biostudies-literatureBlanco-Miguez AEuropean Research CouncilNCI NIH HHS1804-1819.e9https://www.ebi.ac.uk/biostudies/studies/S-EPMC10635906biostudies-literatureUnknown31(11)The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based oCell host & microbeExtension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.PMC10635906716575101045015865466U01 CA230551Segata NAmend LCova LDe Filippis FRiedel THitch TCABerry SEManghi PSpector TDWolf JGalvez EJCHuang KDClavel TThomas AMErcolini DSchober IStrowig TPasolli ELesker TROvermann JTett ADavies RBlanco-Miguez APuncochar MValles-Colomer MfalseExtension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based o2023-01-01T00:00:00Z2023 Nov2026-05-29T03:56:06.196Z2024-11-07T02:46:47.726ZS-EPMC106359063788397610.1016/j.chom.2023.09.013