{"title":"隐藏在众目睽睽之下:从基因组和宏基因组数据筛选中发现的新的辛科和Rhabdochlydiaceae多样性。","authors":"Helen R. Davison, Gregory D.D. Hurst","doi":"10.1016/j.syapm.2023.126468","DOIUrl":null,"url":null,"abstract":"<div><p><em>Chlamydiota</em> are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic <em>Chlamydiota</em> are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of <em>Chlamydiota</em> diversity and its hosts, in particular the Order <em>Parachlamydiales</em>. We extract one <em>Rhabdochlamydiaceae</em> and three <em>Simkaniaceae</em> Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names “<em>Sacchlamyda saccharinae”</em> (Family <em>Rhabdochlamydiaceae)</em> and “<em>Amphrikana amoebophyrae”</em> (Family <em>Simkaniaceae</em>), as well as a third new clade of environmental MAGs “<em>Acheromyda pituitae</em>” (Family <em>Rhabdochlamydiaceae</em>). The extent of uncharacterized diversity within the <em>Rhabdochlamydiaceae</em> and <em>Simkaniaceae</em> is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in <em>Parachlamydiales</em> metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 6","pages":"Article 126468"},"PeriodicalIF":3.3000,"publicationDate":"2023-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data\",\"authors\":\"Helen R. Davison, Gregory D.D. Hurst\",\"doi\":\"10.1016/j.syapm.2023.126468\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><em>Chlamydiota</em> are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic <em>Chlamydiota</em> are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of <em>Chlamydiota</em> diversity and its hosts, in particular the Order <em>Parachlamydiales</em>. We extract one <em>Rhabdochlamydiaceae</em> and three <em>Simkaniaceae</em> Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names “<em>Sacchlamyda saccharinae”</em> (Family <em>Rhabdochlamydiaceae)</em> and “<em>Amphrikana amoebophyrae”</em> (Family <em>Simkaniaceae</em>), as well as a third new clade of environmental MAGs “<em>Acheromyda pituitae</em>” (Family <em>Rhabdochlamydiaceae</em>). The extent of uncharacterized diversity within the <em>Rhabdochlamydiaceae</em> and <em>Simkaniaceae</em> is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in <em>Parachlamydiales</em> metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.</p></div>\",\"PeriodicalId\":22124,\"journal\":{\"name\":\"Systematic and applied microbiology\",\"volume\":\"46 6\",\"pages\":\"Article 126468\"},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2023-09-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Systematic and applied microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0723202023000772\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Systematic and applied microbiology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0723202023000772","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data
Chlamydiota are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names “Sacchlamyda saccharinae” (Family Rhabdochlamydiaceae) and “Amphrikana amoebophyrae” (Family Simkaniaceae), as well as a third new clade of environmental MAGs “Acheromyda pituitae” (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in Parachlamydiales metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.
期刊介绍:
Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology: