Microbial Genomics最新文献

{"title":"Whole-genome sequencing and comparative genomic analysis of <i>Irpex lacteus</i> isolated from the female reproductive tract.","authors":"Yixuan Wang, Shujuan Zhang, Shi-Ling Han, Xiaomeng Ge, Shenghan Gao, Qianhui Zhu, Yadong Liu, Songnian Hu, Ziwen Jiang, Yinmei Dai, Lei Cai, Yu Vincent Fu","doi":"10.1099/mgen.0.001416","DOIUrl":"https://doi.org/10.1099/mgen.0.001416","url":null,"abstract":"<p><p><i>Irpex lacteus</i> is a fungus typically found on angiosperm branches and trunks. Here, we report the isolation of a novel strain of <i>I. lacteus</i> from the cervix uteri of a female patient diagnosed with endometriosis and COVID-19 at Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Using whole-genome sequencing, we generated a high-quality draft genome for this human-derived strain. Comparative genomic analysis revealed significant variations amongst <i>I. lacteus</i> strains colonizing distinct environments. Functional annotations indicated that environmental adaptation has influenced specific functional traits in the strains. Moreover, potential virulence factors were identified, implying a risk of opportunistic infections associated with <i>I. lacteus</i>. This study elucidates the adaptive characteristics of <i>I. lacteus</i> across ecological niches and provides genomic insights into its opportunistic colonization.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216321","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":"Genomic analysis of invasive and non-invasive disease-causing <i>Streptococcus pneumoniae</i> isolated from children between 2014 and 2023 in Suzhou, China.","authors":"Lili Huang, Alannah C King, Yue Liu, Harry C H Hung, Stephen D Bentley, Yue Jiang, Panpan Lv, Xuebin Xu, Stephanie W Lo, Mingliang Chen","doi":"10.1099/mgen.0.001398","DOIUrl":"https://doi.org/10.1099/mgen.0.001398","url":null,"abstract":"<p><p>In 2017, 553,000 clinical cases of <i>Streptococcus pneumoniae</i> in children were reported in China, although the pneumococcal conjugate vaccine (PCV), which targets the pneumococcal capsule, is not included in the Chinese National Immunization Program (NIP) for children. Therefore, the PCV uptake rate is very low. To investigate the <i>S. pneumoniae</i> population over the past 10 years in China, we collected 418 S. <i>pneumoniae</i> isolates from children with pneumococcal diseases in Suzhou, China, 2014-2023, and whole-genome sequenced them. A total of 27 serotypes expressed by 36 Global Pneumococcal Sequence Clusters (GPSCs) that encompassed 72 sequence types were identified, with serotype 19F (38.3%, <i>n</i>=160) and GPSC1 (60.8%, <i>n</i>=254) as the predominant serotype and lineage, respectively. We found that the majority (64.8%, <i>n</i>=271) of samples represented serotypes that are covered by the GSK 10-valent PCV (PCV10) formulation and that even more were covered by the SII PCV10 formulation (89.2%, <i>n</i>=373). Almost all (94.3%, <i>n</i>=394) samples represented serotypes that are included within the 13-valent PCV (PCV13) vaccine formulation. This suggests that the inclusion of the PCV in the NIP would lead to significant benefits for child health. Also, we observed that no significant differences were seen in the serotypes or lineages in cases of invasive and non-invasive pneumococcal diseases.Additionally, we investigated the prevalence of antimicrobial resistance within the population and found that 99.8% (<i>n</i>=417) of isolates were predicted to be resistant to at least one antibiotic tested. This again supports the need to increase PCV uptake to prevent infections with antibiotic-resistant <i>S. pneumoniae</i> and to reduce the number of infections in general, consequently lowering the consumption of antibiotics. In summary, the PCV13 vaccine could potentially cover over 90% of invasive and non-invasive <i>S. pneumoniae</i> isolates in Suzhou, China. Therefore, increasing the uptake of PCVs by including PCV13 in the NIP would lead to significant benefits for child health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208944","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":"The pet café is a neglected site for transmission of antimicrobial-resistant <i>Escherichia coli</i> in urban life.","authors":"Ruan-Yang Sun, Xiao-Ling Long, Ya-Li Ruan, Xi-Ran Wang, Xiao-Hui Wu, Jian Sun, Xiao-Ping Liao, Ya-Hong Liu, Hao Ren, Xin-Lei Lian","doi":"10.1099/mgen.0.001412","DOIUrl":"10.1099/mgen.0.001412","url":null,"abstract":"<p><p>The process of urbanization has brought with it several novel lifestyles, but it remains to be seen whether such lifestyles are the potential driver behind the spread of antimicrobial resistance (AMR) in modern society. Hence, this study employs the pet café as a proof of concept to observe how one pathway of AMR transmission occurs within a megacity. A total of 111 samples were collected from consumers, workers, animals and the surrounding environment from three pet cafés in Guangzhou, and 163 bacterial strains were isolated, with <i>Escherichia coli</i> (<i>n</i>=60) being the most dominant species. The sequence type and genomic diversity of <i>E. coli</i> were observed in all three cafés. Notably, 19 highly related ST328 strains were isolated in a single pet café from both workers (skin and faeces) and animals (faeces), suggesting transmission between distinct hosts. The number of SNPs between ST328 <i>E. coli</i> isolated in this study and strains from other provinces in China was minimal, with the possibility of clonal transmission. In terms of AMR, 90% of the isolates exhibited resistance to at least three distinct classes of antimicrobials (multidrug resistance). Multiple antimicrobial resistance genes (ARGs) such as <i>tet</i>(X4) were detected in this study, and plasmid, especially hybrid plasmid, is the main transmission vector of these ARGs. Our findings highlight that the pet café is a neglected site for the transfer of ARGs among <i>Enterobacteriaceae</i>, with a propensity for continuous contamination through either clonal or horizontal transmission of ARGs.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128094","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 analysis of <i>Legionella pneumophila</i> in the drinking water system of a large building over 25 years.","authors":"Helena M B Seth-Smith, Adrian Egli, Sylvia Gautsch, Michael M Bornstein, Eva M Kulik","doi":"10.1099/mgen.0.001393","DOIUrl":"10.1099/mgen.0.001393","url":null,"abstract":"<p><p><i>Legionella pneumophila</i>, the causative agent of Legionnaires' disease, is often found in the plumbing systems of buildings, from where it can be transmitted to humans via inhalation or aspiration of contaminated water drops. Annual routine water sampling from the potable water system of an occupational healthcare building in Basel over 25 years was performed in accordance with national guidelines. Overall, 309 water samples were collected at 38 time points over the period of 25 years. <i>L. pneumophila</i> was recovered from 120 water samples (38.8%) from 26 time points. No clinical infections were recorded during this period. Initial decontamination measures were successful for ~12 years, after which an increase in the total number of <i>Legionella</i> c.f.u. as well as of <i>L. pneumophila</i>-positive sites was noticed in 2007. Whole genome sequencing (WGS) analysis of <i>n</i>=123 isolates from <i>n</i>=113 samples showed all <i>L. pneumophila</i> to be sequence type 45 (sequence-based typing scheme). The isolates are closely related, with only 408 SNPs among all isolates after the bioinformatic removal of recombination events. Over the 25 years, a single lineage deriving from a recent common ancestor colonized the water system of this building. The phylogeny of isolate genomes can be interpreted as inferring good water circulation and possible recolonization from a common source after cleaning, with genome evolution and insertion/loss of large elements evident. Regular monitoring of waterlines in healthcare settings helps to identify concentrations of <i>Legionella</i> spp., and WGS is recommended for detailed investigation.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128143","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":"Gene conversion and duplication contribute to genetic variation in an outbreak of <i>Mycobacterium tuberculosis</i>.","authors":"Christoph Stritt, Michelle Reitsma, Ana Maria Garcia Marin, Galo Goig, Anna Dötsch, Sonia Borrell, Christian Beisel, Iñaki Comas, Daniela Brites, Sebastien Gagneux","doi":"10.1099/mgen.0.001396","DOIUrl":"https://doi.org/10.1099/mgen.0.001396","url":null,"abstract":"<p><p>Repeats are the most diverse and dynamic but also the least well-understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias, they have received much less attention. Long-read DNA sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen <i>Mycobacterium tuberculosis</i> from Pacific Biosciences HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We found that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which could be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. Whilst recombination events were less frequent than point mutations, they affected large regions and introduced multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involved <i>ppe18</i> and <i>ppe57</i>, two genes possibly involved in immune subversion. The vast majority of variants were present in single isolates, such that phylogenetic resolution was only marginally increased when estimating a tree from complete genomes. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this 'monomorphic' bacterial pathogen awaits investigation.