Microbial Genomics最新文献

{"title":"Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7.","authors":"Qingqiu Jiang, Zhihao Guo, Lu Tan, Yanwen Shao, Guoqian Gu, Xiaomin Zhao, Haidong Wang, Runsheng Li","doi":"10.1099/mgen.0.001684","DOIUrl":"10.1099/mgen.0.001684","url":null,"abstract":"<p><p>Viral non-structural proteins are key mediators of host-virus interplay, including RNA modification dynamics. The function of the transmissible gastroenteritis virus (TGEV) gene 7, which encodes a non-structural protein, remains poorly understood. Using Oxford Nanopore direct RNA sequencing, we explored the host and viral RNA landscapes modulated by TGEV gene 7 in Swine testis cells. Deletion of the TGEV gene 7 halved viral RNA replication yet significantly increased m6A modification levels on both the viral genome and host mRNAs. This epitranscriptomic rewiring was accompanied by reciprocal shifts in the m6A regulators FTO (eraser) and RBM15 (writer). Despite comparable bulk transcriptome changes, gene 7 deletion introduced additional differentially expressed genes, showing stronger enrichment of antiviral and chemokine pathways, indicating heightened innate immunity. PolyA analysis uncovered a gene 7-dependent extension of viral, but not host, polyA tails. These findings highlight RNA-modification machinery as a potential target for coronavirus control and provide a framework for vaccine strategies exploiting gene 7 attenuation.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics and gene association analysis support probiotic potential in a subset of <i>Staphylococcus xylosus</i> isolates.","authors":"Kaylee Dawn Rich, Zhangbin Cai, Diego B Nobrega, Jennifer Ronholm, Jeroen De Buck","doi":"10.1099/mgen.0.001708","DOIUrl":"https://doi.org/10.1099/mgen.0.001708","url":null,"abstract":"<p><p>Mastitis is a major disease in dairy cattle, often caused by <i>Staphylococcus aureus</i> infection and increasingly complicated by antimicrobial resistance. As a result, bacterial strains able to effectively provide colonization resistance in the bovine mammary gland are being explored as potential probiotics to reduce reliance on antimicrobial treatments. Among these, some non-<i>S</i>. <i>aureus</i> staphylococci species have shown promise; however, their effects appear to be highly strain-dependent. In this study, a combination of machine learning approaches alongside standard genomic and phylogenetic analyses was used to compare and select putative probiotic <i>Staphylococcus xylosus</i> strains. The genomes of 82 S. <i>xylosus</i> and 16 closely related <i>Staphylococcus</i> isolates from milk samples obtained from the Canadian Bovine Mastitis Research Network were assembled and annotated. In addition to identifying orthologous gene families and reconstructing phylogenetic relationships, each genome was screened for virulence factors, antimicrobial resistance (AMR) genes and bacteriocins. Random forest modelling and association rule learning were then applied to identify combinations of genes associated with isolates from milk samples collected from quarters exhibiting low inflammation, assessed using somatic cell counts (SCC). This approach identified 63 genes that frequently co-occurred in isolates from low SCC samples (low SCC <25,000 cells ml^-1) but were largely absent in those from high SCC samples (≥200,000 cells ml^-1). These gene sets were used as biomarkers in conjunction with phylogenetic and clustering analyses to guide the selection of a subset of <i>S. xylosus</i> isolates with potential probiotic properties.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Public and patient involvement: exploring public partnership in pathogen whole-genome sequencing research and its data visualisation.","authors":"Suzanne Rotheram, Hannah Trivett, Jane Whitehurst, Caitlin Collins, Jake Carson, Sophie Staniszeweska, Xavier Didelot","doi":"10.1099/mgen.0.001691","DOIUrl":"10.1099/mgen.0.001691","url":null,"abstract":"<p><p>Pathogen genomics is increasingly used in publicly funded studies and has important implications for understanding infectious diseases and their spread. However, unlike many other research areas, it has seen little patient and public involvement (PPI), thereby missing opportunities to enhance both research processes and outcomes. This project addressed that gap by exploring the potential contribution of PPI to pathogen genomics, using whole-genome sequencing (WGS) data visualisation as an exemplar.Following ethical approvals, three 2 h PPI workshops involving five public contributors and six academic contributors were held online. Sessions were documented using visual meeting notes. Workshops were audio-recorded, transcribed and analysed using an iterative thematic analysis.Two interconnected themes were identified. First, effective public involvement required collaborative sense-making, achieved through co-producing a shared knowledge base, establishing consistent terminology and developing effective practices for knowledge exchange. Second, participants highlighted three priority areas for meaningful PPI in future pathogen genomics research: (i) prioritising research questions, (ii) contributing to decisions about data collection and use and (iii) supporting the communication of findings.Although pathogen genomics is technically complex, this did not prevent productive discussion about how, where and why PPI could be integrated into research. Expanding PPI in this area could help align pathogen WGS research with patient priorities, inform approaches to data governance and improve the accessibility of research outputs to the public. Realising this potential, however, will require active engagement from researchers in the field.