Microbial Genomics最新文献

{"title":"Corrigendum: Genetic heterogeneity in the Salmonella Typhi Vi capsule locus: a population genomic study from Fiji.","authors":"Aneley Getahun Strobel, Andrew J Hayes, Wytamma Wirth, Mikaele Mua, Tiko Saumalua, Orisi Cabenatabua, Vika Soqo, Varanisese Rosa, Nancy Wang, Jake A Lacey, Dianna Hocking, Mary Valcanis, Adam Jenney, Benjamin P Howden, Sebastian Duchene, Kim Mulholland, Richard A Strugnell, Mark R Davies","doi":"10.1099/mgen.0.001310","DOIUrl":"https://doi.org/10.1099/mgen.0.001310","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080390","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":"Whole-genome sequencing of <i>Acinetobacter baumannii</i> clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020), revealed the predominance of the Global Clone 2 lineage.","authors":"Nurul Saidah Din, Farahiyah Mohd Rani, Ahmed Ghazi Alattraqchi, Salwani Ismail, Nor Iza A Rahman, David W Cleary, Stuart C Clarke, Chew Chieng Yeo","doi":"10.1099/mgen.0.001345","DOIUrl":"10.1099/mgen.0.001345","url":null,"abstract":"<p><p>Carbapenem-resistant <i>Acinetobacter baumannii</i> is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 <i>A</i>. <i>baumannii</i> isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011-2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (<i>n</i>=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu <i>A. baumannii</i> clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2_Pasteur of the Global Clone 2 lineage identified as the dominant ST (<i>n</i>=76/126; 60.3%). The ST2_Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195_Oxford (<i>n</i>=35) and ST208_Oxford (<i>n</i>=17). Various antimicrobial resistance genes were identified with the <i>bla</i> _OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (<i>n</i>=90/126; 71.4%). Plasmid-encoded <i>rep</i> genes were identified in nearly all (<i>n</i>=122/126; 96.8%) of the isolates with the majority being Rep_3 family (<i>n</i>=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2_Pasteur isolates harbouring them. This study provided a genomic snapshot of the <i>A. baumannii</i> isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2_Pasteur lineage, indicating the entrenchment of this clone in the hospital.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189807","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":"<i>Clostridioides difficile</i> recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences.","authors":"Emmanuel O Ngbede, Vera Junker, Baban Kolte, Martinique Frentrup, Judith Boldt, Warren N Fawley, Mark H Wilcox, Ed J Kuijper, Wiep Klaas Smits, Ulrich Nübel","doi":"10.1099/mgen.0.001342","DOIUrl":"https://doi.org/10.1099/mgen.0.001342","url":null,"abstract":"<p><p>Genomic data on <i>Clostridioides difficile</i> from the African continent are currently lacking, resulting in the region being under-represented in global analyses of <i>C. difficile</i> infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare <i>C. difficile</i> isolates from diarrhoeic human patients (<i>n</i>=142), livestock (<i>n</i>=38), poultry manure (<i>n</i>=5) and dogs (<i>n</i>=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global <i>C. difficile</i> population. In addition, selected isolates were tested for antimicrobial susceptibility (<i>n</i>=33) and characterized by PCR ribotyping (<i>n</i>=53). Hierarchical clustering of core-genome multilocus sequence typing (cgMLST) allelic profiles revealed large diversity at the level HC150 (i.e. clusters of related genomes with maximally 150 pairwise allelic differences), which was previously shown to correlate with PCR ribotypes (RT). While several globally disseminated strains were detected, including HC150_1 (associated with RT078), HC150_3 (RT001) and HC150_3622 (RT014), 42 HC150 clusters (79%) represented unique genotypes that were new to the public genomic record, and 16 (30%) of these were novel PCR ribotypes. Considerable proportions of the <i>C. difficile</i> isolates displayed resistance to fluoroquinolones, macrolides and linezolid, potentially reflecting human and animal antibiotic consumption patterns in the region. Notably, our comparative phylogenomic analyses revealed human-human, human-livestock and farm-farm sharing of near-identical <i>C. difficile</i> genomes (≤2 core-genome allelic differences), suggesting the continued spread of multiple strains across human and animal (pig, poultry, cattle and dog) host populations. Our findings highlight the interconnectivity between livestock production and the epidemiology of human CDI and inform the need for increased CDI awareness among clinicians in this region. A large proportion of <i>C. difficile</i> strains appeared to be unique to the region, reflecting both the significant geographic patterning present in the <i>C. difficile</i> population and a general need for additional pathogen sequencing data from Africa.