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016482","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":"Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of <i>Listeria monocytogenes</i>.","authors":"Stefanie Lüth, Jannika Fuchs, Carlus Deneke","doi":"10.1099/mgen.0.001389","DOIUrl":"https://doi.org/10.1099/mgen.0.001389","url":null,"abstract":"<p><p>Whole-genome sequencing (WGS) has become the key approach for molecular surveillance of <i>Listeria monocytogenes</i>. Genome comparison analysis can reveal transmission routes that cannot be found with classic epidemiology. A widespread standard for use in genome comparison analysis involves data from short-read sequencing, generated on Illumina or Ion Torrent devices. To date, little is known about the compatibility of data from both platforms. This knowledge is essential when it comes to the central analysis of data, for example, in the case of outbreaks. We used WGS data from 47 <i>L</i>. <i>monocytogenes</i> isolates of the strain collection of the German National Reference Laboratory for <i>L. monocytogenes</i>, generated on either Illumina or Ion Torrent devices, to analyse the impact of the sequencing technology on downstream analyses. In our study, only the assembler SPAdes delivered qualitatively comparable results. In the gene-based core genome multilocus sequence typing (cgMLST), the same-strain allele discrepancy between the platforms was 14.5 alleles on average, which is well above the threshold of 7 alleles routinely used for cluster detection in <i>L. monocytogenes</i>. An application of a strict frameshift filter in cgMLST analysis could push the mean discrepancy below this threshold but reduced discriminatory power. The impact of the platform on the read-based single nucleotide polymorphism analysis was lower than that on the cgMLST. Overall, it was possible to improve compatibility in various ways, but perfect compatibility could not be achieved.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044048","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 heavy water-adapted bacterial communities.","authors":"Juan Rivas-Santisteban, José M Martínez, Cristina Escudero, Rebecca Hernández-Antolín, Laura Cid-Barrio, Gary J Ellis, Esteban Domingo, Carlos Sánchez, Francisco Sobrino, Ricardo Amils","doi":"10.1099/mgen.0.001414","DOIUrl":"https://doi.org/10.1099/mgen.0.001414","url":null,"abstract":"<p><p>Micro-organisms can survive and thrive in unusual and extreme environments. Here, we present a metagenomic analysis of living bacteria found in highly pure, deleterious heavy water (>99% D₂O), stored in sealed plastic containers for more than 30 years, without any external supply. Deep DNA sequencing analyses have revealed that the most abundant genetic signatures were primarily associated with <i>Pseudomonadota</i> and <i>Bacteroidota</i>. These bacteria exhibited shorter gene lengths and depletion of polar and metabolically costly amino acids compared to the related species from light water environments. Genes related to DNA transposition, repair and modification were notably abundant, particularly mutant forms of the IS3 transposable elements family. We also explore potential carbon and energy sources and discuss the evolutionary implications of bacteria capable of surviving in such an extreme human-made environment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174069","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":"Detection of novel <i>Plasmodium falciparum</i> haplotypes under treatment pressure in paediatric severe malaria.","authors":"Balotin Fogang, Emilie Guillochon, Claire Kamaliddin, Gino Agbota, Sem Ezinmegnon, Maroufou Jules Alao, Philippe Deloron, Gwladys Bertin, Antoine Claessens","doi":"10.1099/mgen.0.001386","DOIUrl":"https://doi.org/10.1099/mgen.0.001386","url":null,"abstract":"<p><p><b>Background.</b> In Africa, the clearance time for <i>Plasmodium falciparum</i> severe malaria varies significantly, likely due to the complexity of <i>P. falciparum</i> infections and the sequestration phenomenon exhibited by this parasite. This study aims to evaluate different methods to study the intra-host dynamics of polyclonal infections during parasite clearance under antimalarial treatment. Additionally, it seeks to determine the association between parasite clearance rate following artesunate or quinine treatment and the genetic complexity of <i>P. falciparum</i> in Beninese children with severe malaria.<b>Methods.</b> Sixty-five <i>P. falciparum</i> severe malaria individuals diagnosed by microscopy and treated with artesunate or quinine were sampled every 8 h for 24 h. Using whole-genome sequencing (WGS) data, we estimated the multiplicity of infection (MOI) with three algorithms (<i>Fws</i>, THE REAL McCOIL and RoH). We then characterized the <i>P. falciparum</i> genetic complexity in WGS-identified polyclonal infections using amplicon sequencing (AmpSeq) on DNA extracted from plasma and the red blood cell pellet.<b>Results.</b> AmpSeq demonstrated greater sensitivity in detecting multiple genomes within isolates compared to WGS methods. The MOI from AmpSeq was significantly higher in red blood cell pellets compared to plasma (2.4 vs. 1.8 distinct microhaplotypes per isolate). However, at parasitaemia over 1,000 parasites per microlitre, the same MOI was detected in both plasma and pellet samples in 85.4% of the isolates. We observed a high variability in parasite clearance rate among participants, but it was not associated with parasite MOI at diagnosis. Interestingly, in 60.9% of participants, previously undetected microhaplotypes appeared in circulation 16 h after treatment initiation.<b>Conclusion.