Broad diversity of human gut bacteria accessible via a traceable strain deposition system

Abstract

Numerous bacteria in the human gut microbiome remains unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, none are publicly accessible. This is partly due to issues with the deposition of strains to public culture collections. We address these key issues (microbial unknowns, lack of public access to isolates) by proposing a framework that facilitates large-scale submission of isolates, exemplified by a rich collection of human gut isolates that is taxonomically described, functionally novel, and made publicly available. An innovative bulk strain submission system was established by large-scale generation and curation of persistent strain identifiers (https://straininfo.dsmz.de). This was used to create the Human intestinal Bacterial Collection (www.hibc.rwth-aachen.de), which contains 340 strains representing 198 species within 29 families and 7 phyla, of which 32 previously unknown taxa are taxonomically described and named. These included three butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease. Plasmids were identified to be prolific within the HiBC isolates, with almost half (46%) of strains containing one or more plasmids (up to 6). Megaplasmids were identified within two strains, one of them is globally present within multiple Bacteroidales species. The strain submission framework and public collection of easily searchable and available gut bacterial isolates presented here will facilitate the work of many by enabling functional studies.