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066577","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":"Exploring SNP filtering strategies: the influence of strict vs soft core.","authors":"Mona L Taouk, Leo A Featherstone, George Taiaroa, Torsten Seemann, Danielle J Ingle, Timothy P Stinear, Ryan R Wick","doi":"10.1099/mgen.0.001346","DOIUrl":"10.1099/mgen.0.001346","url":null,"abstract":"<p><p>Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample. However, as sample size and genome diversity increase, a strict core can shrink markedly, discarding potentially informative data. Here, we propose and provide evidence to support the use of a 'soft core' that tolerates some missing data, preserving more information for phylogenetic analysis. Using large datasets of <i>Neisseria gonorrhoeae</i> and <i>Salmonella enterica</i> serovar Typhi, we assess different core thresholds. Our results show that strict cores can drastically reduce informative sites compared to soft cores. In a 10 000-genome alignment of <i>Salmonella enterica</i> serovar Typhi, a 95% soft core yielded ten times more informative sites than a 100% strict core. Similar patterns were observed in <i>N. gonorrhoeae</i>. We further evaluated the accuracy of phylogenies built from strict- and soft-core alignments using datasets with strong temporal signals. Soft-core alignments generally outperformed strict cores in producing trees displaying clock-like behaviour; for instance, the <i>N. gonorrhoeae</i> 95% soft-core phylogeny had a root-to-tip regression <i>R</i> ² of 0.50 compared to 0.21 for the strict-core phylogeny. This study suggests that soft-core strategies are preferable for large, diverse microbial datasets. To facilitate this, we developed <i>Core-SNP-filter</i> (https://github.com/rrwick/Core-SNP-filter), an open-source software tool for generating soft-core alignments from whole-genome alignments based on user-defined thresholds.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984006","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":"The dominant lineage of an emerging pathogen harbours contact-dependent inhibition systems.","authors":"Cristian V Crisan, Joanna B Goldberg","doi":"10.1099/mgen.0.001332","DOIUrl":"https://doi.org/10.1099/mgen.0.001332","url":null,"abstract":"<p><p>Bacteria from the <i>Stenotrophomonas maltophilia</i> complex (Smc) are important multidrug-resistant pathogens that cause a broad range of infections. Smc is genomically diverse and has been classified into 23 lineages. Lineage Sm6 is the most common among sequenced strains, but it is unclear why this lineage has evolved to be dominant. Antagonistic interactions can significantly affect the evolution of bacterial populations. These interactions may be mediated by secreted contact-dependent proteins, which allow inhibitor cells to intoxicate adjacent target bacteria. Contact-dependent inhibition (CDI) requires three proteins: CdiA, CdiB and CdiI. CdiA is a large, filamentous protein exported to the surface of inhibitor cells through the pore-like CdiB. The CdiA C-terminal domain (CdiA-CT) is toxic when delivered into target cells of the same species or genus. CdiI immunity proteins neutralize the toxicity of cognate CdiA-CT toxins. We found that all complete Smc genomes from the Sm6 lineage harbour at least one CDI locus. By contrast, less than a quarter of strains from other lineages have CDI genes. Smc CdiA-CT domains are diverse and have a broad range of predicted functions. Most Sm6 strains harbour non-cognate <i>cdiI</i> genes predicted to provide protection against foreign toxins from other strains. Finally, we demonstrated that an Smc CdiA-CT toxin has antibacterial properties and is neutralized by its cognate CdiI.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033497","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":"Diversification of <i>bla</i> _OXA-48-harbouring plasmids among carbapenemase-producing <i>Enterobacterales</i>, 11 years after a large outbreak in a general hospital in the Netherlands.","authors":"Pieter W Smit, Carla van Tienen, Fabian Landman, Sabrina Zagers, Marije den Drijver, Arjan Burggraaf, Daan W Notermans, Marjolein Damen, Antoni P A Hendrickx, Casper Jamin","doi":"10.1099/mgen.0.001335","DOIUrl":"10.1099/mgen.0.001335","url":null,"abstract":"<p><p><b>Introduction.