HiBC: a publicly available collection of bacterial strains isolated from the human gut

Thomas C. A. Hitch, Johannes M. Masson, Charlie Pauvert, Johanna Bosch, Selina Nüchtern, Nicole S. Treichel, Marko Baloh, Soheila Razavi, Afrizal Afrizal, Ntana Kousetzi, Andrea M. Aguirre, David Wylensek, Amy C. Coates, Susan A. V. Jennings, Atscharah Panyot, Alina Viehof, Matthias A. Schmitz, Maximilian Stuhrmann, Evelyn C. Deis, Kevin Bisdorf, Maria D. Chiotelli, Artur Lissin, Isabel Schober, Julius Witte, Thorsten Cramer, Thomas Riedel, Marie Wende, Katrin A. Winter, Lena Amend, Alessandra Riva, Stefanie Trinh, Laura Mitchell, Jonathan Hartman, David Berry, Jochen Seitz, Lukas C. Bossert, Marianne Grognot, Thorsten Allers, Till Strowig, Michael Pester, Birte Abt, Lorenz C. Reimer, Jörg Overmann and Thomas Clavel ()
Additional contact information
Thomas C. A. Hitch: University Hospital of RWTH Aachen
Johannes M. Masson: University Hospital of RWTH Aachen
Charlie Pauvert: University Hospital of RWTH Aachen
Johanna Bosch: University Hospital of RWTH Aachen
Selina Nüchtern: University Hospital of RWTH Aachen
Nicole S. Treichel: University Hospital of RWTH Aachen
Marko Baloh: University Hospital of RWTH Aachen
Soheila Razavi: University Hospital of RWTH Aachen
Afrizal Afrizal: University Hospital of RWTH Aachen
Ntana Kousetzi: University Hospital of RWTH Aachen
Andrea M. Aguirre: University Hospital of RWTH Aachen
David Wylensek: University Hospital of RWTH Aachen
Amy C. Coates: University Hospital of RWTH Aachen
Susan A. V. Jennings: University Hospital of RWTH Aachen
Atscharah Panyot: University Hospital of RWTH Aachen
Alina Viehof: University Hospital of RWTH Aachen
Matthias A. Schmitz: University Hospital of RWTH Aachen
Maximilian Stuhrmann: University Hospital of RWTH Aachen
Evelyn C. Deis: University Hospital of RWTH Aachen
Kevin Bisdorf: University Hospital of RWTH Aachen
Maria D. Chiotelli: University Hospital of RWTH Aachen
Artur Lissin: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Isabel Schober: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Julius Witte: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Thorsten Cramer: University Hospital of RWTH Aachen
Thomas Riedel: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Marie Wende: Helmholtz Centre for Infection Research
Katrin A. Winter: Helmholtz Centre for Infection Research
Lena Amend: Helmholtz Centre for Infection Research
Alessandra Riva: University of Vienna
Stefanie Trinh: University Hospital of RWTH Aachen
Laura Mitchell: University of Nottingham
Jonathan Hartman: RWTH Aachen University
David Berry: University of Vienna
Jochen Seitz: University of Duisburg-Essen
Lukas C. Bossert: RWTH Aachen University
Marianne Grognot: University Hospital of RWTH Aachen
Thorsten Allers: University of Nottingham
Till Strowig: Partner Site Hannover-Braunschweig
Michael Pester: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Birte Abt: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Lorenz C. Reimer: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Jörg Overmann: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Thomas Clavel: University Hospital of RWTH Aachen

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: Abstract Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains are accessible to the scientific community. We have therefore created a publicly available collection of bacterial strains isolated from the human gut. The Human intestinal Bacteria Collection (HiBC) ( https://www.hibc.rwth-aachen.de ) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

Date: 2025
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DOI: 10.1038/s41467-025-59229-9

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