Microbial Genomics最新文献

{"title":"Evaluation of <i>Klebsiella pneumoniae</i> pathogenicity through holistic gene content analysis.","authors":"Miyu Isogai, Kumiko Kawamura, Tetsuya Yagi, Shizuo Kayama, Motoyuki Sugai, Yohei Doi, Masahiro Suzuki","doi":"10.1099/mgen.0.001295","DOIUrl":"10.1099/mgen.0.001295","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of <i>K. pneumoniae</i> is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical <i>K. pneumoniae</i> strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of <i>K. pneumoniae</i> strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (<i>rmpA</i>, <i>iucA</i>, <i>iutA</i>, <i>irp2</i>, <i>fyuA</i>, <i>ybtS</i>, <i>iroN</i>, <i>allS</i> and <i>clbA</i>) compared to the major group. Pathogenicity was assessed using <i>Galleria mellonella</i> larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the <i>G. mellonella</i> infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 9","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11571079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142290819","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 study substantiates the intensive care unit as a reservoir for carbapenem-resistant <i>Klebsiella pneumoniae</i> in a teaching hospital in China.","authors":"Shuo Jiang, Zheng Ma, Huiluo Cao, Li Mo, Jinlan Jin, Bohai Yu, Kankan Chu, Jihua Hu","doi":"10.1099/mgen.0.001299","DOIUrl":"10.1099/mgen.0.001299","url":null,"abstract":"<p><p>Carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP) has recently emerged as a notable public health concern, while the underlying drivers of CRKP transmission among patients across different healthcare facilities have not been fully elucidated. To explore the transmission dynamics of CRKP, 45 isolates were collected from both the intensive care unit (ICU) and non-ICU facilities in a teaching hospital in Guangdong, China, from March 2020 to August 2023. The collection of clinical data and antimicrobial resistance phenotypes was conducted, followed by genomic data analysis for these isolates. The mean age of the patients was 75.2 years, with 18 patients (40.0%) admitted to the ICU. The predominant strain in hospital-acquired CRKP was sequence type 11 (ST11), with k-locus type 64 and serotype O1/O2v1 (KL64:O1/O2v1), accounting for 95.6% (43/45) of the cases. The CRKP ST11 isolates from the ICU exhibited a low single nucleotide polymorphism (SNP) distance when compared to isolates from other departments. Genome-wide association studies identified 17 genes strongly associated with SNPs that distinguish CRKP ST11 isolates from those in the ICU and other departments. Temporal transmission analysis revealed that all CRKP isolates from other departments were genetically very close to those from the ICU, with fewer than 16 SNP differences. To further elucidate the transmission routes among departments within the hospital, we reconstructed detailed patient-to-patient transmission pathways using hybrid methods that combine TransPhylo with an SNP-based algorithm. A clear transmission route, along with mutations in potential key genes, was deduced from genomic data coupled with clinical information in this study, providing insights into CRKP transmission dynamics in healthcare settings.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 9","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349687","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":"Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.","authors":"Daniel G Barber, Christian A Davies, Iain P Hartley, Richard K Tennant","doi":"10.1099/mgen.0.001298","DOIUrl":"https://doi.org/10.1099/mgen.0.001298","url":null,"abstract":"<p><p>Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 9","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11412367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142290820","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":"pQEB1: a hospital outbreak plasmid lineage carrying <i>bla</i> _KPC-2.","authors":"Robert A Moran, Mahboobeh Behruznia, Elisabeth Holden, Mark I Garvey, Alan McNally","doi":"10.1099/mgen.0.001291","DOIUrl":"10.1099/mgen.0.001291","url":null,"abstract":"<p><p>While conducting genomic surveillance of carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene <i>bla</i> _KPC-2. The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of <i>Citrobacter freundii</i>, two STs of <i>Enterobacter cloacae</i>, and three species of <i>Klebsiella</i>. Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an <i>Enterobacter hormaechei</i> isolated from a blood sample at the QE in 2016 and a <i>Klebsiella pneumoniae</i> isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS<i>26</i>-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 9","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109158","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>Vibrio cholerae</i> serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965.","authors":"Caroline Rouard, Elisabeth Njamkepo, Marie-Laure Quilici, Scott Nguyen, Victoria Knight-Connoni, Renáta Šafránková, Francois-Xavier Weill","doi":"10.1099/mgen.0.001282","DOIUrl":"10.1099/mgen.0.001282","url":null,"abstract":"<p><p>Several authors have attributed the explosive outbreak of gastroenteritis that occurred in Czechoslovakia in 1965 to a toxigenic strain of <i>Vibrio cholerae</i> serogroup O37 based on unverified metadata associated with three particular strains from the American Type Culture Collection. Here, by sequencing the original strain preserved at the Czech National Collection of Type Cultures since 1966, we show that the strain responsible for this outbreak was actually a <i>V. cholerae</i> O5 that lacks the genes encoding the cholera toxin, the toxin-coregulated pilus protein and <i>Vibrio</i> pathogenicity islands present in <i>V. cholerae</i> O37 strains.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 9","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133123","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":"Development and implementation of a core genome multilocus sequence typing scheme for <i>Haemophilus influenzae</i>.","authors":"Made Ananda Krisna, Keith A Jolley, William Monteith, Alexandra Boubour, Raph L Hamers, Angela B Brueggemann, Odile B Harrison, Martin C J Maiden","doi":"10.1099/mgen.0.001281","DOIUrl":"10.1099/mgen.0.001281","url":null,"abstract":"<p><p><i>Haemophilus influenzae</i> is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in <i>H. influenzae</i> necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for <i>H. influenzae</i> using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (<i>N</i> = 14) and high-quality draft <i>H. influenzae</i> genomes (<i>N</i> = 2297). The draft genome dataset was divided into a development dataset (<i>N</i> = 921) and a validation dataset (<i>N</i> = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (<i>R</i> ² = 0.945). We used this cgMLST scheme to define a high-resolution population structure for <i>H. influenzae</i>, which enhances the genomic analysis of this clinically relevant human pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907045","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":"Comparative genomic analysis identifies potential adaptive variation in <i>Mycoplasma ovipneumoniae</i>.","authors":"Kimberly R Andrews, Thomas E Besser, Thibault Stalder, Eva M Top, Katherine N Baker, Matthew W Fagnan, Daniel D New, G Maria Schneider, Alexandra Gal, Rebecca Andrews-Dickert, Samuel S Hunter, Kimberlee B Beckmen, Lauren Christensen, Anne Justice-Allen, Denise Konetchy, Chadwick P Lehman, Kezia Manlove, Hollie Miyasaki, Todd Nordeen, Annette Roug, E Frances Cassirer","doi":"10.1099/mgen.0.001279","DOIUrl":"https://doi.org/10.1099/mgen.0.001279","url":null,"abstract":"<p><p><i>Mycoplasma ovipneumoniae</i> is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared <i>M. ovipneumoniae</i> genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of <i>M. ovipneumoniae</i> assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three <i>M. ovipneumoniae</i> genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of <i>M. ovipneumoniae</i> has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109156","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":"Whole-genome sequencing of Western Canadian <i>Borrelia</i> spp. collected from diverse tick and animal hosts reveals short-lived local genotypes interspersed with longer-lived continental genotypes.","authors":"Jennifer N Russell, Min-Kuang Lee, Miguel I Uyaguari-Diaz, Ashton N Sies, Danae M Suchan, William Hsiao, Erin Fraser, Muhammad G Morshed, Andrew D S Cameron","doi":"10.1099/mgen.0.001276","DOIUrl":"10.1099/mgen.0.001276","url":null,"abstract":"<p><p>Changing climates are allowing the geographic expansion of ticks and their animal hosts, increasing the risk of <i>Borrelia</i>-caused zoonoses in Canada. However, little is known about the genomic diversity of <i>Borrelia</i> from the west of the Canadian Rockies and from the tick vectors <i>Ixodes pacificus</i>, <i>Ixodes auritulus</i> and <i>Ixodes angustus</i>. Here, we