Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome
Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.
Authors
- Viktoria Weinberger (ORCID: https://orcid.org/0009-0001-7787-0755)
- Laura Schmidberger
- Alexander Mahnert (ORCID: https://orcid.org/0000-0001-7083-8894)
- Rokhsareh Mohammadzadeh
- Michael Predl (ORCID: https://orcid.org/0000-0002-3556-4661)
- Stefanie Duller (ORCID: https://orcid.org/0000-0002-0927-3270)
- Łukasz Szydłowski (ORCID: https://orcid.org/0009-0001-1667-251X)
- Christine Moissl‐Eichinger
- Verena Zrim
- Adrian Moser
- Marcus Blohs (ORCID: https://orcid.org/0000-0001-6488-1298)
- Dagmar Kolb (ORCID: https://orcid.org/0000-0002-6387-7446)
- Thomas Rattei (ORCID: https://orcid.org/0000-0002-0592-7791)
- Dominique Pernitsch
- Christoph Högenauer (ORCID: https://orcid.org/0000-0003-4566-0806)
- Christina Kumpitsch (ORCID: https://orcid.org/0000-0002-2077-2839)
- Tomasz Kościółek (ORCID: https://orcid.org/0000-0002-9915-7387)
- Ruth A. Schmitz (ORCID: https://orcid.org/0000-0002-6788-0829)
- Melanie Dragovan
- Tamara Zurabischvili
- Simone Vrbancic
- Anna Eberhard
- Torben Kühnast
Institutions
- Silesian University of Technology (PL)
- Jagiellonian University (PL)
- University of Vienna (AT)
- Medical University of Graz (AT)
- Christian-Albrechts-Universität zu Kiel (DE)
- BioTechMed-Graz (AT)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-08-31
- DOI
- https://doi.org/10.1038/s41467-024-52037-7
- Citations
- 13
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 3.04
Funders
- Austrian Science Fund
- Universität Wien
- Karl-Franzens-Universität Graz
- Medizinische Universität Graz