts, refine target product profiles, and build reliable models of vaccine impact. Here we describe TiNTS, a prospective household study in Blantyre, Malawi, which will measure real-time eNTS incidence, transmission, and antibody responses to close these evidence gaps and accelerate rational vaccine deployment.

METHODS: We will recruit all members of at least 60 households in Ndirande, Blantyre, Malawi. Stool samples will be collected every other day for at least four weeks and tested for NTS using culture and pan- Salmonella PCR on growth media. Environmental samples collected at enrolment will be tested using the same methods. Symptoms and exposure risks will be recorded throughout.We will collect blood samples at enrolment, after four weeks, and four weeks after the first eNTS episode in each household. We will measure serum IgG responses to Salmonella Typhimurium and Enteritidis LPS antigens. We will extend follow-up if participants continue shedding or if the first household case occurs with fewer than 14 days of follow-up remaining.All culture-positive isolates and PCR-positive broths will undergo Illumina sequencing to enable genome and metagenome reconstruction for transmission inference.

CONCLUSIONS: TiNTS will define the burden, transmission patterns, and immune response to eNTS. Findings will inform vaccine modelling, trial design, and targeted introduction strategies.},
}

@article {pmid41281952,
year = {2025},
author = {Marangon, E and Ramsby, BD and Luter, HM and Bell, SC and Laffy, P and Webster, NS and Hentschel, U and Fiore, C and Oatley, G and Thomas, T and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Cliona cf. orientalis Thiele (1900) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {342},
pmid = {41281952},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Cliona cf. orientalis (Porifera; Demospongiae; Clionaida; Clionaidae). The genome sequence has a total length of 217.17 megabases. Most of the assembly (98.28%) is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,502 protein-coding genes. Furthermore, three prokaryotic binned genomes were generated, including a high-quality metagenome-assembled genome (MAG) of the family Parvibaculaceae. Although Symbiodiniaceae sequences were also identified, a complete genome assembly could not be generated due to low coverage.},
}

@article {pmid41280484,
year = {2025},
author = {Zhu, Y and Pan, R and den Haan, R and Jiang, Y and Xin, F},
title = {Recent progress on the bioconversion of lignocellulose to fuels and chemicals.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {443},
pmid = {41280484},
issn = {2190-572X},
abstract = {With the continuous strengthening of green and sustainable development, chemical production is entering a new era. Lignocellulose, a widely available renewable biomass, offers potential for biofuel and chemical production; however, its complex structure hinders efficient utilization. Accordingly, this review will first summarize the required enzymes for its degradation based on the structural characteristics of lignocellulose. Oriented by bioconversion technology, pretreatment methods of lignocellulose are elaborated in detail. Additionally, we introduce four mainstream process configurations including separate hydrolysis and fermentation, simultaneous saccharification and fermentation, simultaneous saccharification and co-fermentation, consolidated bioprocessing. As is well known, the production of biofuels and bio-based platform chemicals is critically important for ensuring energy security and reducing greenhouse gas emissions. Thus, this review summarizes typical high value-added products synthesized from lignocellulose, including biofuels (bioethanol, biobutanol, biodiesel, biohydrogen), bulk chemicals (lactic acid, succinic acid, malic acid), and fine chemicals (vanillin, xylitol, carotenoids). Finally, we discuss the technological challenges and innovative solutions of lignocellulose bioconversion, while briefly mentioning the life cycle assessment.},
}

@article {pmid41280427,
year = {2025},
author = {Soni, PK and Kala, A and Agarwal, P and Deka, R and Rahman, H and Vijayalakshmy, K and Chaudhary, LC},
title = {Taxonomic and functional shifts in the rumen microbiome of buffalo calves under long-term strategic supplementation of phyto-feed additives.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1647762},
pmid = {41280427},
issn = {2297-1769},
abstract = {INTRODUCTION: The present study aimed to understand the shift in the rumen microbiome of buffaloes fed diets with and without phyto-additives. The rationale was based on the hypothesis that plant-based additives can modulate the microbial population in the rumen, potentially reducing methane production and enhancing fiber degradation. Given the possibility that prolonged use of the same additives may lead to microbial adaptation and diminished efficacy, the study also investigated the effects of periodically switching additives.

METHODS: Three male buffalo calves were fed a control diet, while another three received additive-supplemented diets. Two additive formulations were used: FAI (a blend of garlic Allium sativum, ajwain Trachyspermum ammi, harad Terminalia chebula, and soapnut Sapindus mukorossi) and FAII (ajwain oil). The additives were alternated every 15 days to prevent microbial adaptation. After 21 days of feeding, rumen liquor samples were collected 2 hours post-feeding for metagenomic analysis. The study included both in vivo and in vitro assessments of rumen fermentation.

RESULTS: Metagenomic analysis revealed that dominant bacterial phyla included Prevotella, Bacteroides, Succiniclasticum, Fibrobacter, Clostridium, Alistipes, Ruminococcus, and Butyrivibrio, with over 50 bacterial species consistently present across all animals. The main archaeal phylum was Euryarchaeota (>85%), along with notable presence of Candidatus_Bathyarchaeota and Thaumarchaeota. At the genus level, Methanomicrobium and Methanobrevibacter each accounted for approximately 30% of the archaeal community, followed by Methanosphaera, Methanosarcina, and Methanomassiliicoccus. While total abundances of Archaea and Bacteroidota were not significantly different among groups, specific taxa within these phyla showed marked changes.

DISCUSSION: The inclusion of phyto-additives in the buffalo diet influenced the rumen microbiome composition by reducing methanogen populations, particularly Methanobrevibacter, and enhancing fiber-degrading microbial communities. These microbial shifts were associated with improved fiber utilization and decreased methane emissions. Rotating the additives every 15 days appeared to sustain their efficacy over time, potentially by preventing microbial adaptation. This approach may offer a sustainable strategy to optimize rumen function and reduce enteric methane emissions in ruminants.},
}

@article {pmid41280102,
year = {2025},
author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, L and Yeow, C and Alvarado, LV and Adams, PD and Banfield, J and Siegel, JB and Prywes, N and Shih, PM},
title = {Diversity-driven biochemical survey reveals dimeric structural origin of rubisco.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.686826},
pmid = {41280102},
issn = {2692-8205},
abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sampled and synthesized a library of diverse rubisco sequences with an emphasis on clades that have previously not been characterized. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily -- in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize the largest rubisco described to date, originating from a cryptic, early-branching subclade with novel structural folds that have previously not been observed in the rubisco superfamily. By integrating biochemical data with an updated phylogenetic framework, we propose a revised nomenclature for the rubisco protein family that reflects current insights and will better accommodate future discoveries.},
}

@article {pmid41280077,
year = {2025},
author = {Diaz, L and Kong, AX and Zhang, P and Chi, J and Pham, K and Johnson, M and Eno, A and Douglas, I and Mao, Y and MacDonald, JW and Cui, JY and Bammler, T and Gu, H and Geng, Y},
title = {Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41280077},
issn = {2692-8205},
abstract = {Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPF's contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrate's rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.},
}

@article {pmid41279986,
year = {2025},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and , and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.685084},
pmid = {41279986},
issn = {2692-8205},
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, we used constraint-based metabolic modelling to associate an increased risk of AD with altered production of microbiome-derived metabolites. In this study, we investigated whether these previous results can also be identified in AD patients. Therefore, we created personalised whole-body metabolic models from gut metagenomics samples from 34 AD dementia patients, 51 individuals with mild cognitive impairments, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found an increased capacity of AD host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD dementia patients and patients with mild cognitive impairments. The metabolic predictions were then mechanistically linked to gut microbial changes in AD. This analysis identified that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron were key factors driving the predicted metabolic changes. Furthermore, the predicted altered microbial influences on blood metabolites were also associated with allelic variations in the APOE risk gene in healthy individuals, which confirmed our previous findings. In conclusion, we identified blood metabolites whose perturbations in AD may be influenced by gut microbiota and predicted the key microbial drivers for these metabolic influences. These findings may facilitate the development of microbiome-informed treatments of AD.},
}

@article {pmid41279864,
year = {2025},
author = {Andersen, SE and Kirsch, JM and Singh, N and Garret, SR and Whitney, JC and Hesselberth, JR and Duerkop, BA},
title = {Serine recombinases are conserved genetic markers of antiphage defense systems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.07.681051},
pmid = {41279864},
issn = {2692-8205},
abstract = {Antiphage defense systems confer bacteriophage (phage) resistance in bacteria. Renewed interest in phage therapy indicates a need to understand the breadth and molecular mechanisms of antiphage defenses. Traditionally, strategies to identify antiphage defenses lack throughput or are biased toward model bacteria. Herein, we developed a bioinformatic pipeline that uses a serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our informatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage effector domains and prokaryotic Schlafen proteins support phage defense. Our work shows that serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.},
}

@article {pmid41279814,
year = {2025},
author = {Lucas, A and Reale, M and Wolf, YI and Duong, B and Zhang, Y and Wickramasinghe, J and Behlman, L and Jones, SM and Higgins, S and Moustafa, AM and Elbasir, A and Amaravadi, R and Mitchell, T and Huang, A and Auslander, N},
title = {Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.686285},
pmid = {41279814},
issn = {2692-8205},
abstract = {The gut microbiome has been causally linked to the efficacy of immune-checkpoint inhibitor therapy (ICI), prompting numerous clinical trials of microbiome-targeting strategies. Yet, mechanisms by which gut microbiota shape immune responses remain elusive as taxonomic biomarkers have failed to generalize across multiple cohorts. In this study, we develop a taxonomy-agnostic framework to identify microbial biomarkers of ICI response and immune-related adverse event (irAE) occurrence from metagenomic sequencing. Applying this approach to four independent melanoma cohorts from clinical centers across the United States, we uncover gut microbial proteins produced by diverse bacterial taxa that consistently predict ICI response. Notably, we uncover a previously uncharacterized operon involved in cellular redox homeostasis that is encoded by different bacteria and reliably predicts irAE occurrence. We further validated the predictive power of this operon in a prospectively sequenced melanoma cohort. Our results demonstrate that taxa-agnostic microbial protein biomarkers are robust, generalizable, and provide a path towards pretreatment risk stratification for melanoma patients initiating ICI therapy.},
}

@article {pmid41279647,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.25.645238},
pmid = {41279647},
issn = {2692-8205},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached bacteria and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.},
}

@article {pmid41279399,
year = {2025},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, J and Yin, Y},
title = {Mucinolysome in gut microbiomes of farm animals and humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682383},
pmid = {41279399},
issn = {2692-8205},
abstract = {Mucins are glycoproteins that create a protective barrier protecting host tissues from microbial pathogens and are instrumental for host health. Here, we provide evidence that mucin glycan degradation in the gut can be mediated by mucinolysomes, defined as extracellular multi-enzyme complexes specializing in mucin glycan degradation. We computationally predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of anaerobic Limousia bacteria, including seven MAGs from human samples of six countries. All 65 genomes were found to display core mucinolysome components, consisting of 3∼6 scaffoldins (containing up to 12 cohesin modules) and up to 22 dockerin-containing mucin glycan-degrading CAZymes (carbohydrate active enzymes). The organization of mucinolysomes allows the assembly of up to 24 CAZymes in the same complex. We validated that a cultivated Limousia strain ET540 from chicken cecum can support growth on mucins as its sole carbon source, triggering the expression of most mucinolysome-related genes, including both scaffoldins and CAZymes. We also modeled the assembly of proteins into a multi-enzyme complex by predicting the cohesin-dockerin interactions among most of the mucinolysome proteins using AlphaFold3. While mucinolysosome-encoding Limousia have low abundance in different animal hosts, their abundance and prevalence are higher in farm animals than in humans, highlighting a potentially important role in livestock gut ecosystems. Our findings reveal a novel mechanism of mucin glycan degradation and provide a framework to explore microbial contributions to gut health and host-microbe interactions across species.},
}

@article {pmid41279300,
year = {2025},
author = {Yancey, CE and Brumfield, KD and Buss, J and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.09.681436},
pmid = {41279300},
issn = {2692-8205},
abstract = {Advances in next generation sequencing have made it possible to explore microbial community dynamics and regulation of functionally important genes through metagenomics and metatranscriptomics. However, the use of meta-omics to link enzyme function directly with complex, community-level phenotypes remain largely unexplored. To overcome this gap, we developed a novel framework that integrates ecological concepts by microbial community perturbation with association analysis to a targeted phenotype. Specifically, we introduce a hypothesis-free "bait and switch" strategy demonstrated through salt marsh soil microcosm pulse experiments to detect and characterize novel enzymes responsible for chitin degradation. Soil microbial communities were "baited" with shell compost, a chitin-rich substrate, to trigger community succession toward chitin degraders and gene upregulation of chitinases. A "switch" was then employed, by addition of glucose, inducing rapid downregulation of genes putatively responsible for chitin degradation. Results demonstrate the feasibility of this approach to identify functionally important enzymes, in this example, 48 hours after chitin addition. The bait and switch community perturbation provides a framework for discovery of polymer degrading enzymes present in complex microbial communities and serves as a proof of concept applicable for linking enzyme function with emergent community level phenotypes.},
}

