Microbial Genomics最新文献

{"title":"GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.","authors":"Calum J Walsh, Meghana Srinivas, Timothy P Stinear, Douwe van Sinderen, Paul D Cotter, John G Kenny","doi":"10.1099/mgen.0.001255","DOIUrl":"10.1099/mgen.0.001255","url":null,"abstract":"<p><p>Sequence comparison of 16S rRNA PCR amplicons is an established approach to taxonomically identify bacterial isolates and profile complex microbial communities. One potential application of recent advances in long-read sequencing technologies is to sequence entire rRNA operons and capture significantly more phylogenetic information compared to sequencing of the 16S rRNA (or regions thereof) alone, with the potential to increase the proportion of amplicons that can be reliably classified to lower taxonomic ranks. Here we describe <i>GROND</i> (<i>G</i>enome-derived <i>R</i>ibosomal <i>O</i>pero<i>n D</i>atabase), a publicly available database of quality-checked 16S-ITS-23S rRNA operons, accompanied by multiple taxonomic classifications. <i>GROND</i> will aid researchers in analysis of their data and act as a standardised database to allow comparison of results between studies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284107","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":"Discovery and genetic characterization of novel paramyxoviruses from small mammals in Hubei Province, Central China","authors":"Jia-le Xu, Jin-tao Chen, Bing Hu, Wei-wei Guo, Jing-jing Guo, Chao-rui Xiong, Ling-xin Qin, Xin-nai Yu, Xiao-min Chen, Kun Cai, Yi-rong Li, Man-qing Liu, Liang-jun Chen and Wei Hou","doi":"10.1099/mgen.0.001229","DOIUrl":"https://doi.org/10.1099/mgen.0.001229","url":null,"abstract":"Paramyxoviruses are a group of single-stranded, negative-sense RNA viruses, some of which are responsible for acute human disease, including parainfluenza virus, measles virus, Nipah virus and Hendra virus. In recent years, a large number of novel paramyxoviruses, particularly members of the genus <span>Jeilongvirus</span>, have been discovered in wild mammals, suggesting that the diversity of paramyxoviruses may be underestimated. Here we used hemi-nested reverse transcription PCR to obtain 190 paramyxovirus sequences from 969 small mammals in Hubei Province, Central China. These newly identified paramyxoviruses were classified into four clades: genera <span>Jeilongvirus</span>, <span>Morbillivirus</span>, <span>Henipavirus</span> and <span>Narmovirus</span>, with most of them belonging to the genus <span>Jeilongvirus</span>. Using Illumina sequencing and Sanger sequencing, we successfully recovered six near-full-length genomes with different genomic organizations, revealing the more complex genome content of paramyxoviruses. Co-divergence analysis of jeilongviruses and their known hosts indicates that host-switching occurred more frequently in the evolutionary histories of the genus <span>Jeilongvirus</span>. Together, our findings demonstrate the high prevalence of paramyxoviruses in small mammals, especially jeilongviruses, and highlight the diversity of paramyxoviruses and their genome content, as well as the evolution of jeilongviruses.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"9 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828750","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":"Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing.","authors":"Nicholas D Sanderson, Katie M V Hopkins, Matthew Colpus, Melody Parker, Samuel Lipworth, Derrick Crook, Nicole Stoesser","doi":"10.1099/mgen.0.001246","DOIUrl":"10.1099/mgen.0.001246","url":null,"abstract":"<p><p>Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Pseudomonas aeruginosa</i> and <i>Staphylococcus aureus</i>, and nine genetically diverse <i>E. coli</i> bloodstream infection-associated isolates from different phylogroups and sequence types, both with and without BSA. These sequences were <i>de novo</i> assembled and compared against Illumina-corrected reference genomes. In this small evaluation of 13 isolates we found that nanopore long-read-only R10.4.1/kit 14 assemblies with updated basecallers trained using bacterial methylated DNA produce accurate assemblies with ≥40×depth, sufficient to be cost-effective compared with hybrid ONT/Illumina sequencing in our setting.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140859603","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":"Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.","authors":"Gwyn Dahlquist-Axe, Francesca J Standeven, Camilla F Speller, Andrew Tedder, Conor J Meehan","doi":"10.1099/mgen.0.001251","DOIUrl":"10.1099/mgen.0.001251","url":null,"abstract":"<p><p>The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912291","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":"Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.","authors":"Steven G Sutcliffe, Susanne A Kraemer, Isaac Ellmen, Jennifer J Knapp, Alyssa K Overton, Delaney Nash, Jozef I Nissimov, Trevor C Charles, David Dreifuss, Ivan Topolsky, Pelin I Baykal, Lara Fuhrmann, Kim P Jablonski, Niko Beerenwinkel, Joshua I Levy, Abayomi S Olabode, Devan G Becker, Gopi Gugan, Erin Brintnell, Art F Y Poon, Renan Valieris, Rodrigo D Drummond, Alexandre Defelicibus, Emmanuel Dias-Neto, Rafael A Rosales, Israel Tojal da Silva, Aspasia Orfanou, Fotis Psomopoulos, Nikolaos Pechlivanis, Lenore Pipes, Zihao Chen, Jasmijn A Baaijens, Michael Baym, B Jesse Shapiro","doi":"10.1099/mgen.0.001249","DOIUrl":"10.1099/mgen.0.001249","url":null,"abstract":"<p><p>Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087977","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":"SaLTy: a novel <i>Staphylococcus aureus</i> Lineage Typer.","authors":"Liam Cheney, Michael Payne, Sandeep Kaur, Ruiting Lan","doi":"10.1099/mgen.0.001250","DOIUrl":"10.1099/mgen.0.001250","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 <i>S</i>. <i>aureus</i> was associated with 20 000 deaths in the USA alone. Dividing <i>S. aureus</i> isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of <i>S. aureus</i> genome sequences when describing the fundamental population structure of the species. In this study, we developed <i>Staphylococcus aureus</i> Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (<i>n</i>=21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing <i>mecA</i> (SCC<i>mec</i>) which is carried by methicillin-resistant <i>S. aureus</i> (MRSA). Most lineages had isolates lacking SCC<i>mec</i> and the four largest lineages varied in SCC<i>mec</i> over time. Classifying isolates into SaLTy lineages, which were further SCC<i>mec</i> typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of <i>S. aureus</i> genome data. SaLTy will aid the characterisation of <i>S. aureus</i> populations and ongoing surveillance of sub-groups that threaten human health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912394","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>Actinomycetota</i> bioprospecting from ore-forming environments.","authors":"César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy Parkinson","doi":"10.1099/mgen.0.001253","DOIUrl":"10.1099/mgen.0.001253","url":null,"abstract":"<p><p>Natural products from <i>Actinomycetota</i> have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922265","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":"Genomics and physiology of <i>Catenibacillus</i>, human gut bacteria capable of polyphenol <i>C</i>-deglycosylation and flavonoid degradation.","authors":"Tobias Goris, Annett Braune","doi":"10.1099/mgen.0.001245","DOIUrl":"10.1099/mgen.0.001245","url":null,"abstract":"<p><p>The genus <i>Catenibacillus</i> (family <i>Lachnospiraceae</i>, phylum <i>Bacillota</i>) includes only one cultivated species so far, <i>Catenibacillus scindens,</i> isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal <i>Catenibacillus</i> strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated <i>Catenibacillus decagia</i>, and showed its ability to deglycosylate <i>C</i>-coupled flavone and xanthone glucosides and <i>O</i>-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of <i>C. scindens</i> and ten faecal metagenome-assembled genomes assigned to the genus <i>Catenibacillus</i>, we performed a comparative genome analysis and searched for genes encoding potential <i>C</i>-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of <i>Catenibacillus</i> strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both <i>C. scindens</i> and <i>C. decagia</i> encode a flavonoid <i>O</i>-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid <i>C</i>-deglycosylation system of <i>Dorea</i> strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for <i>C</i>-deglycosylation. The diversity of <i>dgpA</i> and <i>dgpBC</i> gene clusters might explain the broad <i>C</i>-glycoside substrate spectrum of <i>C. scindens</i> and <i>C. decagia</i>. The other <i>Catenibacillus</i> genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several <i>Catenibacillus</i> species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087970","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":"Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment.","authors":"Becca L Handley, Oliver Sokana, Kennedy Kwasi Addo, Josef Wagner, María Fookes, Emma Harding-Esch, Michael Marks, Nicholas R Thomson, Ronan M Doyle","doi":"10.1099/mgen.0.001234","DOIUrl":"10.1099/mgen.0.001234","url":null,"abstract":"<p><p>Cutaneous ulcers are common in yaws-endemic areas. Although often attributed to '<i>Treponema pallidum</i> subsp. <i>pertenue'</i> and <i>Haemophilus ducreyi</i>, quantitative PCR has highlighted a significant proportion of these ulcers are negative for both pathogens and are considered idiopathic. This is a retrospective analysis utilising existing 16S rRNA sequencing data from two independent yaws studies that took place in Ghana and the Solomon Islands. We characterized bacterial diversity in 38 samples to identify potential causative agents for idiopathic cutaneous ulcers. We identified a diverse bacterial profile, including <i>Arcanobacterium haemolyticum</i>, <i>Campylobacter concisus</i>, <i>Corynebacterium diphtheriae</i>, <i>Staphylococcus</i> spp<i>.</i> and <i>Streptococcus pyogenes</i>, consistent with findings from previous cutaneous ulcer microbiome studies. No single bacterial species was universally present across all samples. The most prevalent bacterium, <i>Campylobacter ureolyticus</i>, appeared in 42% of samples, suggesting a multifactorial aetiology for cutaneous ulcers in yaws-endemic areas. This study emphasizes the need for a nuanced understanding of potential causative agents. The findings prompt further exploration into the intricate microbial interactions contributing to idiopathic yaw-like ulcers, guiding future research toward comprehensive diagnostic and therapeutic strategies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912397","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":"Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen.","authors":"Julie Ramírez Martínez, Sonia Guillou, Stéphanie Le Prieur, Pauline Di Vittorio, Florelle Bonal, Demetris Taliadoros, Elise Gueret, Elisabeth Fournier, Eva H Stukenbrock, Romain Valade, Pierre Gladieux","doi":"10.1099/mgen.0.001241","DOIUrl":"10.1099/mgen.0.001241","url":null,"abstract":"<p><p>Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. <i>Pyrenophora teres</i> is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of <i>P. teres</i> remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of <i>P. teres</i> in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140863238","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}