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13071077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic epidemiology of <i>Mycobacterium tuberculosis</i> in Malawi: using global phylogeography to understand the impact of geographically focused interventions.","authors":"Alexander B Beams, Yexuan Song, Jennifer McNichol, Bradley R Jones, Benjamin Sobkowiak, Peter MacPherson, Marriott Nliwasa, Victor Ndhlovu, Mphatso D Phiri, Ted Cohen, Caroline Colijn","doi":"10.1099/mgen.0.001674","DOIUrl":"10.1099/mgen.0.001674","url":null,"abstract":"<p><p>Genomic surveillance of pathogens important to public health, such as <i>Mycobacterium tuberculosis</i> (Mtb), offers the opportunity to characterize the geographic movements of pathogens on a range of spatial and temporal scales and to explore the consequences of these inferred movements on the impacts of public health interventions. Pathogen movements can affect the impact of interventions that are geographically focused, with interventions in high-transmission areas, potentially leading to indirect benefits in other locations due to the prevention of transmission. We supplemented a large genomic surveillance dataset from Blantyre, Malawi (518 Lineage 4 sequences and 103 Lineage 1 sequences) with publicly available sequences collected across the world from 2015 to 2019 (910 Lineage 4 sequences and 445 Lineage 1 sequences) to reconstruct global and regional movements of Mtb in order to clarify the extent of importation into Blantyre. Standard phylogeographic methods are unsuitable for this task because they do not account for sampling heterogeneity across locations, so we build on a new method called sampling-aware ancestral state inference, incorporating wide disparities in the sampling fractions between different regions across the world, and also the fact that sampling only occurred from 2015 to 2019. Reconstructed phylogenetic trees contain strong signals of spatial localization of individual clades, with very limited numbers of introductions to, or exports from, Blantyre, and considerable movements within the city itself. Inferring which zone of the Blantyre nodes of the tree was in allows us to perform simple simulations of geographically focused interventions such as active case finding (ACF). We find that zone-focused ACF in Blantyre is likely to have modest impacts, with a focus on Zones 2 and 4 likely to have the most impact. As genomic surveillance becomes more commonplace, analyses such as this may be useful for public health practitioners developing interventions to reduce local TB transmission and incidence.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rolling out <i>Plaque-2-seq</i>: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques.","authors":"Slawomir Michniewski, Rebecca Glenny, Andrew Kinsella, Kane Porter, Kayne Wright, Sophie Harrison, Nzubechukwu I Ugokwe, Amani Alrashidi, Srwa J Rashid, Chisomaga Eke, Jack C D Lee, Faizal Patel, Theo Josephs, Arezoo Pedramfar, Max Coleman, Hasanain F Y Al-Dahash, Gibson A Sabuholo, Navodya S Roemer, Hannah Sampson, Gerald N Misol, Branko Rihtman, David J Scanlan, Elspeth Smith, Graham Stafford, Willem van Schaik, Richard J Puxty, Edouard Galyov, Martha R J Clokie, Spyridon Megremis, Andrew Millard","doi":"10.1099/mgen.0.001672","DOIUrl":"https://doi.org/10.1099/mgen.0.001672","url":null,"abstract":"<p><p>Rapid, accurate and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequencing and assembling complete bacteriophage genomes using short- or long-read technologies. However, current protocols require large DNA input and are cost-prohibitive, which limits their application to phage collections that typically are large and have low biomass. In order to address this, we have developed <i>Plaque-2-seq</i>, a robust and cost-effective workflow for high-throughput phage genome sequencing that will transform the speed and cost of attaining phage genomes. <i>Plaque-2-seq</i> combines low-input transposase-based library preparation, amplification, nanopore sequencing and optimized assembly steps tailored to phage genomes. We applied the method to phages isolated on seven genetically diverse bacterial hosts: <i>Escherichia</i>, <i>Pseudomonas</i>, <i>Synechococcus</i>, <i>Enterococcus</i>, <i>Klebsiella, Serratia</i> and <i>Enterobacter</i>. High-quality genome assemblies were validated using CheckV and benchmarked against previously sequenced phage isolates. Compared to standard Illumina sequencing, <i>Plaque-2-seq</i> offers up to ~5-10-fold savings in sequencing price for individual labs. Furthermore, it substantially decreases the time required to produce a phage genome, once a plaque is obtained. Offering the ability to routinely obtain hundreds of phage genome sequences a week, with minimal hands-on time. <i>Plaque-2-seq</i> enables systematic genomic characterization of phage isolates, facilitating taxonomic classification, for the development of large-scale phage biobanks.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screen for signatures of positive selection in the core genome of <i>Staphylococcus epidermidis</i>.","authors":"Callum O Rimmer, Jonathan C Thomas","doi":"10.1099/mgen.0.001692","DOIUrl":"10.1099/mgen.0.001692","url":null,"abstract":"<p><p><i>Staphylococcus epidermidis</i> is a commensal skin bacterium and the leading cause of medical-device-associated infections. Although previous studies have investigated the phylogenetic diversity of the species, the level of positive selection on the core genome has yet to be explored in <i>S. epidermidis</i>. Here, we present a comprehensive genome-wide screen for signatures of positive selection in this species. A curated dataset of 1,003 whole-genome sequences was created, which represented the global diversity of <i>S. epidermidis</i>, including all previously identified clades and genetic clusters. A 100-strain subset, which retained the diversity of the collection, was created by pruning the species-level tree with treemmer; core genes present in all genomes were extracted with Roary and used for positive selection analysis (<i>n</i>=826). Site-level analysis was performed using PAML with omegaMap for confirmation. Selection along branches separating clades A and B was investigated using PAML branch-site models and HyPhy. PAML site analysis revealed 16 genes under selection, including 6 hypothetical genes, most of which were linked to metabolism or transport. Several genes were associated with antimicrobial resistance, including <i>ileS</i>, which confers resistance to mupirocin. Nearly a third of the genes under selection were components of interconnected pathways that collectively provide essential cofactors for the NirB enzyme subunit. No genes showed evidence of positive selection in both the PAML and HyPhy branch-site analyses. Our analysis reveals the extent to which positive selection is operating on the core genome of <i>S. epidermidis</i>, driving clade-associated mutations in multiple core genes, and identifies candidate genes that may have important roles in the fitness of the species.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13095176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.","authors":"Sam A Mellor, Samuel J Bloomfield, Raphaëlle Palau, George M Savva, John Wain, Alison E Mather","doi":"10.1099/mgen.0.001705","DOIUrl":"10.1099/mgen.0.001705","url":null,"abstract":"<p><p>Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including <i>Pseudomonas</i>, <i>Lactococcus</i> and <i>Psychrobacter</i>. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional shifts of the dual-substrate phosphoribosyl isomerase PriA from primary to specialized metabolism in rare Actinomycetota.","authors":"Luis Rodrigo Rosas-Becerra, Andrés Arredondo-Cruz, Nelly Sélem-Mojica, Francisco Barona-Gómez","doi":"10.1099/mgen.0.001634","DOIUrl":"10.1099/mgen.0.001634","url":null,"abstract":"<p><p>Evolutionary functional innovations can occur while gene families expand and two homologous (or analogous) genes co-occur. PriA is a dual-substrate enzyme family exclusive to <i>Actinomycetota</i>, with activities in l-histidine and l-tryptophan biosynthesis (HisA and TrpF activities) that evolved after the loss of the <i>trpF</i> gene. Since this gene loss, PriA has undergone multiple functional gain and loss events in central metabolism. Here, we report further evolutionary scenarios of PriA. First, in <i>Ornithimicrobiaceae</i>, a rare <i>Actinomycetota</i> family, PriA coexists with HisA, concomitant with the loss of its HisA but not TrpF activity, and is recruited in a physiological genome context. Second, a <i>priA</i> homologue, <i>adeK</i>, is located in the biosynthetic gene cluster of the specialized metabolites adechlorin and 2'-amino-2'-deoxyadenosine. The <i>adeK</i> gene is encoded in several genomes of the <i>Streptosporangiaceae</i> family and coexists with the expected and conserved <i>priA</i>. In this scenario, the PriA enzymes conserve both activities, whereas AdeK has only detectable levels of HisA activity, which might be related to specificity for a chlorinated intermediary during adechlorin biosynthesis. The <i>adeK</i> gene was first identified in strain ATCC-39365, previously designated as <i>Actinomadura</i> sp., but reclassified here as <i>Nonomuraea</i> sp. We further identified unprecedented adechlorin/2'-amino-2'-deoxyadenosine/pentostatin producers within the <i>Microbispora</i> and <i>Streptosporangium</i> genera. Phylogenomic analysis revealed additional recruitments of <i>priA</i> and <i>hisG</i> homologues into diverse uncharacterized biosynthetic gene clusters taxonomically related to the nucleoside antibiotics adechlorin, pentostatin and pyrazomycin. These findings highlight how enzyme family expansions and recruitment drive metabolic functional innovation in <i>Actinomycetota</i>, involving both gene loss and gain throughout central and specialized metabolism, and how evolutionary genome mining allows unbiased natural product discovery.