@article {pmid41279291,
year = {2025},
author = {Camargo, AP and Baltoumas, FA and Ndela, EO and Fiamenghi, MB and Merrill, BD and Carter, MM and Pinto, Y and Chakraborty, M and Andreeva, A and Ghiotto, G and Shaw, J and Proal, AD and Sonnenburg, JL and Bhatt, AS and Roux, S and Pavlopoulos, GA and Nayfach, S and Kyrpides, NC},
title = {A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.01.686033},
pmid = {41279291},
issn = {2692-8205},
abstract = {Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic representation, sparse taxonomic classification, and insufficient functional annotation, hindering detailed investigation into phage biology. Here, we present the Unified Human Gastrointestinal Virome (UHGV), a collection of 873,994 viral genomes from globally diverse populations that addresses these limitations. UHGV provides high-quality virome references with extensive host predictions, comprehensive functional annotations, protein structures, a classification framework for comparative analysis, and a web portal to facilitate data access. Using UHGV to profile worldwide metagenomes, we found that host range breadth is strongly associated with phage prevalence. Additionally, we identified diversity-generating retroelements and DNA methyltransferases as key factors enabling phage populations to access diverse hosts, revealing how specific genomic features contribute to global phage distribution patterns. UHGV is available at http://uhgv.jgi.doe.gov.},
}

@article {pmid41279261,
year = {2025},
author = {Schuran, FA and Mishra, N and López-Agudelo, VA and Sommer, N and Bernardes, JP and Walker, A and Hinrichsen, F and Gong, T and Gilbert, F and Schröder, L and Bhardwaj, A and Künzel, S and Weber-Stiehl, S and Ito, G and Tran, F and Groussin, M and Röcken, C and Matute, J and Schreiber, S and Penninger, JM and Blumberg, RS and Schmitt-Kopplin, P and Baines, JF and Sommer, F and Rosenstiel, P},
title = {Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.20.683425},
pmid = {41279261},
issn = {2692-8205},
abstract = {Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and function of the intestinal epithelium and its associated microbiota, we employed a comprehensive multi-omics approach, including (spatial) transcriptomics, DNA methylation analysis, fecal metagenomics, and metabolomics. Our findings show that PEM persistently alters the intestinal epithelium by depleting Paneth cells and suppressing antimicrobial gene expression - changes linked to DNA methylation that persist despite dietary recovery. In germ-free mice, the sustained epithelial phenotype after was absent. We identified the microbial lipid metabolite 9-HODE and epigenetically deregulated PPAR-driven GDF15 expression as key molecular drivers of the persistent PEM-induced Paneth cell dysfunction. Targeting microbial lipid production and its link to the host GDF15 pathway could offer novel therapeutic strategies for long-term consequences of malnutrition and other Paneth cell-associated diseases.},
}

@article {pmid41279255,
year = {2025},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.686673},
pmid = {41279255},
issn = {2692-8205},
abstract = {UNLABELLED: The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgae polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, macroalgae polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens , to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing were employed to distinguish the natural active fraction from transient gut microbiome taxa. Four media combinations were able to propagate between 96% to 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo . Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.

IMPORTANCE: Seaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes to propagate these active microbial communities in vitro . This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}

@article {pmid41279103,
year = {2025},
author = {Seki, K and Nguyen, MTA and Penev, PI and Banfield, JF and Isaacs, FJ and Jewett, MC},
title = {Engineered orthogonal translation systems from metagenomic libraries expand the genetic code.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.30.685624},
pmid = {41279103},
issn = {2692-8205},
abstract = {Genetic code expansion with non-canonical amino acids (ncAAs) opens new opportunities for the function and design of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation is limited both by a small collection of orthogonal aminoacyl-tRNA synthetases (aaRSs) and tRNAs and by low-throughput methods to discover them. Here, we report the discovery, characterization, and engineering of a UGA suppressing orthogonal translation system mined from metagenomic data. We developed an integrated computational and experimental pipeline to profile the orthogonality of >200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNA [Trp] UCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNA [Trp] UCA is highly active in cell-free and cellular contexts. We then use Ochre , a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion.},
}

@article {pmid41278862,
year = {2025},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole Metagenome Sequencing: not Deep Enough for Complete Microbial Function Recovery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.685665},
pmid = {41278862},
issn = {2692-8205},
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated.We analyzed oral-rinse WMS data from a study cohort including 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data were annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in e.g. case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights.},
}

@article {pmid41278782,
year = {2025},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.23.683462},
pmid = {41278782},
issn = {2692-8205},
abstract = {Studies of whole viral populations--the "virome"--are yielding exciting new insights into biological systems, but methods are still being optimized. Here we describe generation and use of a synthetic viral community to assess several technical challenges important in virome analysis. Our mock community was comprised of phages lambda, T4, M13, MS2, and phi6, together with adeno-associated virus (AAV), murine hepatitis virus (MHV), and vaccinia virus (VV). We spiked the mock community into different human sample types, including stool, saliva, oropharyngeal (OP) wash, and bronchoalveolar lavage (BAL), then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared to direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from virus-rich samples such as from stool and saliva. Three VLP enrichment work flows were compared, and each was found to have strengths and weaknesses. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. Bacteriophage DNA can be modified by at least 12 different chemistries, raising the question of whether these modifications might block recovery in virome analytical protocols. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC), and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.},
}

@article {pmid41278757,
year = {2025},
author = {Luo, RS and Kille, B and Vaughan, EE and Clark, JR and Maresso, AW and Nute, MG and Treangen, TJ},
title = {Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.10.681738},
pmid = {41278757},
issn = {2692-8205},
abstract = {MOTIVATION: Strain-level microbiome profiling has revealed key insights into microbial community composition and strain dynamics. However, accurate strain-level analysis remains challenging due to limited linkage information, ambiguous read mapping, and complicating factors such as genome similarity, sequencing depth, and community complexity. These challenges are especially pronounced for short-read metagenomic data when estimating the relative abundances of multiple strains, a task critical for genotype-phenotype association studies.

RESULTS: To address this gap, we present Strainify, which enables accurate strain-level abundance estimation from short-read metagenomes with as little as 1% genome coverage. Specifically, Strainify combines (1) identification of informative variants via core genome alignment, (2) filtering of confounding variants via a window-based test, and (3) maximum likelihood estimation of strain abundances. A Shannon entropy-weighted version of the model further improves robustness in noisy, low-coverage settings by downweighting sites with low information content. Across simulated communities of varying complexity, Strainify consistently outperformed existing approaches. On mock community sequencing data, Strainify's estimates aligned more closely with reference abundances. When applied to a longitudinal gut microbiome dataset, Strainify successfully recapitulated the reported temporal dynamics of Bacteroides ovatus strain groups, demonstrating its ability to recover biologically meaningful patterns from real-world metagenomes. Together, these results establish Strainify as a robust and versatile solution for accurate strain-level abundance estimation in short-read, low-coverage microbiome studies.

AVAILABILITY: The Strainify code and results are available at: https://github.com/treangenlab/Strainify.},
}

@article {pmid41278729,
year = {2025},
author = {Lu, R and Lee, N and Drake, AK and Fulton, RP and Abutaleb, NS and Seleem, M and Oakland, DN and Garin-Laflam, MP and Pop, M and Luo, XM},
title = {Discovery of Novel Probiotic Species to Improve Infant Health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.27.684727},
pmid = {41278729},
issn = {2692-8205},
abstract = {UNLABELLED: Selecting an appropriate infant formula can be challenging for parents given the wide range of available options, which may lead to suboptimal choices or frequent switching. Our recent studies in mice demonstrated that the maternal microbiota-particularly Limosilactobacillus reuteri present in breast milk-plays a critical role in shaping neonatal immunity by promoting the production of immunoglobulin A (IgA), a key antibody for defense against enteric pathogens. To extend these findings to humans, we analyzed fecal samples from healthy breastfed infants using shotgun metagenomic sequencing combined with whole-bacterial-cell ELISA to assess associations between specific taxa and pathogen-reactive IgA. We found that members of the Oscillibacter species (including Oscillibacter sp. KLE1728, KLE1745, PC13, PEA192, and O. valericigenes) and Morganella (e.g., M. morganii, Morganella sp. EGD-HP17, and Morganella sp. HMSC11D09) were strongly correlated with IgA responses against Salmonella and Shigella . In contrast, IgA reactive to enterohemorrhagic Escherichia coli (EHEC) was associated with other genera, including Staphylococcus . Notably, Lactobacillus species (L. bombi, L. kefiri, L. equi , and L. rhamnosus) were consistently linked to elevated IgA responses against Salmonella, Shigella , and EHEC. Moreover, levels of anti- Salmonella and anti- Shigella IgA were positively correlated with the use of infant formula containing prebiotic fibers or human milk oligosaccharides (5-HMO). Collectively, these findings highlight novel commensal taxa with potential as probiotic candidates to guide the development of next-generation infant formulas aimed at enhancing mucosal immunity and supporting infant health.

IMPORTANCE: Early-life nutrition shapes immune maturation, yet the microbial factors driving mucosal antibody responses remain poorly defined. Through integrated metagenomic and IgA profiling, this study identifies commensal taxa, particularly Lactobacillus, Oscillibacter , and Morganella , associated with pathogen-specific IgA in infants. These taxa may enhance mucosal defense against enteric pathogens, revealing key microbial contributors to early immune development. The findings provide a foundation for designing next-generation infant formulas that leverage targeted probiotics or prebiotics to promote protective IgA responses and gut health.},
}

@article {pmid41278541,
year = {2025},
author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T},
title = {MeTAline: enabling reproducible and scalable metagenomic analyses.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf158},
pmid = {41278541},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; },
abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.},
}

*Metagenomics/methods
*Software
Metagenome
Microbiota/genetics
Reproducibility of Results
Computational Biology/methods

@article {pmid41278535,
year = {2025},
author = {Berg, M and Reiter, T and Emerson, J and Brown, CT and Roux, S},
title = {Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf163},
pmid = {41278535},
issn = {2631-9268},
mesh = {*Soil Microbiology ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; },
abstract = {Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome regions and that long-read sequencing can complement short-read metagenomes by improving assembly contiguity and the recovery of variable regions.},
}

*Soil Microbiology
*Metagenome
*Metagenomics/methods
Sequence Analysis, DNA/methods
Genetic Variation
High-Throughput Nucleotide Sequencing

@article {pmid41278475,
year = {2025},
author = {An, W and Zhang, Y and Liu, Y and Yang, T and Bai, S and Zhou, P and Si, J and Zhao, Y and He, Y and Pan, Y and Jiang, Y},
title = {Impact of metagenomic sequencing on clinical outcomes in patients with suspected central nervous system infections: a retrospective case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1677092},
pmid = {41278475},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; *Central Nervous System Infections/diagnosis/microbiology/cerebrospinal fluid/mortality ; Female ; Middle Aged ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Adult ; Treatment Outcome ; Hospital Mortality ; },
abstract = {OBJECTIVES: Although the value of metagenomic sequencing (mNGS) in diagnosing pathogens in central nervous system infections (CNSi) has been confirmed, its impact on the clinical outcomes of patients remains to be elucidated. This study intended to investigate the clinical impact of cerebrospinal fluid (CSF) mNGS on the outcomes of patients with suspected CNSi.

METHODS: Between January 2022 and July 2024, patients who met both the inclusion and exclusion criteria were enrolled in the study and assigned to either the mNGS group (CSF tested by both mNGS and conventional microbiological tests [CMTs]) or the CMT group (CMTs alone). Following this, propensity score matching (PSM) was applied to balance baseline differences. The primary endpoint, time to clinical improvement, was then compared between the two groups and analyzed in stratified subgroups. Secondary endpoints included the rates of clinical improvement at 14 and 30 days, hospital stay, in-hospital mortality, and the proportion of GCS score <15.

RESULTS: A retrospective analysis of 338 patients was conducted, with 169 cases in each group. In the mNGS group, a comparison of diagnostic performance between the two testing methods demonstrated that mNGS yielded a significantly higher positivity rate in patients with CNSi compared to CMTs (67.5% vs. 18.3%, p < 0.001), identifying 111 pathogens in total, which was substantially more than the 24 detected by CMTs. Subsequent comparison of clinical outcomes between the groups showed that the duration until clinical improvement was significantly reduced in the mNGS group when compared to the CMT group (median: 14 days vs. 17 days; p=0.032). Moreover, a significantly higher percentage of patients in the mNGS group experienced clinical improvement within 14 days compared to those in the CMT group(42.6% vs. 31.4%; p=0.032). Subgroup analysis further revealed that the mNGS group's superiority in clinical improvement over the CMT group was only evident in patients with CNSi, especially when complicated by pneumonia.