</b> Genes encoding OXA-48-like carbapenem-hydrolyzing enzymes are often located on plasmids and are abundant among carbapenemase-producing <i>Enterobacterales</i> (CPE) worldwide. After a large <i>bla</i> _OXA-48 plasmid-mediated outbreak in 2011, routine screening of patients at risk of CPE carriage on admission and every 7 days during hospitalization was implemented in a large hospital in the Netherlands. The objective of this study was to investigate the dynamics of the hospitals' 2011 outbreak-associated <i>bla</i> _OXA-48 plasmid among CPE collected from 2011 to 2021.<b>Methods.</b> A selection of 86 <i>bla</i> _OXA-48-carrying CPE isolates was made from 374 isolates collected over an 11-year study period. Species included <i>Escherichia coli</i> (Eco), <i>Klebsiella pneumoniae</i> (Kpn), <i>Enterobacter cloacae complex</i> (Ecl), <i>Citrobacter freundii</i> (Cfr), <i>Citrobacter koseri</i> (Cko) and <i>Morganella morgani</i> (Mmo). Short-read sequencing was combined with long-read sequencing for all isolates to reconstruct <i>bla</i> _OXA-48-like plasmids and chromosomes of CPE. MASH, MOBsuite, ResFinder, PlasmidFinder and SNP analyses were performed to study diversity. pOXA-48 plasmids were compared to plasmid sequences that were sequenced for the Dutch CPE surveillance in the same time period.<b>Results.</b> In total for the 86 CPE, 2 failed genomic assemblies and 78 <i>bla</i> _OXA-48-encoding plasmids were reconstructed, and six <i>bla</i> _OXA-48 genes were located chromosomally. The 2011 outbreak-associated <i>bla</i> _OXA-48 plasmid of 63.6 kb with IncL replicon was found in Cfr, Ecl, Eco, Kpn and Mmo and primarily between 2011 and 2014 and indicated as LR025105 as MASH nearest neighbour. From 2014 onwards, 11 other types of <i>bla</i> _OXA-48-carrying plasmids with different antibiotic-resistant genes and replicons were discovered, representing the earlier defined distinct pOXA-48 plasmid groups found in the Netherlands. Furthermore, on a national level, the LR025105 plasmid was found after 2015 in many different bacterial backgrounds, highlighting the promiscuous nature of this pOXA-48 plasmid.<b>Conclusion.</b> After a large <i>bla</i> _OXA-48 outbreak in a large hospital in the Netherlands, the composition of the <i>bla</i> _OXA-48 plasmid population in this hospital diversified over time and is in line with national surveillance data. Plasmid sequencing provided valuable insight into the transmission dynamics of <i>bla</i> _OXA-48-encoding plasmids and showed no indication of the persistence of the 2011 <i>bla</i> _OXA-48 plasmid in the hospital environment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951318","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":"Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.","authors":"Vadim Puller, Florian Plaza Oñate, Edi Prifti, Raynald de Lahondès","doi":"10.1099/mgen.0.001330","DOIUrl":"10.1099/mgen.0.001330","url":null,"abstract":"<p><p>Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four established profilers as well as the impact of the simulations and that of the common taxonomic references on the perceived performance of these profilers. Finally, we provide guidelines to enhance future profiler comparisons for human microbiome ecosystems: (i) use or create realistic simulations tailored to your biological context (BC), (ii) identify a common feature space suited to your BC and independent of the catalogues used by the profilers and (iii) apply a comprehensive set of metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) and quantification (UniFrac and/or Aitchison distance).