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13055916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing gastrointestinal microbial co-association networks to predict feed efficiency and methane emissions across beef and dairy cattle.","authors":"Pamela A Alexandre, Yuliaxis Ramayo-Caldas, Milka Popova, Ioanna-Theoni Vourlaki, Gilles Renand, Aurélie Vinet, Diego P Morgavi, Antonio Reverter","doi":"10.1099/mgen.0.001689","DOIUrl":"10.1099/mgen.0.001689","url":null,"abstract":"<p><p>Enteric methane emissions from cattle pose a significant environmental concern and represent a substantial energy loss for the animal, necessitating the development of effective mitigation strategies. The gastrointestinal microbiota plays a crucial role in determining both feed efficiency and methane production. Still, the specific microbial signatures that predict these traits across different production systems remain poorly understood. This study aimed to identify common predictive microbial biomarkers for feed efficiency and methane emissions using co-association network analysis across contrasting cattle production systems. Rumen liquid and faecal microbiota from 55 Charolais heifers (beef) and 56 Holstein cows (dairy) were analysed using 16S rRNA gene amplicon sequencing. Phenotypic data included feed efficiency, methane yield and acetate/propionate ratio. Co-association networks were constructed using Partial Correlation and Information Theory to identify amplicon sequence variants (ASVs) directly connected to phenotypes. Multiple regression analysis determined the minimal ASV sets required to achieve optimal predictive accuracy. Rumen microbiomes consistently showed superior predictive performance compared to faecal communities across all traits. Network-selected ASVs explained substantial phenotypic variance across traits and production systems (<i>R</i>²=0.45-0.84), consistently outperforming randomly selected ASVs by 0.13-0.44 <i>R</i>² units. The ACET:PROP ratio showed the highest predictive accuracy (<i>R</i>²=0.84 in Charolais rumen, 0.77 in Holstein rumen), while minimal ASV sets achieved 93-97% of the full model's performance using 33-65% fewer ASVs (6-17 ASVs). <i>Bacteroidaceae</i> was consistently enriched across phenotypes in rumen networks, regardless of production system. Contrary to expectations, most associations were production system-specific, with notable exceptions including negative correlations between the ACET:PROP ratio and <i>Prevotella</i>/<i>Ruminococcus</i> genera and negative associations with members of the <i>Succinivibrionaceae</i> family for methane-related traits. The anatomical site-specific and production system-specific nature of most associations underscores the importance of context-specific approaches.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13075996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147674747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization.","authors":"Nicholas Pucci, Daniel R Mende","doi":"10.1099/mgen.0.001702","DOIUrl":"https://doi.org/10.1099/mgen.0.001702","url":null,"abstract":"<p><p>Human milk glycan (HMG) metabolism, especially by bifidobacteria, is crucial for infant gut colonization and healthy microbiome development. Bifidobacterial species and even strains are highly variable in their ability and in their enzymatic repertoire for HMG metabolism. The enzymes involved in HMG metabolism often have many non-HMG-related homologues, necessitating fine-grained annotation for accurate assessment of bifidobacterial HMG metabolic capabilities. However, current annotation tools provide only broad glycoside hydrolase (GH) (sub)family classifications. Here, we present <i>bifidoAnnotator</i>, a tool for fine-grained annotation and visualization of bifidobacterial GH genes involved in HMG utilization. <i>bifidoAnnotator</i> leverages MMseqs2 (Many-against-Many sequence searching) to map protein sequences against a manually curated database of over 22,000 bifidobacterial GH proteins, organized into 13 families and 108 functional clusters, each assigned a validation status (i.e. experimentally validated, putative or hypothetical). The tool performs hierarchical annotation at family and cluster levels, identifying consistently annotated protein variants rather than just broad family assignments, and generates publication-ready heatmaps for comparative analysis. Benchmarking on a gold standard dataset demonstrated that bifidoAnnotator has superior performance (95.9% precision, 100% recall) compared with six established tools and is an order of magnitude faster than the most accurate competitor. <i>bifidoAnnotator</i>'s superior performance and computational efficiency represent a meaningful advance in high-throughput genomic annotation workflows, enabling detailed characterization of strain-level functional diversity in bifidobacterial HMG metabolism.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13120772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}