CONCLUSION: The combination of mNGS with CMT significantly improves the clinical outcome of CNSi patients, offering greater clinical utility than traditional methods alone.},
}

Humans
Retrospective Studies
Male
*Central Nervous System Infections/diagnosis/microbiology/cerebrospinal fluid/mortality
Female
Middle Aged
*Metagenomics/methods
Case-Control Studies
Aged
Adult
Treatment Outcome
Hospital Mortality

@article {pmid41278474,
year = {2025},
author = {Huang, R and Zhang, Y and Dong, C and Chen, J and Zou, H and Liu, Y and Guo, M and Gao, H and Ke, Q and Wu, W},
title = {Clinical application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1661213},
pmid = {41278474},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; *Pneumonia/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Intensive Care Units ; Adult ; Fungi/genetics/isolation & purification/classification ; *Pneumonia, Bacterial/diagnosis/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Severe pneumonia is a significant cause of mortality among ICU patients. Metagenomic next-generation sequencing (mNGS) is an advanced, comprehensive, unbiased diagnostic tool for pathogen identification in infectious diseases. This study aimed to evaluate the clinical efficacy of mNGS for diagnosing severe pneumonia.

METHODS: This study retrospectively analyzed 323 patients with suspected severe pneumonia admitted to the intensive care unit (ICU) of Wuhan University Renmin Hospital between January 2022 and December 2023. Bronchoalveolar lavage fluid (BALF) samples were collected from all 323 patients, and blood samples were obtained from 80 patients. Both mNGS and conventional microbial testing (CMT) were performed on the collected BALF and blood samples to analyze the pathogen spectrum. The diagnostic performance of mNGS and CMT was systematically evaluated and compared.

RESULTS: The overall positivity rate of mNGS was significantly greater than that of CMT (93.5% vs. 55.7%, p < 0.001). mNGS demonstrated significantly greater sensitivity than did CMT (94.74% vs. 57.24%, p < 0.001) but lower specificity (26.32% vs. 68.42%, p < 0.01). mNGS identified 36 bacterial species, 14 fungal species, 7 viral species, and 1 Chlamydia species, whereas CMT detected 21 bacterial species and 9 fungal species. According to the pathogen spectrum, Klebsiella pneumoniae, Acinetobacter baumannii, and Candida albicans were the predominant pathogens associated with severe pneumonia. The detection rate of mixed infections was significantly higher with mNGS than with CMT (62.8% vs. 18.3%, p < 0.001).

CONCLUSIONS: Compared with CMT methods, mNGS has significant advantages in pathogen detection for severe pneumonia. Owing to its broad detection range and high sensitivity, mNGS serves as a valuable complementary approach to traditional culture-based methods.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Male
Retrospective Studies
Female
*Metagenomics/methods
Middle Aged
Aged
Bronchoalveolar Lavage Fluid/microbiology/virology
Sensitivity and Specificity
*Pneumonia/diagnosis/microbiology
*Bacteria/genetics/isolation & purification/classification
Intensive Care Units
Adult
Fungi/genetics/isolation & purification/classification
*Pneumonia, Bacterial/diagnosis/microbiology
Aged, 80 and over

@article {pmid41278471,
year = {2025},
author = {Wang, Y and Guo, P and Chen, Y and Zhu, H and Yu, X and Deng, J},
title = {Comparison and evaluation of metagenomic next-generation sequencing (mNGS) and real-time PCR for the detection of Mycobacterium tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694179},
pmid = {41278471},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Real-Time Polymerase Chain Reaction/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Metagenomics/methods ; Male ; Female ; Adult ; *Tuberculosis/diagnosis/microbiology ; Middle Aged ; Sputum/microbiology ; Aged ; *Molecular Diagnostic Techniques/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Young Adult ; Adolescent ; },
abstract = {OBJECTIVE: This study aimed to evaluate and compare the performance of metagenomic next-generation sequencing (mNGS) and real-time polymerase chain reaction (RT-PCR) for the detection of Mycobacterium tuberculosis (MTB) in patients with suspected tuberculosis (TB).

METHODS: Samples from patients undergoing routine clinical testing for MTB using both mNGS and RT-PCR were included. The diagnostic agreement between the two methods was assessed. Discordant results were further validated using the Xpert MTB/RIF assay on cryopreserved aliquots.

RESULTS: A total of 556 samples from suspected TB patients were analyzed. The majority were lower respiratory tract specimens, including bronchoalveolar lavage fluid (BALF; 94.06%), sputum (3.24%), and extrapulmonary samples (2.70%). Compared with Xpert MTB/RIF and clinical diagnosis as composite reference standard, both mNGS and RT-PCR showed high sensitivity (92.31% and 90.38%, respectively) and perfect specificity (100%). There was a high level of agreement between mNGS and RT-PCR, with a positive agreement of 82.69%, negative agreement of 98.25%, overall agreement of 98.38%, and a kappa value of 0.896 (P < 0.001). Concordance was higher in samples with lower RT-PCR cycle threshold (Ct) values: 100% at Ct ≤ 15, 100% at 15
CONCLUSION: Both RT-PCR and mNGS demonstrate high overall agreement for MTB detection, with concordance strongly influenced by microbial burden. These findings support the complementary use of these methods in the diagnosis of TB.},
}

Humans
*Mycobacterium tuberculosis/genetics/isolation & purification
*Real-Time Polymerase Chain Reaction/methods
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
*Metagenomics/methods
Male
Female
Adult
*Tuberculosis/diagnosis/microbiology
Middle Aged
Sputum/microbiology
Aged
*Molecular Diagnostic Techniques/methods
Bronchoalveolar Lavage Fluid/microbiology
Young Adult
Adolescent

@article {pmid41278154,
year = {2025},
author = {Zheng, L and Duan, SL and Wang, K},
title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {31},
number = {42},
pages = {113170},
pmid = {41278154},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; },
abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.},
}

Humans
*Gastrointestinal Microbiome/immunology/genetics
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Intestinal Mucosa/microbiology/immunology/pathology
*Crohn Disease/microbiology/therapy/immunology
*Colitis, Ulcerative/microbiology/therapy/immunology
Genetic Predisposition to Disease
Dysbiosis/microbiology/immunology/therapy
*Inflammatory Bowel Diseases/microbiology/therapy
Metagenomics
Animals
Metabolomics
Immunity, Mucosal

@article {pmid41278038,
year = {2025},
author = {Li, B and Liao, Y and Li, J},
title = {Legionella-induced suppurative cervical lymphadenitis in a child diagnosed by metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1655298},
pmid = {41278038},
issn = {2296-2360},
abstract = {Legionella pneumophila, primarily associated with respiratory infections, rarely causes extrapulmonary disease. Conventional diagnostic methods for Legionella are often limited. Here we report a case of suppurative cervical lymphadenitis caused by L. pneumophila. And we highlight the critical role of mNGS in enabling rapid and accurate pathogen identification, guiding effective targeted therapy for rare and challenging infections.},
}

@article {pmid41278006,
year = {2025},
author = {Minch, B and Moniruzzaman, M},
title = {BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf284},
pmid = {41278006},
issn = {2635-0041},
abstract = {MOTIVATION: Viruses in the kingdom Bamfordvirae, specifically giant viruses (NCLDVs) in the phylum Nucleocytoviricota and smaller members in the Preplasmiviricota phylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom, such as giant viruses, polinton-like viruses, and virophages, have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets.

RESULTS: Here, we present, BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, and Preplasmiviricota genome identification and annotation. BEREN's performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs and Preplasmiviricota genomes. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis.

BEREN is available at https://gitlab.com/benminch1/BEREN, and results from testing BEREN on a real-world metagenome are available in the Supplementary Files.},
}

@article {pmid41277975,
year = {2025},
author = {Wang, B and Li, W and Xue, N and Xi, R and Wang, Y and Fang, L and Wang, Q and Liang, X and Xiao, Y and Yang, X and Wu, X},
title = {Co-application of biochar and compost enhanced soil carbon sequestration in urban green space.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1707894},
pmid = {41277975},
issn = {1664-302X},
abstract = {The mechanism of biochar and compost as soil amendments in urban green spaces remains unclear. Using Euonymus kiautschovicus as a model system, this study established eight treatment gradients, 0 (CK), single biochar applications: 4% (BC4), 8% (BC8), 12% (BC12), 7.5% compost (COM), and their combinations BCC4 (BC4 + 7.5% COM), BCC8 (BC8 + 7.5% COM), BCC12 (BC12 + 7.5% COM). Through metagenomic sequencing and metagenome-assembled genomes (MAGs) analysis, we investigated soil microbiome structure, carbon sequestration functional genes, and their interactions in response to amendments. The combined application of medium-low dose biochar (4-8%) with compost significantly optimized the physicochemical properties and microbial functions in soils. Compared to single amendments, hybrid treatments synergistically enhanced soil moisture content. Specifically, BCC8 increased by 27% compared to the CK, organic carbon levels reached 12.8 g/kg with BCC12, and available nutrients showed 45% higher available phosphorus with BCC4. Metagenomic analysis revealed that hybrid treatments reshaped microbial community structure, with BCC8 significantly enriching Acidobacteria (8.72%) and Nitrospira (1.42%), driving an increased abundance of carbon fixation genes. Among key carbon fixation pathways, the reductive tricarboxylic acid cycle (rTCA) exhibited the highest gene abundance (mean 15.03), dominated by MAG176. The Calvin-Benson-Bassham (CBB) cycle displayed broad adaptability, with MAG59 identified as a core carbon-fixing strain. This study has significant implications for the application of biochar-compost combinations in carbon management of urban green spaces.},
}

@article {pmid41277970,
year = {2025},
author = {Chapagain, C and Khezri, A and Ali, J and Smistad, M and Sølverød, LS and Ahmad, R},
title = {Optimizing sample preparation for culture-free nanopore sequencing to enable rapid pathogen and antimicrobial resistance profiling in bovine mastitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680165},
pmid = {41277970},
issn = {1664-302X},
abstract = {Long-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk is challenging due to the complex milk matrix, low bacterial count, and high somatic cell content. This study primarily aimed to further optimize our previously developed culture-free nanopore sequencing protocol for milk samples from mastitis cases. Additional optimizations included combining centrifugation, gradient centrifugation, and fat fraction treatment with Tween 20 and citric acid. Subsequently, four DNA extraction kits (Blood and Tissue, Molysis Complete5, HostZero, and SPINeasy Host depletion) were evaluated for their ability to remove host DNA and enrich bacterial DNA for long-read sequencing with Oxford Nanopore technologies. qPCR was used to quantify bacterial and bovine DNA, allowing comparison of host depletion efficiency among the kits. Our results show that simple centrifugation effectively concentrates bacterial cells, removing the need for chemical treatments. The HostZero kit consistently produced higher DNA yields, improved DNA integrity, and more effective host DNA depletion. Using nanopore sequencing, both Gram-positive and Gram-negative mastitis pathogens, along with their AMR genes, were successfully detected. Overall, this study underscores the importance of an effective DNA extraction method for the direct sequencing of mastitis milk samples. Additionally, our findings support the potential of direct metagenomic sequencing as a rapid, culture-free approach for identifying mastitis pathogens and their resistance profiles.},
}

@article {pmid41277885,
year = {2025},
author = {Solís, VE and Bangratz, M and Brugo Carivali, MF and Comte, A and Luciani, CE and Lacombe, S and Fontana, ML and Filloux, D and Pachecoy, MI and Fernandez, E and Dirchwolf, PM and Ayala, JOA and Julian, C and Kruger, RD and Hébrard, E and Fernandez, FD and Perotto, MC and Roumagnac, P and Gutiérrez, SA and Poulicard, N and Celli, MG},
title = {Near-complete genome sequences of a rice necrosis mosaic virus isolate infecting rice in Argentina.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059825},
doi = {10.1128/mra.00598-25},
pmid = {41277885},
issn = {2576-098X},
abstract = {While rice necrosis mosaic virus (RNMV) has only been described in Asia, we identified this virus on a rice plant from Argentina using a viral metagenomic approach. We further confirmed this result by RT-PCR and small-RNA Illumina sequencing to obtain the near-complete genome and to confirm actual infection by RNMV.},
}

@article {pmid41277537,
year = {2025},
author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH},
title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1190},
pmid = {41277537},
issn = {1362-4962},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; },
abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.},
}

