Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.

Aitor Blanco-Míguez, Eric J C Gálvez, Edoardo Pasolli, Francesca De Filippis, Lena Amend, Kun D Huang, Paolo Manghi, Till-Robin Lesker, Thomas Riedel, Linda Cova, Michal Punčochář, Andrew Maltez Thomas, Mireia Valles-Colomer, Isabel Schober, Thomas C A Hitch, Thomas Clavel, Sarah E Berry, Richard Davies, Jonathan Wolf, Tim D Spector, Jörg Overmann, Adrian Tett, Danilo Ercolini, Nicola Segata, Till Strowig

Journal: Cell host & microbe 2023;31(11):1804-1819.e9

PMID: 37883976

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Abstract

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 on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.

Address: Department CIBIO, University of Trento, Trento, Italy.; Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.; Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.; Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.; Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany.; Department of Nutritional Sciences, King's College London, London, UK.; Zoe Ltd., London, UK.; Department of Twin Research, King's College London, London, UK.; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Technical University of Braunschweig, Braunschweig, Germany.; Centre for Microbiology and Environmental Systems Science, University of Vienna, Wien, Austria.; Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.; Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Centre for Individualized Infection Medicine, Hannover, Germany. Electronic address: [email protected].

DOI: 10.1016/j.chom.2023.09.013

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MeSH Terms: Humans, Male, Gastrointestinal Microbiome, Metagenome, Microbiota, Phylogeny, Prevotella, Female