</b> These findings demonstrate that combining different haplotyping techniques effectively determines parasite genetic complexity. Additionally, plasma can be effectively used for parasite genotyping at sufficient parasitaemia levels. The parasite clearance rate of severe malaria is independent of parasite MOI. However, genotyping a single blood sample upon hospital admission does not capture the full spectrum of parasite genotypes present in the infection.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989893","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 characterization of <i>Pseudomonas aeruginosa</i> from canine otitis highlights the need for a One Health approach to this opportunistic pathogen.","authors":"L Newstead, T Smith-Zaitlik, C Kelly, E Roberts, S Street, G K Paterson","doi":"10.1099/mgen.0.001407","DOIUrl":"https://doi.org/10.1099/mgen.0.001407","url":null,"abstract":"<p><p>In humans, <i>Pseudomonas aeruginosa</i> is well known as a prominent opportunistic pathogen associated with antimicrobial resistance (AMR), which presents a major challenge to successful treatment. This is also the case in animals, particularly in companion dogs where <i>P. aeruginosa</i> is a common cause of otitis. Despite its clinical significance, little data are available on the genomics and epidemiology of <i>P. aeruginosa</i> in dogs. To address this, we have genome-sequenced 34 canine otitis <i>P. aeruginosa</i> isolates from a veterinary referral hospital and analysed these along with a further 62 publicly available genomes from canine isolates. Phylogenetic analysis revealed that all three <i>P. aeruginosa</i> phylogroups<i>,</i> A-C<i>,</i> are represented amongst a diverse bacterial population isolated from dogs. We identify examples of persistent or recurrent infection by the same strain of up to 309 days between sampling, demonstrating the difficulty of successfully eradicating infection. Isolates encoded a variety of AMR genes with genomic and phenotypic AMR correlating poorly for β-lactams but showing complete concordance between fluoroquinolone resistance and quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV. Pangenome-wide analysis between 80 canine otitis isolates (34 newly sequenced here and a further 46 publicly available) and a reference collection of 491 human isolates found no genes which were over-represented or specific to either host species, indicating similar strains infect both humans and dogs. This agrees with the sharing of multilocus sequence types between dogs and humans, including the isolation here of ST235 from three dogs, a lineage prominent among the multidrug resistant (MDR) and extensively drug-resistant (XDR) international high-risk clones of <i>P. aeruginosa</i> causing human infections. The presence of such 'high-risk' clones in companion dogs is concerning given their potential impact on animal health and the potential for zoonotic spread. These data provide new insight into this difficult-to-treat veterinary pathogen and promote the need for a One Health approach to tackling it.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007872","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":"Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the <i>Proteobacteria</i>.","authors":"Alex S Grossman, Nicholas C Mucci, Sarah J Kauffman, Jahirul Rafi, Heidi Goodrich-Blair","doi":"10.1099/mgen.0.001406","DOIUrl":"10.1099/mgen.0.001406","url":null,"abstract":"<p><p>Type 11 secretion systems (T11SS) are broadly distributed amongst <i>Proteobacteria</i>, with more than 3,000 T11SS family outer membrane proteins (OMPs) comprising ten major sequence similarity network clusters. Of these, only seven, all from animal-associated cluster 1, have been experimentally verified as secretins of cargo, including adhesins, haemophores and metal-binding proteins. To identify novel cargo of a more diverse set of T11SS, we identified gene families co-occurring in gene neighbourhoods with either cluster 1 or marine microbe-associated cluster 3 T11SS OMP genes. We developed bioinformatic controls to ensure that perceived co-occurrences are specific to T11SS, and not general to OMPs. We found that both cluster 1 and cluster 3 T11SS OMPs frequently co-occur with single-carbon metabolism and nucleotide synthesis pathways, but that only cluster 1 T11SS OMPs had significant co-occurrence with metal and haem pathways, as well as with mobile genetic islands, potentially indicating the diversified function of this cluster. Cluster 1 T11SS co-occurrences included 2,556 predicted cargo proteins, unified by the presence of a C-terminal <i>β</i>-barrel domain, which fall into 141 predicted UniRef50 clusters and approximately ten different architectures: four similar to known cargo and six uncharacterized types. We experimentally demonstrate T11SS-dependent secretion of an uncharacterized cargo type with homology to plasmin-sensitive protein. Unexpectedly, genes encoding marine cluster 3 T11SS OMPs only rarely co-occurred with the C-terminal <i>β</i>-barrel domain and instead frequently co-occurred with DUF1194-containing genes. Overall, our results show that with sufficiently large-scale and controlled genomic data, T11SS-dependent cargo proteins can be accurately predicted.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111036","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}