@article {pmid41276871,
year = {2025},
author = {Torres-Beltrán, M and Hernández-Guzman, M and Barcelos, C and Chong-Robles, J and Sidón-Ceseña, K and García-Maldonado, JQ and Aguirre-Macedo, ML and Lago-Lestón, A},
title = {Alternative carbon and energy metabolisms linked to hydrocarbon degradation are widely distributed across the different microbial communities from deep-sea sediments of the Gulf of Mexico.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00823-1},
pmid = {41276871},
issn = {2524-6372},
support = {201441/WT_/Wellcome Trust/United Kingdom ; Postdoctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; Master fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; Doctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
abstract = {In marine sediments, microorganisms' roles in recycling organic and inorganic molecules, including hydrocarbons, are critical for ecosystem function. Genomic studies in the Gulf of Mexico (GoM) reveal that microbial community composition and function are shaped by environmental gradients, with hydrocarbon degradation relying on consortia dynamics rather than single species, highlighting their collective ecological importance. Our study evaluated the prokaryotic microbial community in deep-sea GoM sediments, under a depth gradient, in Coatzacoalcos and Perdido regions, two areas influenced by crude-oil efflux and petroleum extraction. Findings indicated depth was the primary driver of microbial community structure, with distinct compositional shifts between shallow (< 1000 m) and deep (> 1200 m) sediments, showcasing microbial adaptation to deep-sea nutrient-limited conditions. Furthermore, functional gene analysis revealed depth-specific metabolic partitioning, with Deltaproteobacteria dominating amino acid and energy metabolism in shallow sediments, while Alphaproteobacteria and Thaumarchaeota prevailed in deeper zones. This underlines the importance of microbial community shifts in composition and structure in ensuring environmental resilience. In addition, relatively low-abundance but critical hydrocarbon degradation genes were detected, primarily in shallow/transition zones, indicating niche-specific potential for bioremediation despite their apparent limited representation. This research contributes to advancing our understanding of alternative carbon and energy metabolisms linked to hydrocarbon degradation that are widely distributed across different microbial communities inhabiting deep-sea marine sediments.},
}

@article {pmid41275986,
year = {2025},
author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , },
title = {Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism.},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jrn.2025.10.015},
pmid = {41275986},
issn = {1532-8503},
abstract = {BACKGROUND AND HYPOTHESIS: Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.

METHODS: We conducted a non-randomized, open-label, three-phase pilot trial, to investigate the effect of daily oral oligofructose-enriched inulin (p-inulin) on stool functional metagenome and changes in plasma, urine and stool metabolites in 13 CKD patients. The study comprised a pre-treatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).

RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In the plasma metabolic biosynthetic pathways for valine, leucine and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and non-polar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.

CONCLUSION: P-inulin administration to CKD patients resulted a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.},
}

@article {pmid41275762,
year = {2025},
author = {Stevenson, EM and Buckling, A and Cole, M and Hayes, A and Lindeque, PK and Murray, AK},
title = {Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments.},
journal = {Environment international},
volume = {206},
number = {},
pages = {109944},
doi = {10.1016/j.envint.2025.109944},
pmid = {41275762},
issn = {1873-6750},
abstract = {Microplastic particles are extremely prevalent environmental pollutants which support microbial biofilms known as the 'plastisphere'. Antimicrobial resistant (AMR) and pathogenic bacteria have been detected in these communities, but it is currently unknown whether microplastics pose a unique risk in terms of AMR or pathogen enrichment. In addition, previous work has been largely lab-based, so it is difficult to understand the role of different substrates in supporting AMR pathogens within the environment, and how this varies as a function of levels of pollution from wastewater. This study investigated in situ bacterial colonisation dynamics on microplastics alongside natural, inert and free-living controls. Samples were incubated along a transect predicted to decrease in anthropogenic pollution, and taxonomy, AMR gene and pathogen presence were assessed using whole metagenome sequencing. Several AMR gene (e.g. aminoglycosides, oxazolidinones and tetracyclines) and pathogen classes (e.g. Flavobacteriia, Chlamydiia and Sphingobacteriia) of concern were detected, and increased in relative abundance in biofilms moving downstream, with polystyrene and HDPE nurdle communities posing a particular risk by supporting AMR bacteria. This work contributes to our understanding of how microplastics may support AMR development, persistence and dispersal in natural systems. In addition, these findings highlight the importance of considering the combined impacts of co-contaminants in wastewater settings, especially following spills into surface water.},
}

@article {pmid41275684,
year = {2025},
author = {Liu, Q and Chen, J and Xu, R and Huang, C and Ren, N and Gao, S and Li, W and Xin, X and Lv, S and Yang, S and Ben, W and Wang, AJ},
title = {Bacterial, viral and environmental interactions shape antibiotic resistance genes in China's anaerobic-anoxic-oxic wastewater treatment systems.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124911},
doi = {10.1016/j.watres.2025.124911},
pmid = {41275684},
issn = {1879-2448},
abstract = {The dissemination of antibiotic resistance genes (ARGs) threatens global public health. Urban wastewater treatment plants (WWTPs), serving as critical reservoirs and dissemination hubs for ARGs, are driven by complex bacteria-virus interactions and environmental factors in activated sludge. This study employed metagenomics and 16S rRNA gene sequencing of activated sludge from 28 A[2]O WWTPs across China to decipher the national distribution of ARGs and their associations with bacterium-phage systems and environmental factors. Research outcomes: fluoroquinolone resistance genes (adeF) and sulfonamide resistance genes (sul1, sul2) dominated ARG abundance (mean 41.7 %, 11.51 %), with significant regional differentiation (PERMANOVA, R[2] = 0.153, p = 0.043). The involvement of bacteria and viruses was significantly associated with ARG dissemination. Among these, Proteobacteria and Actinobacteria were identified as pivotal putative bacterial vectors. Additionally, Myoviridae was predicted to be the predominant viral host for ARGs, while Siphoviridae and Demerecviridae were preferentially associated with specific ARG types. Correlation analysis indicated that ions, such as cobalt, zinc and cadmium, were positively correlated with specific ARG subtypes, whereas arsenic was consistently negatively correlated with most ARG subtypes. Additionally, the oxidation-reduction potential was significantly linked to ARG abundance. This study reveals complex ARG association patterns from the perspective of bacteria-virus interactions and environmental factors, providing insights and a valuable reference for future phage-based control strategies and regional antibiotic resistance pollution policies.},
}

@article {pmid41275679,
year = {2025},
author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J},
title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124956},
doi = {10.1016/j.watres.2025.124956},
pmid = {41275679},
issn = {1879-2448},
abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.},
}

@article {pmid41275070,
year = {2025},
author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G},
title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66733-5},
pmid = {41275070},
issn = {2041-1723},
support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.},
}

@article {pmid41274992,
year = {2025},
author = {Becsei, Á and Stéger, J and Visontai, D and Munk, P and Aarestrup, FM and Csabai, I and Papp, K},
title = {A case study using sewage metagenomic data for assessment of text-to-SQL capabilities in large language models.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28341-7},
pmid = {41274992},
issn = {2045-2322},
support = {No. 874735 (VEO)//European Union's Horizon 2020 research and innovation programme/ ; U24AI183840//National Institute Of Allergy And Infectious Diseases of the National Institutes of Health/ ; RRF-2.3.1-21-2022-00004//National Research, Development, and Innovation Office of Hungary within the framework of the MILAB Artificial Intelligence National Laboratory/ ; },
abstract = {Relational databases offer an efficient solution for storing and retrieving complex data sets, yet the requirement for SQL programming expertise presents a significant challenge for many life science users. We explore whether a cutting-edge large language model can effectively translate plain English queries into SQL scripts (Text-to-SQL), thereby simplifying database interaction and eliminating the typical usage barriers. A complex database comprising 19 interconnected tables of metagenomic analyses from 239 sewage samples across five European cities was available. A large language model was provided with details of the database's structure and background information on its contents. We evaluated the functionalities of this "SewageGPT" tool and assessed the accuracy of its responses to complex questions and visualisation of results. Providing a detailed description of the database enabled SewageGPT to accurately respond to complex inquiries, accelerating the database querying process. Knowledge of the database content proved beneficial, as it minimized the risk of ambiguities in queries; however, ambiguities can lead to incorrect responses. Therefore, human oversight remains crucial, particularly for questions that lack detail or involve ambiguities. The integration of state-of-the-art large language models with direct database connectivity substantially enhances the efficiency of query generation, statistical analysis and visualization of the results.},
}

@article {pmid41274878,
year = {2025},
author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R},
title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66497-y},
pmid = {41274878},
issn = {2041-1723},
support = {R01HD109830//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32HD105364//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD080444//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.},
}

@article {pmid41274873,
year = {2025},
author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J},
title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66612-z},
pmid = {41274873},
issn = {2041-1723},
abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.},
}

@article {pmid41274479,
year = {2025},
author = {Xu, X and Hong, X and Zeng, W and Yan, R and Li, F and Meng, C and Shi, X and Luo, J and Wang, G},
title = {Stereoselective synthesis of (S)-3-Hydroxy-3-phenylpropionate with a novel carbonyl reductase identified from a soda lake metagenome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149193},
doi = {10.1016/j.ijbiomac.2025.149193},
pmid = {41274479},
issn = {1879-0003},
abstract = {This study aimed to discover novel carbonyl reductases from a soda lake metagenome for the efficient synthesis of the chiral drug intermediate (S)-ethyl 3-hydroxy-3-phenylpropionate ((S)-EHPP). A carbonyl reductase (denoted as SLCR1) was identified and found to share less than 30 % sequence identity with known functionally characterized NAD(P)-dependent oxidoreductases, suggesting its novelty. The recombinant enzyme demonstrated optimal activity at 50 °C and pH 7.0, along with excellent stability at 45 °C and within a pH range of 6.0-7.5. Semi-rational design was applied to enhance the catalytic efficiency of SLCR1 toward ethyl benzoylacetate (EBA). After three rounds of mutagenesis and screening, a triple mutant (I212F/I176L/R216L) was obtained, which exhibited a ~ 29-fold improvement in catalytic efficiency compared to the wild-type. Molecular docking indicated that the triple mutant achieves superior catalytic efficiency and binding affinity at the expense of reduced structural stability. In whole-cell biocatalysis co-expressing the mutant enzyme and Bacillus subtilis glucose dehydrogenase (GDH), 150 mM EBA was fully consumed within 1 h, affording (S)-EHPP with 95 % conversion yield and > 99 % enantiomeric excess (e.e.). To the best of our knowledge, this biocatalytic system sets a new benchmark by enabling unprecedented single-batch substrate loading (150 mM) coupled with a remarkably short completion time of 1 h. This study demonstrates an efficient one-step synthesis of (S)-EHPP through the discovery of a novel carbonyl reductase, engineered enhancement, and optimized biocatalysis, providing a promising basis for the industrial production of chiral intermediates.},
}

@article {pmid41274194,
year = {2025},
author = {Jin, L and Xinting, L and Shuaiyang, Z and Qiaoyun, R and Obaid, MK and Peiwen, D and Guiquan, G and Guangyuan, L and Hong, Y},
title = {Comparative metagenomic profiling of microbial pathogen diversity in Haemaphysalis longicornis and Hyalomma dromedarii ticks.},
journal = {Veterinary parasitology},
volume = {341},
number = {},
pages = {110656},
doi = {10.1016/j.vetpar.2025.110656},
pmid = {41274194},
issn = {1873-2550},
abstract = {Ticks are globally important vectors of human and animal pathogens. This study characterized microbial communities in Haemaphysalis longicornis (from humid Zhangjiachuan County) and Hyalomma dromedarii (from arid Minqin County, Gansu Province, China) using metagenomic sequencing. We identified diverse bacteria and viruses including known pathogens (Anaplasma phagocytophilum, Totivirus spp., Escherichia spp.) and potentially novel agents (Totivirus-like and Trachysalambria curvirostris-associated sequences). These results highlight the role of these tick species in pathogen transmission across different environments and emphasize the need for region-specific surveillance. Our findings contribute to the understanding of tick-borne disease risks and inform strategies for targeted control.},
}

@article {pmid41273975,
year = {2025},
author = {Yuan, C and Zhao, X and Qing, C and Li, P},
title = {Phylogenetic diversity and divergent arsenite oxidation of photoarsenotrophs in geothermal springs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140531},
doi = {10.1016/j.jhazmat.2025.140531},
pmid = {41273975},
issn = {1873-3336},
abstract = {A unique metabolic process coupling anoxygenic photosynthesis with arsenite oxidation plays a critical role in arsenic (As) biogeochemical cycling within terrestrial thermal springs. While previous studies have identified restricted ranges of photoarsenotrophic bacteria, their phylogenetic diversity and physiological characteristics remain poorly understood. In this study, we obtain 12 putative metagenome-assembled genomes (MAGs) of photoarsenotrophs from global geothermal springs using metagenomics. These MAGs belong to five thermophilic taxa: Chloroflexales, Burkholderiales, Rhizobiales, Steroidobacterales, Rhodobacterales, significantly expanding the photoarsenotrophic bacteria diversity beyond the previously recognized Gammaproteobacteria. We identified the first Betaproteobacteria lineage supported by integrated physiological characterization, phylogenomics and genomic analysis, which belonging to Calidifontimicrobium sediminis of the order Burkholderiales. Comparative genomic analysis revealed their divergent arsenite oxidase systems: strains G02091 and YIM 73032 employ the arx gene cluster (ARX system), whereas strain SYSU G00088 have evolved the aio gene cluster (AIO system). Our finding extends the known phylogenetic range of photoarsenotrophy, and reveals metabolic versatility of among these bacteria, offering insights into their ecological roles in As cycling, as well as a potential biological resource for its remediation in environments.},
}

@article {pmid41273973,
year = {2025},
author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z},
title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140564},
doi = {10.1016/j.jhazmat.2025.140564},
pmid = {41273973},
issn = {1873-3336},
abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.},
}

@article {pmid41273932,
year = {2025},
author = {Tang, J and Kang, Z and Cui, S and Xu, H and Ren, H and Li, P and Han, J and Zou, Y},
title = {Exploration of molecular diagnosis for HHV-6 encephalitis in immunocompetent individuals: A study combining mNGS and PCR.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117196},
doi = {10.1016/j.diagmicrobio.2025.117196},
pmid = {41273932},
issn = {1879-0070},
abstract = {PURPOSE: To evaluate clinical features, diagnosis, treatment, and prognosis of HHV-6 encephalitis in immunocompetent adults, a rare and challenging condition.