report the whole-genome shotgun sequences of 51 <i>Borrelia</i> isolates from multiple tick species collected on a range of animal hosts between 1993 and 2016, located primarily in coastal British Columbia. The bacterial isolates represented three different species from the Lyme disease-causing <i>Borrelia burgdorferi sensu lato</i> genospecies complex [<i>Borrelia burgdorferi sensu stricto</i> (<i>n</i>=47), <i>Borrelia americana</i> (<i>n</i>=3) and <i>Borrelia bissettiae</i> (<i>n</i>=1)]. The traditional eight-gene multi-locus sequence typing (MLST) strategy was applied to facilitate comparisons across studies. This identified 13 known <i>Borrelia</i> sequence types (STs), established 6 new STs, and assigned 5 novel types to the nearest sequence types. <i>B. burgdorferi</i> s. s. isolates were further differentiated into ten <i>ospC</i> types, plus one novel <i>ospC</i> with less than 92 % nucleotide identity to all previously defined <i>ospC</i> types. The MLST types resampled over extended time periods belonged to previously described STs that are distributed across North America. The most geographically widespread ST, ST.12, was isolated from all three tick species. Conversely, new <i>B. burgdorferi</i> s. s. STs from Vancouver Island and the Vancouver region were only detected for short periods, revealing a surprising transience in space, time and host tick species, possibly due to displacement by longer-lived genotypes that expanded across North America.This article contains data hosted by Microreact.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11296321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875283","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":"Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.","authors":"Melissa J Jansen van Rensburg, Duncan J Berger, Iman Yassine, David Shaw, Andy Fohrmann, James E Bray, Keith A Jolley, Martin C J Maiden, Angela B Brueggemann","doi":"10.1099/mgen.0.001280","DOIUrl":"10.1099/mgen.0.001280","url":null,"abstract":"<p><p>Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11321556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976130","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":"Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome.","authors":"Yuka Adachi Katayama, Ryoma Kamikawa, Takashi Yoshida","doi":"10.1099/mgen.0.001285","DOIUrl":"10.1099/mgen.0.001285","url":null,"abstract":"<p><p>Although the production of carbon monoxide (CO) within the human body has been detected, only two CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut. Therefore, the phylogenetic diversity of the human gut CO-utilizing prokaryotes remains unclear. Here, we unveiled more than a thousand representative genomes containing genes for putative nickel-containing CO dehydrogenase (pCODH), an essential enzyme for CO utilization. The taxonomy of genomes encoding pCODH was expanded to include 8 phyla, comprising 82 genera and 248 species. In contrast, putative molybdenum-containing CODH genes were not detected in the human gut microbial genomes. pCODH transcripts were detected in 97.3 % (<i>n</i>=110) of public metatranscriptome datasets derived from healthy human faeces, suggesting the ubiquitous presence of prokaryotes bearing transcriptionally active pCODH genes in the human gut. More than half of the pCODH-encoding genomes contain a set of genes for the autotrophic Wood-Ljungdahl pathway (WLP). However, 79 % of these genomes commonly lack a key gene for the WLP, which encodes the enzyme that synthesizes formate from CO₂, suggesting that potential human gut CO-utilizing prokaryotes share a degenerated gene set for WLP. In the other half of the pCODH-encoding genomes, seven genes, including putative genes for flavin adenine dinucleotide-dependent NAD(P) oxidoreductase (FNOR), ABC transporter and Fe-hydrogenase, were found adjacent to the pCODH gene. None of the putative genes associated with CO-oxidizing respiratory machinery, such as energy-converting hydrogenase genes, were found in pCODH-encoding genomes. This suggests that the human gut CO utilization is not for CO removal, but potentially for fixation and/or biosynthesis, consistent with the harmless yet continuous production of CO in the human gut. Our findings reveal the diversity and distribution of prokaryotes with pCODH in the human gut microbiome, suggesting their potential contribution to microbial ecosystems in human gut environments.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017965","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}