</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971502","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":"<i>Shigella sonnei</i> and <i>Shigella flexneri</i> infection in <i>Caenorhabditis elegans</i> led to species-specific regulatory responses in the host and pathogen.","authors":"Bao Chi Wong, Hock Siew Tan","doi":"10.1099/mgen.0.001339","DOIUrl":"https://doi.org/10.1099/mgen.0.001339","url":null,"abstract":"<p><p>In recent decades, <i>Shigella sonnei</i> has surpassed <i>Shigella flexneri</i> as the leading cause of shigellosis, possibly due to species-specific differences in their transcriptomic responses. This study used dual RNA sequencing to analyse the transcriptomic responses of <i>Caenorhabditis elegans</i> and the two <i>Shigella</i> species at early (10 minutes) and late (24 hours) stages of infection. While the nematode defence response was downregulated during both <i>Shigella</i> infections, only infection by <i>S. sonnei</i> led to downregulation of sphingolipid metabolism, cadmium ion response and xenobiotic response in <i>C. elegans</i>. Furthermore, <i>S. sonnei</i> upregulates biofilm formation and energy generation/conservation during infection, acid resistance-related genes and biofilm regulators compared to <i>S. flexneri</i>. These findings highlight species-specific responses during <i>C. elegans</i> infection.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033492","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":"Multiple introductions of NRCS-A <i>Staphylococcus capitis</i> to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey.","authors":"Emily A Lees, Jessica Gentry, Hermione Webster, Nicholas Sanderson, David Eyre, Daniel Wilson, Sam Lipworth, Derrick Crook, T H Nicholas Wong, Anthony Mark, Katie Jeffery, Stéphane Paulus, Bernadette C Young","doi":"10.1099/mgen.0.001340","DOIUrl":"https://doi.org/10.1099/mgen.0.001340","url":null,"abstract":"<p><p><b>Background.</b> The <i>Staphylococcus capitis</i> NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood.<b>Methods.</b> Demographic and clinical data for 45 neonates with <i>S. capitis</i> and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. <i>S. capitis</i> isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (<i>n</i>=27) and short-read (Illumina) sequencing (<i>n</i>=18). These sequences were compared with <i>S. capitis</i> sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (<i>n</i>=6), <i>S. capitis</i> isolated from surface swabs (found in 5/150 samples), rectal swabs (in 2/69 samples) in NICU patients and NICU environmental samples (in 5/114 samples). Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a complete UK NRCS-A reference genome, for outbreak analysis and comparison with 826 other <i>S. capitis</i> from the UK and Germany.<b>Results.</b> <i>S. capitis</i> bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; <i>P</i>=0.05). A phylogeny of sequenced <i>S. capitis</i> revealed a cluster comprised of 25/27 neonatal sterile site isolates and 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other wards belonged to this cluster. Phylogenetic comparison with published sequences confirmed that the cluster was NRCS-A outbreak strain but found a relatively high genomic diversity (mean pairwise distance of 84.9 SNPs) and an estimated NRCS-A <i>S. capitis</i> molecular clock of 5.1 SNPs/genome/year (95% credibility interval 4.3-5.9). The presence of <i>S. capitis</i> in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A <i>S. capitis</i> carriage identified also experienced <i>S. capitis</i> bacteraemia.<b>Conclusions.</b> <i>S. capitis</i> bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A <i>S. capitis</i> strain, distinct from non-NICU clinical samples. Multiple introductions of <i>S. capitis</i>, rather than prolonged environmental persistence, were seen over 5 years of infections.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951263","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":"An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the <i>Acidobacteriota</i>.","authors":"Ella McReynolds, Mostafa S Elshahed, Noha H Youssef","doi":"10.1099/mgen.0.001344","DOIUrl":"10.1099/mgen.0.001344","url":null,"abstract":"<p><p>Members of the phylum <i>Acidobacteriota</i> inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various <i>Acidobacteriota</i> lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes <i>Terriglobia</i>, <i>Vicinamibacteria</i>, <i>Blastocatellia</i> and <i>Thermoanaerobaculia</i> were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes <i>Aminicenantia</i> and <i>Holophagae</i> showed preferences to non-soil habitats. However, while specific preferences were observed, most <i>Acidobacteriota</i> lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the <i>Acidobacteriota</i>. The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in the <i>Acidobacteriota</i> suggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of <i>Acidobacteriota</i> as a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059444","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}