METHODS: In this retrospective, single-centre study, we enrolled six immunocompetent adults (mean age 60.67 ± 15.57 years) diagnosed with HHV-6 encephalitis at Hengshui People's Hospital between January 2022 and December 2024. Clinical data, laboratory variables, cerebrospinal fluid (CSF) parameters, brain magnetic resonance imaging (MRI) findings, and electroencephalography (EEG) recordings were systematically collected. CSF samples underwent metagenomic next-generation sequencing (mNGS) for unbiased pathogen detection. All HHV-6-positive findings were subsequently confirmed by quantitative real-time polymerase chain reaction (PCR).

RESULTS: HHV-6 encephalitis presented with fever, unconsciousness, convulsions, headache, and cognitive dysfunction. CSF analysis showed mild intracranial pressure elevation(median 186.67 mmH2O, IQR 157.50-217.50mmH2O), lymphocytic pleocytosis(58.6 ± 31.70 %), and normal or mildly elevated protein(0.234±0.99 g/L) and glucose(median 4.03 mmol/L, IQR 3.42-4.50 mmol/L) levels. MRI revealed high-FLAIR signals in the right temporal lobe in three patients and chronic foci in the frontal lobe and basal ganglia in three others. EEG abnormalities were noted in two patients. mNGS revealed an average of 578±512.09 unique HHV-6 reads, with HHV-6A identified in five patients and HHV-6B in one. All findings were confirmed by quantitative PCR. Prompt ganciclovir therapy led to complete recovery without sequelae in all six cases.

CONCLUSIONS: mNGS enables rapid detection of the rare but treatable HHV-6 meningitis in immunocompetent adults that conventional tests miss, prompting early antiviral therapy and better outcomes.},
}

@article {pmid41273911,
year = {2025},
author = {Zhang, Z and Wang, R and An, Z and Liu, Y and Zhao, J and Zhang, T and Ye, X and Liu, P and Jia, H},
title = {Polystyrene and its dissolved organic matter accelerate antibiotic resistance gene dissemination in anaerobic digestion by posing resistance pressure on functional microorganisms.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124997},
doi = {10.1016/j.watres.2025.124997},
pmid = {41273911},
issn = {1879-2448},
abstract = {Microplastics (MPs) in sludge can release dissolved organic matter (MP-DOM) and affects the dissemination of co-existing antibiotic resistance genes (ARGs). However, the contributions and mechanisms of MPs themselves and released MP-DOM on ARGs dissemination during anaerobic digestion (AD) remain unclear. This study investigated the dissemination potential of ARGs under MP and MP-DOM treatment by combining metagenomic sequencing with partial least squares structural equation modeling (PLS-SEM). Results showed that both treatments increased the abundances of ARGs, virulence factor genes and mobile genetic elements, with 1.25-1.79 fold enhancement relative to control, highlighting ARGs dissemination in AD. Notably, MP-DOM exhibited a stronger enhancement than MPs. The enhancement was mainly ascribed to the resistance pressure on functional microbial communities becoming ARGs hosts by increasing membrane permeability and type IV secretion system activation through reactive oxygen species generation, as evidenced by the 108.2 % and 120.5 % increases in VirD4 expression under MPs and MP-DOM, respectively. Different from the induced selection pressure of MPs on ARGs dissemination, MP-DOM mainly exerted a strongly biological effect by stimulating stress-adaptive carbohydrate metabolism (glycolysis and pentose phosphate) within hydrolytic microorganisms (Clostridium and Defluviicoccus) in the microbially-driven AD environment. This study identifies a dominant factor yet previously overlooked driver of MP-DOM that amplifies ARGs dissemination in sludge AD, providing new insights into the risks of plastic-derived contaminants.},
}

@article {pmid41273495,
year = {2025},
author = {Liu, Z and Shao, X and Jin, Y and Shan, X and Zhang, H and Liang, Q and Lu, W and Zhou, G and Lan, H and Zhang, Y},
title = {GO/iron series enhance performance of anaerobic system for treatment of sulfate-containing organic wastewater.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {472},
pmid = {41273495},
issn = {1573-0972},
support = {2024TSGC0781//Shandong Province Science and Technology Small and Medium sized Enterprise Inno vation Ability Enhancement Project/ ; 2024ZDYF010019//Key R&D Program of Rizhao City/ ; ZR2021MB085//Shandong Provincial Natural Science Foundation/ ; },
mesh = {*Wastewater/chemistry/microbiology ; Anaerobiosis ; *Sulfates/metabolism/chemistry ; *Graphite/chemistry ; Methane/metabolism ; Biological Oxygen Demand Analysis ; *Iron/chemistry ; Bioreactors/microbiology ; Ferric Compounds/chemistry ; Biofuels ; Bacteria/metabolism/genetics/classification ; *Water Purification/methods ; },
abstract = {This study combined with the analysis of co-metabolic microbial communities and investigated the enhancing effects of graphene oxide (GO)/iron series (GO/Fe[0], GO/Fe3O4 and GO/Fe2O3) on anaerobic treatment of sulfate-laden organic wastewater at varying chemical oxygen demand to sulfate ion (COD/SO4[2-]) ratios (COD/SO4[2-]=2.5, COD/SO4[2-]=1.25 and COD/SO4[2-]=0.8). Our results indicate that all GO/iron series significantly improved CODCr and SO4[2-] removal efficiencies and methane production and the enhancement effect was more pronounced at lower COD/SO4[2-] ratios. At COD/SO4[2-]=0.8, compared to the blank control system, the CODCr and SO4[2-] removal efficiencies and the biogas production rate of the GO/Fe3O4 and GO/Fe2O3 system were enhanced by 14.1%, 18.3%, and 24.7%; 5.8%, 9.6%, and 23.3% respectively. Notably, with GO/Fe[0] exhibiting the most significant improvement, the CODCr removal efficiency, SO4[2-] removal efficiency and biogas production were improved by 34.4%, 41.1% and 42.5%, respectively, relative to the blank control. This mechanism is primarily attributed to the corrosion of Fe[0] under anaerobic conditions, which releases electrons and H2 (supplying electron donors for hydrogenotrophic methanogens) and produces elevated levels of soluble Fe[2+] which precipitates sulfide (reducing H2S toxicity). Furthermore, they optimized the system's pH (GO/Fe[0]:7.30-7.69; GO/Fe3O4: 7.30-7.57; GO/Fe2O3: 7.17-7.54; blank: 6.99-7.18), and oxidation-reduction potential (ORP) (GO/Fe[0]: -350~-370 mV; GO/Fe3O4 and GO/Fe2O3: -303~-325 mV; blank: -303~-325 mV) and enhanced the physicochemical properties of the activated sludge. Metagenomic sequencing revealed that the addition of GO/iron series maintained the stability of the microbial community structure, thereby conferring stronger shock resistance to the system. This research provides a scientific basis for exploring the application of anaerobic systems in treating sulfate-containing organic wastewater.},
}

*Wastewater/chemistry/microbiology
Anaerobiosis
*Sulfates/metabolism/chemistry
*Graphite/chemistry
Methane/metabolism
Biological Oxygen Demand Analysis
*Iron/chemistry
Bioreactors/microbiology
Ferric Compounds/chemistry
Biofuels
Bacteria/metabolism/genetics/classification
*Water Purification/methods

@article {pmid41272806,
year = {2025},
author = {Zhang, CJ and Hou, J and Zhou, J and Zou, D and Zhang, H and Ma, Q and Li, M},
title = {Methane cycling microorganisms drive seasonal variation of methane emission in mangrove ecosystems.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {149},
pmid = {41272806},
issn = {2524-6372},
abstract = {Coastal mangroves are one of the significant hotspots of natural methane (CH4) emissions, yet the seasonal dynamics of these emissions and the underlying microbial drivers remain poorly understood. A clearer understanding of these processes is critical for predicting and mitigating methane emissions from these crucial ecosystems. In this study, we conducted a seasonal investigation (from March 2021 to January 2022) in mangrove sediments of the Futian Natural Reserve. We measured in situ methane fluxes and analyzed the microbial community structure via 16S rRNA gene sequencing, metagenomics and metatranscriptomics. Our results revealed significant seasonal variations in methane emissions, with the highest rates occurring in summer. Based on relative abundance of 16S rRNA gene amplicons and methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) gene sequences obtained from metagenomes, we identified three dominant methanogenic lineages (hydrogenotrophic Methanomicrobiales, acetoclastic Methanosaeta and H2-dependent methylotrophic Methanomassiliicoccales), two anaerobic methanotrophic archaea (ANME-1 and ANME-2b) and one group of aerobic methanotrophic bacteria (Methylococcaceae). Metatranscriptomic data further illuminated that the transcripts of methanogenic mcrA genes were significantly higher in summer and autumn, while the transcriptional activity of anaerobic (ANME-mcrA) and aerobic (pmoA) methanotrophs were most pronounced in autumn. Correlation analyses established a significantly negative relationship between methane emissions and salinity levels. This study highlights that salinity is a key environmental factor mediating methane emissions in mangroves, likely through suppressing methanogenic activity. Our findings thus reveal that seasonal microbial interactions regulate mangrove methane flux, providing critical insights for modeling global methane budgets and guiding climate-smart mangrove management.},
}

@article {pmid41272756,
year = {2025},
author = {Dubovitskiy, N and Kurskaya, O and Solomatina, M and Loginova, A and Derko, A and Khozyainova, A and Denisov, E and Shemyakin, E and Shestopalov, A and Sharshov, K},
title = {Metagenomic identification, isolation, and complete genome characterization of two novel picornaviruses in wild duck from Northeastern Siberia.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-025-03017-w},
pmid = {41272756},
issn = {1743-422X},
support = {225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; },
abstract = {Duck hepatitis A virus (DHAV, Avihepatovirus ahepati species) is a well-known pathogen of domestic ducks, causing fatal disease in ducklings and posing a significant burden to duck poultry farms. Avihepatovirus ahepati is the sole species within the genus Avihepatovirus and is classified into three distinct genotypes: DHAV-1, DHAV-2, and DHAV-3. In our study, we detected and isolated two strains belonging to the Picornaviridae family from Anas crecca in Northeastern Asia. One of the isolates is related to the DHAV-1 group; however, its polyprotein gene sequence shares only 77.83% nucleotide identity and 89.68% amino acid identity with the most closely related DHAV-1 sequence available, suggesting it represents a highly divergent lineage. The second isolated duck picornavirus shows 60.16% nucleotide identity to the polyprotein gene sequence of the previously described duck picornavirus strain detected during an outbreak in domestic ducks in China. The identification of these two novel picornaviruses in wild ducks, along with their efficient replication in duck embryos and primary cell cultures, emphasizes the need for comprehensive studies of their prevalence in wild ducks and their biological traits to assess potential risks for wildlife and poultry farming. The obtained complete genome sequences and viral isolates enhance our understanding of the diversity, evolution, and ecology of avian picornaviruses.},
}

@article {pmid41272260,
year = {2025},
author = {Akyazı, H and Güldür, FÇ and Beyzi, E},
title = {Anode surface modification with reduced graphene oxide (rGO) and molybdenum (Mo) enhances microbial diversity and chemical oxygen demand (COD) removal in microbial fuel cells.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41272260},
issn = {1614-7499},
support = {FCD-2023-8721//Gazi Üniversitesi/ ; },
abstract = {This study aimed to investigate the effects of anode surface modifications on microbial community composition and chemical oxygen demand (COD) removal efficiency in microbial fuel cells (MFCs). Four different anode electrodes were fabricated: bare nickel foam (NF), reduced graphene oxide-coated nickel foam (rGO/NF), and rGO/NF modified with 30 wt% and 50 wt% molybdenum (Mo). These electrodes were tested in a single-chamber, membraneless, air-cathode MFC. Surface morphology was characterized using scanning electron microscopy (SEM), and microbial diversity was assessed through 16S rRNA metagenomic sequencing. Distinct microbial profiles were observed across the electrode types. The NF anode supported high abundances of Mesoterricola sediminis (22.2%), Klebsiella pneumoniae (10.1%), and other facultative species. The rGO/NF electrode promoted colonization by Cutibacterium acnes (8.1%) and Paracidovorax avenae (5.4%). On the 30Mo/rGO/NF electrode, notable species included Escherichia coli (8.4%) and Salmonella enterica (6.0%). The 50Mo/rGO/NF anode exhibited the highest microbial diversity, with species such as Streptomyces sp. RerS4 (6.9%) and Micromonospora endophytica (6.5%) being predominant. The highest COD removal efficiency (88.58%) was achieved using the 50Mo/rGO/NF anode. These findings demonstrate that molybdenum-modified rGO coatings enhance both microbial colonization and electrochemical performance, offering a promising strategy for improving MFC efficiency in wastewater treatment applications.},
}

@article {pmid41271719,
year = {2025},
author = {Martiny, HM and Munk, P and Fuschi, A and Becsei, Á and Pyrounakis, N and Brinch, C and , and Larsson, DGJ and Koopmans, M and Remondini, D and Csabai, I and Aarestrup, FM},
title = {Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10278},
pmid = {41271719},
issn = {2041-1723},
support = {NNF16OC0021856: Global Surveillance of Antimicrobial Resistance//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
mesh = {*Sewage/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; North America ; Geography ; Cities ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance genes (ARGs) have rapidly emerged and spread globally, but the pathways driving their spread remain poorly understood. We analyzed 1240 sewage samples from 351 cities across 111 countries, comparing ARGs known to be mobilized with those identified through functional metagenomics (FG). FG ARGs showed stronger associations with bacterial taxa than the acquired ARGs. Network analyses further confirmed this and showed potential for source attribution of both known and novel ARGs. The FG resistome was more evenly dispersed globally, whereas the acquired resistome followed distinct geographical patterns. City-wise distance-decay analyses revealed that the FG ARGs showed significant decay within countries but not across regions or globally. In contrast, acquired ARGs showed decay at both national and regional scales. At the variant level, both ARG groups had significant national and regional distance-decay effects, but only FG ARGs at a global scale. Additionally, we observed stronger distance effects in Sub-Saharan Africa and East Asia compared to North America. Our findings suggest that differential selection and niche competition, rather than dispersal, shape the global resistome patterns. A limited number of bacterial taxa may act as reservoirs of latent FG ARGs, highlighting the need of targeted surveillance to mitigate future resistance threats.},
}

*Sewage/microbiology
*Bacteria/genetics/drug effects/classification/isolation & purification
Metagenomics
*Drug Resistance, Bacterial/genetics
Genes, Bacterial/genetics
North America
Geography
Cities
Anti-Bacterial Agents/pharmacology

@article {pmid41271709,
year = {2025},
author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C},
title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10295},
pmid = {41271709},
issn = {2041-1723},
mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; },
abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.},
}

*Caves/microbiology
*Ecosystem
Carbon Dioxide/metabolism
Metagenome
Geologic Sediments/microbiology
Microbiota/genetics
Hydrogen/metabolism
Metagenomics
*Bacteria/genetics/metabolism/classification
Biodiversity
Carbon Monoxide/metabolism
Biofilms
Gammaproteobacteria/genetics/metabolism

@article {pmid41271554,
year = {2025},
author = {Wang, J and Chen, Y and Chen, T and Cai, H and Chen, Q and Sun, W and Ni, J},
title = {Genomic blueprint enables early intervention in cyanobacterial risk management.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2025.11.005},
pmid = {41271554},
issn = {2095-9281},
abstract = {While existing early-warning systems struggle to achieve cross-species cyanobacterial risk prediction with the required synchronicity and accuracy in aquatic ecosystems, our study pioneers a genome architecture-driven monitoring paradigm through decoding 317 cyanobacterial metagenome-assembled genomes from the world's largest phosphorus-limiting water transfer system, the Middle Route of the South-to-North Water Diversion Canal (MR-SNWDC). We found an evolutionary blueprint where genome minimization (<3 Mbp) confers ecological dominance under phosphorus scarcity. These streamlined genomes showed predominance and remarkable seasonal dynamics and demonstrated metabolic specialization in phosphorus turnover, light harvesting, and carbon fixation compared to larger genomes. Importantly, we identified a 3 Mbp genomic threshold distinguishing low-risk cyanobacterial consortia from their toxin-producing counterparts. This genome-proxy system enables preemptive risk mitigation by predicting toxic transitions through genome size tracking, fundamentally advancing algal management from reactive monitoring to proactive regulation in water transfer networks.},
}

@article {pmid41271358,
year = {2025},
author = {Li, Z and Chen, Y and Zheng, J and Su, J and Lu, Y and Xia, Y and Luo, H},
title = {From fungi to lactic acid bacteria: Dominant microorganisms govern stage-specific esters biosynthesis in pit microecology of strong-flavor baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 2},
pages = {117797},
doi = {10.1016/j.foodres.2025.117797},
pmid = {41271358},
issn = {1873-7145},
mesh = {*Esters/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Fungi/metabolism/genetics ; *Wine/microbiology/analysis ; *Flavoring Agents/metabolism ; Butyrates/metabolism ; Food Microbiology ; Taste ; },
abstract = {Esters are vital flavor compounds in strong-flavor baijiu (SFB). However, their biosynthetic mechanisms during pit fermentation are not fully understood. This study employed integrated metagenomic and metabolomic analyses to investigate stage-specific microecological dynamics governing ester biosynthesis and identified three distinct fermentation stages. Stage P1 (days 0-15) featured initial ester accumulation driven by fungal dominance (e.g., Saccharomyces, Aspergillus, and Rhizopus) and high α-diversity. Elevated esterase (EST) genes mainly involved to the ethyl acetate and ethyl butyrate synthesis. Stage P2 (15-35 d) exhibited minimal changes in esters content (except ethyl lactate increase linked to 42 EST genes). During this stage, acidogenic microorganisms, primarily Acetilactobacillus (> 64 % relative abundance), Lactobacillus, and Clostridium, proliferated and co-aggregated with methanogens, including Methanosarcina and Methanobacterium. In Stage P3 (35-117 d), Lactobacillus-Acetilactobacillus consortium (> 74 %) exhibited rapid ester accumulation alongside acids and alcohols increases, with high EST abundance for ethyl caproate and ethyl butyrate synthesis. Dominant microorganisms govern the ester synthesis, with catalytic dominance shifting from fungal (Aspergillus, Saccharomyces, etc.) to lactic acid bacteria (Lactobacillus, Acetilactobacillus, etc.) systems across stages. Five physicochemical properties exerted the stage-dependent control: pH and reducing sugars shaped the microbial structure in P1 (R[2] = 0.40, 0.46); temperature and ethanol drove community simplification in P2 (R[2] = 0.35, 0.64); Acidity and ethanol regulated functional dominance in P3 (R[2] = 0.85, 0.64). PLS-SEM confirmed direct inhibition/promotion effects on α/β-diversity. This microecology-guided framework provided references for manipulation of ester profiles via phase-specific environmental control, offering a scientific basis for improving the quality of SFB flavor.},
}

*Esters/metabolism
Fermentation
*Lactobacillales/metabolism
*Fungi/metabolism/genetics
*Wine/microbiology/analysis
*Flavoring Agents/metabolism
Butyrates/metabolism
Food Microbiology
Taste

@article {pmid41270974,
year = {2025},
author = {Wang, L and Zhao, Z and Zhao, Y and Dong, S and Feng, S and Cao, L and Song, K},
title = {Comparative Diagnostic Accuracy of Metagenomic Next-Generation Sequencing and Targeted Next-Generation Sequencing for Periprosthetic Joint Infection: A Systematic Review and Meta-Analysis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106661},
doi = {10.1016/j.jinf.2025.106661},
pmid = {41270974},
issn = {1532-2742},
abstract = {OBJECTIVES: The aim of this meta-analysis was to assess the diagnostic performance of metagenomic next-generation sequencing and targeted next-generation sequencing for periprosthetic joint infection (PJI).

BACKGROUND: Next-generation sequencing (NGS) is increasingly used for diagnosing periprosthetic joint infection (PJI), but its clinical utility remains poorly defined. Discrepancies between metagenomic NGS (mNGS) and targeted NGS (tNGS) results pose a significant clinical challenge for PJI diagnosis. To address this, we conducted a systematic review and meta-analysis comparing the diagnostic accuracy of mNGS and tNGS for PJI.

METHODS: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We comprehensively searched PubMed, EMBASE, Cochrane Library, Web of Science, and Scopus from inception through June 1, 2025. Two reviewers independently extracted data and assessed study quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), and the area under the hierarchical summary receiver operating characteristic curve (AUC) were calculated.

RESULTS: Following screening and eligibility assessment, 23 studies were included in the analysis. The pooled sensitivity and specificity for diagnosing PJI were 0.89 (95% CI: 0.84-0.93) and 0.92 (95% CI: 0.89-0.95) for mNGS, and 0.84 (95% CI: 0.74-0.91) and 0.97 (95% CI: 0.88-0.99) for tNGS. The DORs were 58.56 (95% CI: 38.41-89.26) for mNGS and 106.67 (95% CI: 40.93-278.00) for tNGS. The areas under the summary receiver-operating characteristic curves (AUCs) were 0.935 (95% CI: 0.90-0.95) for mNGS and 0.911 (95% CI: 0.85-0.95) for tNGS. Comparisons of DOR and AUC between mNGS and tNGS revealed no statistically significant differences (P > 0.05).

CONCLUSIONS: This meta-analysis indicates that mNGS demonstrates higher sensitivity and a numerically greater AUC than tNGS for diagnosing PJI, with acceptable specificity, although the difference in AUC was not statistically significant. Conversely, tNGS exhibits higher specificity and DOR, alongside acceptable sensitivity, making it valuable for confirming PJI. Overall, the diagnostic accuracy of both next-generation sequencing (NGS) methods is comparable, with each possessing distinct advantages and limitations.},
}

@article {pmid41270973,
year = {2025},
author = {Zhu, TY and Guo, JY and Zhang, D and Weng, L and Yang, QW and Peng, JM and Du, B},
title = {A Comparative Study of DNA- and RNA-Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Tract Infections.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106659},
doi = {10.1016/j.jinf.2025.106659},
pmid = {41270973},
issn = {1532-2742},
abstract = {OBJECTIVES: To compare the clinical utility of DNA- and RNA-metagenomic next-generation sequencing (mNGS) for pathogen detection in lower respiratory tract infections (LRTIs), and evaluate strategies to optimize RNA-mNGS performance.

METHODS: We retrospectively analyzed 82 patients with suspected LRTI undergoing simultaneous DNA-mNGS and RNA-mNGS testing. The concordance of two methods in detecting microorganisms was assessed. Performance in detecting causative pathogens was compared using multi-label classification metrics. Impacts of RNA-mNGS workflow adjustments were evaluated using mock samples.

RESULTS: In a total of 196 microbial detections, DNA-mNGS and RNA-mNGS showed poor overall agreement (Cohen's κ=0.166, p<0.01). In identifying causative pathogens, RNA-mNGS demonstrated significantly higher precision (1.00 vs. 0.50, p<0.05) and F1 scores (0.80 vs. 0.67, p<0.05) compared to DNA-mNGS. DNA-mNGS possessed higher sensitivity for bacteria, fungi, and atypical pathogens, while RNA-mNGS excelled in detecting RNA viruses. Improved RNA-mNGS sensitivity and significant DNA-RNA read correlations were observed in causative pathogens at high abundance. Neither homogenization nor increased sequencing depth improved RNA-mNGS testing.

CONCLUSIONS: DNA-mNGS and RNA-mNGS exhibited low overall consistency. However, RNA-mNGS showed superior precision in identifying causative pathogens in LRTI and additional capacity for RNA virus detections, while DNA-mNGS possessed essential sensitivity for low abundance pathogens.},
}

@article {pmid41270957,
year = {2025},
author = {Xu, Y and Zhao, J and Huang, N and Wang, Z and Liu, L and Wang, Y and Qu, Q and Li, Q and Yang, Q and Wang, G and Liu, G and Wang, Q and Wu, W},
title = {Metagenomic characterization of the resistome, bacteriome and mobilome in raw milk from intensive farming systems.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.017},
pmid = {41270957},
issn = {2090-1224},
abstract = {INTRODUCTION: Intensive farming, as the dominant paradigm in global dairy production, exacerbates antimicrobial resistance (AMR) risks via concentrated animal operations and routine antimicrobial prophylaxis. Nevertheless, the spatiotemporal dissemination patterns of antibiotic resistance genes (ARGs) in regional intensive dairy systems remain insufficiently elucidated.

OBJECTIVES: Elucidating the spatiotemporal dissemination patterns of ARGs in regional intensive dairy systems by characterizing ARGs across diverse sample matrices.

METHODS: This investigation employed an integrated approach, combining metagenomic sequencing with comprehensive experimental validation, including bacterial isolation, antimicrobial susceptibility testing, PCR based detection of ARGs, biofilm formation assays, and conjugation experiments to characterize the antibiotic resistome across 539 samples (encompassing raw milk, forage, water, and breast swabs) collected from 42 intensive farms in Shandong, China.

RESULTS: DY exhibited the most pronounced microbial diversity (16,347 species) and the highest ARG abundance (547 subtypes), which were predominantly β-lactamase genes (56.3 %). Multidrug-resistant determinants were pervasive across all sample types. Klebsiella pneumoniae (K. pneumoniae) was identified as a high-risk vector, showing 96.43 % resistance to β-lactam antibiotics and a 25 % rate of multidrug resistance (MDR). Crucially, conjugation experiments confirmed the horizontal transfer of the blaSHV gene to Escherichia coli (E. coli), demonstrating its potential for cross-species transmission. Furthermore, a significant correlation (P < 0.05) was found between biofilm formation and enhanced β-lactam resistance, implicating biofilms in the maintenance of resistance.

CONCLUSION: This pioneering regional ARG atlas delineates K. pneumoniae's epidemiological significance in Shandong's intensive dairy continuum. Our findings advocate for precision intervention strategies and establish the utility of metagenomics for operational surveillance.},
}

@article {pmid41270896,
year = {2025},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}

@article {pmid41270740,
year = {2025},
author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z},
title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116517},
doi = {10.1016/j.celrep.2025.116517},
pmid = {41270740},
issn = {2211-1247},
abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.},
}

@article {pmid41270667,
year = {2025},
author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T},
title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.},
journal = {Chemosphere},
volume = {393},
number = {},
pages = {144767},
doi = {10.1016/j.chemosphere.2025.144767},
pmid = {41270667},
issn = {1879-1298},
abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.},
}

@article {pmid41270588,
year = {2025},
author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK},
title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180981},
doi = {10.1016/j.scitotenv.2025.180981},
pmid = {41270588},
issn = {1879-1026},
abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.},
}

@article {pmid41270407,
year = {2025},
author = {Zhang, T and Zhang, P and Zhang, J and Hu, Z and Zhang, J and Wah, TY and He, Y},
title = {Interfacial electron transfer between artificial carbon nanowires clusters and Cyt c: Enabling electron transport for methanogenesis.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124994},
doi = {10.1016/j.watres.2025.124994},
pmid = {41270407},
issn = {1879-2448},
abstract = {Intercellular electron transfer via microbial nanowires and Cytochrome c (Cyt c) is a key mechanism for syntrophic metabolism in anaerobic digestion, yet this functionality is encoded in only a limited number of microbial genomes. To address this limitation, we developed artificial carbon nanowire clusters (ACNCs) derived from plastic/sludge precursors, featuring densely arranged nanowires (Φ 20-60 nm), which form a conductive network supporting microbial colonization and electron transport. Calculations of pseudocapacitance and double-layer capacitance derived from cyclic voltammetry (CV), along with electrochemical impedance spectroscopy (EIS) characterization, revealed enhanced interfacial electron transfer between Cyt c and ACNC compared to biochar (BC) and, carbon nanotubes (CNT). Mott-Schottky analysis revealed superior energy level alignment between ACNC and Cyt c in comparison to BC/CNT, resulting in an enhanced current response in the ACNCCyt c complex, which is critical for efficient electron transfer. Circular dichroism and EPR spectroscopy revealed that ACNC induced an increase in β-sheet content in Cyt c, optimizing its electron transfer orientation. In microbial communities, ACNC supplementation enriched electroactive populations. Metagenomic analysis showed a 1.67-fold increase in Methanothrix abundance and a 1.16-fold upregulation of multiheme cytochromes (MtrC/Ech/Rnf), leading to a 123 % elevation in methanation rates compared to BC.},
}

@article {pmid41269405,
year = {2025},
author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q},
title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {102},
pmid = {41269405},
issn = {1559-0267},
support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; },
abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.},
}

Humans
*Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology
*Skin/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
Precision Medicine
Animals
Dysbiosis
Disease Susceptibility
Probiotics
Cellular Microenvironment/immunology

@article {pmid41269281,
year = {2025},
author = {Yazhini, A and Morice, É and Jochheim, A and Lieser, B and Söding, J},
title = {Evaluation of metagenome binning: advances and challenges.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf617},
pmid = {41269281},
issn = {1477-4054},
support = {101111457//Marie Skłodowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; },
abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.},
}

*Metagenome
*Metagenomics/methods
*Deep Learning
Computational Biology/methods
Humans
Algorithms

@article {pmid41268511,
year = {2025},
author = {Almeida, NEC and Kalil, AC and Gomez, CA},
title = {Prostatic Abscess due to Ureaplasma parvum in a Heart Transplant Recipient: Diagnostic Challenges and Clinical Utility of Metagenomics Next-Generation Sequencing (NGS).},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {7511507},
pmid = {41268511},
issn = {2090-6625},
abstract = {Ureaplasma spp. are small and fastidious bacteria that may cause urogenital infections in healthy adults and, in rare cases, invasive disease. These bacteria have been increasingly recognized in immunocompromised patients and have been associated with hyperammonemia syndrome, particularly in lung transplant recipients. In this context, we present a unique clinical case of Ureaplasma parvum prostate abscess, a condition rarely observed in heart transplant recipients, diagnosed using next-generation sequencing (NGS).},
}

@article {pmid41268311,
year = {2025},
author = {Han, JA and Lee, J and An, HJ and Yi, ES and Kim, Y and Koo, BK and Lee, H and Kim, EY and Lee, HS},
title = {Exploring the Panax ginseng Meyer soil metagenome to uncover antagonistic bacteria against ginseng root rot disease.},
journal = {Journal of ginseng research},
volume = {49},
number = {6},
pages = {767-775},
pmid = {41268311},
issn = {1226-8453},
abstract = {BACKGROUND: Ginseng, renowned for its health benefits, is often cultivated with pesticides, which contradicts its health-enhancing properties. To address this, we identified Bacillus velezensis ARRI17 through a 5-year monitoring of ginseng yield on a national scale and comparative metagenome analysis. ARRI17 is a biocontrol agent that enhances ginseng growth and disease resistance under authentic field conditions.

METHODS: We identified ARRI17 through metagenomic analysis of soil samples collected from ginseng fields classified as high-yield (3.54 ± 0.46 kg per 1.62 m[2]) or low-yield (0.9 ± 0.21 kg per 1.62 m[2]), based on comparisons to the national 5-year average yield of 2.13 ± 0.35 kg per 1.62 m[2]. The biocontrol efficacy of ARRI17 was validated under laboratory conditions and field trials. Additionally, we analyzed the genomic and physiological characteristics of ARRI17 to clarify its antifungal mechanisms and adaptability to diverse environments.

RESULTS: ARRI17 exhibited strong inhibitory activity against multiple ginseng fungal pathogens, including Ilyonectria mors-panacis, in both controlled and field conditions. The application of ARRI17 improved ginseng growth parameters and reduced disease incidence in infested soil. Genomic analysis revealed that ARRI17 produces antimicrobial compounds, such as Iturin A, confirmed by HPLC. Furthermore, ARRI17 naturally thrived in rice straw compost, a traditional biofertilizer used in ginseng cultivation, suggesting its long-term presence and compatibility with standard ginseng farming practices.

CONCLUSION: Bacillus velezensis ARRI17 is an effective biocontrol agent that promotes ginseng growth and enhances disease resistance. Its natural compatibility with traditional farming practices, especially its presence with rice straw compost, positions ARRI17 as a promising and sustainable alternative.},
}

@article {pmid41268301,
year = {2025},
author = {Zhang, D and Zhou, M and Qiu, Y and Xu, H and Liu, H and Liu, Y and Xie, L},
title = {Cross-generational mechanisms of maternal gut microbiota in modulating offspring autism spectrum disorder risk: from the gut-brain axis to translational challenges in precision interventions.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1642240},
pmid = {41268301},
issn = {1663-4365},
abstract = {Autism Spectrum Disorder (ASD) manifests as a group of neurodevelopmental disorders with high clinical and genetic heterogeneity, characterized by core features including social communication deficits, repetitive behaviors, and restricted interests. Current research primarily focuses on genetic variations, immune dysregulation, synaptic dysfunction, and gene-environment interactions. Nowadays, accumulating evidence indicates that maternal gut microbiota dysbiosis, induced by high-fat diets, antibiotic overuse, and urbanization, significantly correlates with abnormal fetal neurodevelopment and increased ASD risk. This review systematically delineates three transplacental mechanisms whereby maternal dysbiosis regulates fetal neurodevelopment: Metabolite-mediated pathways, Immune pathway activation, and Epigenetic reprogramming. Meanwhile, the key translational challenges are highlighted. At last, metagenomics-metabolomics-fetal neuroimaging, Development of microbiota metabolite-treated brain organoids, and Artificial Intelligence-driven (AI-driven) probiotic screening were proposed as research directions in future.},
}

@article {pmid41268226,
year = {2025},
author = {Liu, Y and Zhang, Y and Li, Y and Yang, J},
title = {Liver abscess caused by Bacteroides thetaiotaomicron complicated by purulent pericarditis: a case report.},
journal = {American journal of translational research},
volume = {17},
number = {10},
pages = {8164-8170},
pmid = {41268226},
issn = {1943-8141},
abstract = {BACKGROUND: Liver abscess complicated by purulent pericarditis is a rare clinical condition. To date, no cases of liver abscess caused by Bacteroides thetaiotaomicron with concomitant purulent pericarditis have been reported. We present a rare case of this dual pathology to improve clinicians' understanding of liver abscess-related complications and uncommon pathogens.

CASE PRESENTATION: A 33-year-old female was admitted with hypothermia, chest tightness, and vomiting. Upon admission, laboratory tests showed elevated inflammatory markers. Ultrasound imaging revealed both pericardial effusion and a hepatic abscess, leading to a diagnosis of liver abscess complicated by purulent pericarditis. Metagenomic next-generation sequencing (mNGS) of pericardial fluid identified Bacteroides thetaiotaomicron. The patient received anti-infective therapy with meropenem and ornidazole, combined with pericardial effusion drainage. During the later stage of treatment, the patient developed thoracic empyema, necessitating thoracic drainage. Following treatment, the inflammatory markers significantly improved, the liver abscess reduced in size, and the pericardial effusion nearly resolved. At the 8-week follow-up after discharge, clinical and imaging findings were normal.

CONCLUSION: This case highlights the importance of recognizing atypical manifestations in immunocompromised patients and emphasizes the critical role of early comprehensive examination, prompt and effective anti-infective therapy, and puncture drainage for improving patient outcome. Pathogen identification methods such as mNGS can guide more precise treatment strategies, thereby shortening hospitalization and reducing complications.},
}

@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism
Male
Female
*Metabolome
Adult
Middle Aged
*Diet, High-Protein Low-Carbohydrate
*Diet, High-Protein

@article {pmid41267936,
year = {2025},
author = {Ogbuji, NG and Agogbua, JU},
title = {Genomics in plant pathogen identification and control.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1661432},
pmid = {41267936},
issn = {1664-462X},
abstract = {Recent advances in genomics have revolutionized plant pathogen detection and control by enabling faster and more accurate identification compared to traditional culture-based methods. Genomic tools like metagenomics and next generation sequencing (NGS) facilitate the detection of microorganisms (bacteria, fungi, viruses, and nematodes) directly from environmental samples. Genomics also provides information on plant-pathogen interactions, especially the detection of Resistance (R) genes and their role in plant defense against pathogens, aiding in the development of genetic markers for breeding disease-resistance crop species. Gene editing systems such as clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (CRISPR-Cas9), transcription activator-like effector nucleases (TALENs), and Zinc Finger nucleases (ZFNs) allow for precise genetic modification, either by incorporating a beneficial R genes or disabling susceptibility (S) genes of the host plant. RNA interference (RNAi) is another genomic tool used to suppress important pathogenic genes and inhibit disease development. Although the use of genomics in plant pathology is hampered by limitations such as high costs, complexity of data analysis and interpretation, and limited access to sequencing platforms, especially in developing countries, recent innovations and multi-disciplinary collaborations are tackling these issues. In general, genomics offers powerful tools that can be employed in the development of sustainable and effective plant disease management strategies, which will help to enhance crop protection and contribute to global food security.},
}

@article {pmid41267688,
year = {2025},
author = {Song, K and Ren, L and Guo, X and Ren, G and Sun, Y and Tian, X and Hu, C and Pan, M and Yu, Q and Luo, Z and Hao, Y and Lei, P and Yu, H and Yang, S and Chen, Q and Li, Y and Wang, S and He, Y and Hui, Z and Zheng, W and Jiang, J and Wang, L},
title = {Microbiota-responsive oral nano-amifostine enables colorectal-specific radioprotection and tumor immunity via gut microenvironment reprogramming.},
journal = {Advanced composites and hybrid materials},
volume = {8},
number = {6},
pages = {432},
pmid = {41267688},
issn = {2522-0136},
abstract = {UNLABELLED: Radiotherapy for abdominal malignancies is limited by intestinal toxicity and secondary colorectal cancers. Here, we develop an oral, microbiota-responsive nano-amifostine (CS/PEC-AMF NPs) system that achieves site-specific radioprotection in the colorectum without compromising antitumor efficacy. By conjugating amifostine to pectin and encapsulating it with chitosan, the nanoparticles enable pH- and microbiota-triggered release in the large bowel, safeguarding drug bioactivity during gastrointestinal transit. In murine models, CS/PEC-AMF NPs attenuate both acute and chronic radiation-induced bowel injury, restore epithelial integrity, preserve stem cell populations, and promote tight junction repair. Integrated metagenomic and metabolomic analyses reveal that the system normalizes gut microbiota diversity and composition, increases short-chain fatty acid production, and facilitates macrophage polarization towards the anti-inflammatory M2 phenotype. Notably, the formulation synergistically enhances tumor suppression and extends survival in orthotopic colorectal tumor models undergoing radiotherapy and reduces the incidence of secondary colorectal tumors post-irradiation. Mechanistically, transcriptomic analysis demonstrates the suppression of proinflammatory pathways and the promotion of DNA repair programs. This study provides a paradigm for leveraging functional nanomaterials to orchestrate precise, tissue-specific radioprotection and immune modulation, addressing a key challenge in abdominal cancer therapy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42114-025-01492-x.},
}

@article {pmid41267624,
year = {2025},
author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J},
title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70234},
doi = {10.1111/1758-2229.70234},
pmid = {41267624},
issn = {1758-2229},
support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; },
mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; },
abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.},
}

*Eutrophication
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota
RNA, Ribosomal, 16S/genetics
Ecosystem
Metagenomics
Phylogeny

@article {pmid41267035,
year = {2025},
author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z},
title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {236},
pmid = {41267035},
issn = {2049-2618},
support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; },
abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.

RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.

CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Mammals/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Altitude
Tibet
Symbiosis

@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}

*Metagenomics/methods
*Genome, Bacterial
*Metagenome
*Microbiota/genetics
Humans

@article {pmid41266391,
year = {2025},
author = {Pairoh, S and Mhuantong, W and Boonyapakron, K and Yuvaniyama, J and Kanokratana, P and Bunterngsook, B and Lekakarn, H and Arunrattanamook, N and Laothanachareon, T and Champreda, V},
title = {Machine learning-guided discovery of thermophilic carbonic anhydrases from environmental metagenomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40969},
pmid = {41266391},
issn = {2045-2322},
support = {B13F670055//Program Management Unit for Human Resources & Institutional Development, Research and Innovation (PMU-B)/ ; },
mesh = {*Carbonic Anhydrases/genetics/chemistry/metabolism ; *Machine Learning ; *Metagenome ; Metagenomics/methods ; Hot Springs/microbiology ; },
abstract = {Thermophilic carbonic anhydrases (CAs) are promising biocatalysts for carbon capture utilization and storage (CCUS) due to their stability and efficiency at elevated temperatures. This study presents a machine learning (ML)-guided approach to discover thermostable γ-class CA (γ-CA) from metagenomic datasets derived from Fang Hot Spring, Northern Thailand. To develop classification models, two sets of protein descriptors-dipeptide composition (DPC) and physicochemical/biochemical properties (AAindex)-were used to train classification models. Fourteen ML algorithms were systematically evaluated for each feature set. AdaBoost achieved the best performance for the DPC-based model, while LightGBM performed best with AAindex-based features. External validation with known CA sequences confirmed the ability of the models to discriminate thermophilic from non-thermophilic proteins. Applying the optimized models, we screened 1,534 predicted CAs and identified three high-confidence candidates (TtCA, CrCA, and ToCA). These were heterologously expressed in E. coli, purified, and biochemically validated. All candidates exhibited carbonic anhydrase activity, trimeric oligomeric structures, and high melting temperatures (Tm ranging from 97.0 °C to 109.1 °C). Although their hydration activity was modest compared to α-class CAs, their thermal robustness highlights their potential for industrial CO2 capture. This study demonstrates an approach in which ML integrated with metagenomics enables efficient discovery and validation of robust enzymes from extreme environments, providing a scalable strategy for CCUS applications.},
}

*Carbonic Anhydrases/genetics/chemistry/metabolism
*Machine Learning
*Metagenome
Metagenomics/methods
Hot Springs/microbiology

@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}

Animals
*Enterococcus faecalis/physiology/genetics
Bees/virology/microbiology
*Symbiosis
Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Larva/virology/microbiology
Apoptosis

@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {1OT3HL14715//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}

Adult
Female
Humans
Male
Middle Aged
*Asthma/genetics/microbiology/epidemiology/ethnology
Body Mass Index
Cross-Sectional Studies
Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Hispanic or Latino/genetics
Obesity/microbiology/genetics/complications
Risk Factors
United States/epidemiology

@article {pmid41265635,
year = {2025},
author = {Wang, S and Huang, Y and Wang, N and Zhou, H and Ren, X and Li, K and Xia, Y and Xu, J and Huang, L and Cai, H},
title = {Epstein-Barr virus in suspected intracranial infection: a multicenter, retrospective study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108235},
doi = {10.1016/j.ijid.2025.108235},
pmid = {41265635},
issn = {1878-3511},
abstract = {OBJECTIVES: The clinical relevance of Epstein-Barr virus (EBV) detection in cerebrospinal fluid (CSF) using metagenomic next-generation sequencing (mNGS) in patients with suspected intracranial infections has not been fully clarified. This study aimed to assess the clinical features, imaging characteristics, and outcomes in EBV-positive patients.

METHODS: We retrospectively enrolled patients with suspected intracranial infection who underwent commercial mNGS of CSF samples between December 2019 and October 2023 across 13 hospitals in four cities. Clinical data were collected, and multivariable logistic regression was performed to assess the association between EBV positivity and unfavorable outcomes.

RESULTS: Among 507 patients, 51 (10.1%) were EBV-positive in CSF. EBV-positive cases showed higher CSF mononuclear cell proportions (83.8% vs. 32.8%, p<0.001), lower chloride levels (123.0 vs. 126.1 mmol/L, p=0.019), and more frequent herpesvirus co-detection (21.6% vs. 8.6%, p=0.007). Imaging abnormalities did not differ significantly. After adjustment, multivariable logistic regression showed that EBV was not an independent risk factor for clinical outcomes (OR 1.005, 95% CI 0.516 - 1.972, p = 0.988).

CONCLUSIONS: EBV was detected in 10.1% of patients in CSF samples from patients with suspected intracranial infections. EBV positivity correlated with a lymphocytic CSF profile and co-detection of other herpesviruses but was not independently associated with unfavorable outcomes.},
}

@article {pmid41265331,
year = {2025},
author = {Zeng, Y and Gao, H and Huang, H and Xiong, W and Bin, L and Liao, B and Chen, W and Chen, X and Wen, S and Li, P and Huang, S and Tang, B},
title = {Performance, metabolism, and resistance of an SMX-stressed continuous-flow AGS-MBR system: Microscopic mechanism of macroscopic instability phenomena.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124968},
doi = {10.1016/j.watres.2025.124968},
pmid = {41265331},
issn = {1879-2448},
abstract = {To clarify how long-term sulfamethoxazole (SMX) pressure converts macro-scale performance loss into micro-level mechanistic change, a continuous-flow aerobic granular sludge membrane bioreactor (AGS-MBR) was operated for 140 days at SMX concentrations ranging from 0 to 5 mg L[-1]. At 0.2-1 mg L[-1], the system remained resilient: TN and TP removal stabilized at 90 % and 72.8 %, respectively, and the volume-mean granule diameter remained 282 µm. Metagenomics revealed significant up-regulation of the glycogen-metabolising gene glk and the polyphosphate gene ppk, which fuelled an energy-compensation pathway that supplied ATP and precursors for TB-EPS synthesis and reinforced granule scaffolding. When influent SMX rose to 5 mg L[-1] this compensation collapsed: EPS dropped 45 %, Dv shrank 38 %, granules disintegrated, TN removal fell to 70 % and TP to 44.8 %. The community shifted to a filamentous bacteria dominated state with Thiothrix >25 % relative abundance. Concurrently, the non-pathogen Rubrivivax became a shared host for antibiotic resistance genes (sul1, sul2) and multiple transposases; mobile genetic elements mediated the co-transfer of resistance and virulence genes and eroded functional redundancy. LC-MS further showed that the major transformation products P4 and P6 exhibited 2.3 folds higher chronic toxicity than the parent compound and imposed additional chemical stress on the already impaired granule microbiota. SMX dose dictated a cascade in which metabolic compensation was followed by selection of filamentous hosts prone to gene mobility and finally by chemical toxicity, progressively dismantling granule structure, nutrient removal services and ecological safety. These results elucidate the dose-dependent macro-to-micro cascade under SMX stress and provide insights for mitigating ecological risks in antibiotic laden wastewater.},
}

@article {pmid41264852,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00349},
pmid = {41264852},
issn = {1520-4995},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}

@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}

@article {pmid41263111,
year = {2025},
author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC},
title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1234},
pmid = {41263111},
issn = {1362-4962},
support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; },
abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.},
}

@article {pmid41263098,
year = {2025},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1185},
pmid = {41263098},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}

@article {pmid41262935,
year = {2025},
author = {Zhang, B and Meng, D and Wang, X and Hu, J and Fan, J and Li, X and Yang, Z and He, W and Zhou, D and Cheng, Y and Li, J and Zou, J and Liu, Z},
title = {Additive of cow dung weakened the influences of microbial interactions on nitrogen dynamic during composting of rice husks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641502},
pmid = {41262935},
issn = {1664-302X},
abstract = {Rice husk (RH) and cow dung (CD) are two of the most abundant agricultural solid waste. Converting these residues into peat-free substrates through co-composting supports sustainable agricultural development. A 40-day rice husk composting experiment was conducted to assess the effects of cow dung addition on microbial networks and carbon-nitrogen dynamics using 16S rRNA and metagenomic analyses. Furthermore, Furthermore, we prepared seedling substrates from composts of RH alone and RH combined with CD (RHCD), and evaluated their plant growth-promoting effects. The addition of cow dung (CD) to rice husk (RH) composting increased the average temperature from 52.8 °C to 60.1 °C and acted as a pH buffer, maintaining values around 7.4. CD significantly (p < 0.05) enhanced microbial network complexity, as indicated by larger network size and higher average degree, but disrupted the linear correlations between network properties and carbon or nitrate nitrogen contents (p > 0.05). This decoupling suggests that CD weakened the linkage between microbial interactions and carbon or nitrogen biotransformation processes. CD also significantly suppressed (p < 0.05) denitrification-related genes (norB, nir and nar) after the thermophilic phase, implying reduced nitrogen loss during compost maturation. We further found that larger network size or higher average degree reduced the abundance of key genes involved in assimilatory nitrite reduction (e.g., nirBD), while increasing those related to denitrification (e.g., nirK and nirS). Moreover, seedling substrates derived from RH (95.06%) and RHCD (93.21%) composts achieved higher germination rates of Solanaceae crops than the commercial peat-based substrate (81.48%). Germination rate and seedling biomass were positively correlated with dissolved organic carbon (r = 0.820, p = 0.045) and ammonium nitrogen (r = 0.858, p = 0.029), respectively. These findings advance the understanding of microbial interaction regulating carbon and nitrogen cycling during RH composting, and support the sustainable production of peat-free seedling substrates from agricultural waste.},
}