Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome

Stefanie Duller, Simone Vrbancic, Łukasz Szydłowski, Alexander Mahnert, Marcus Blohs, Michael Predl, Christina Kumpitsch, Verena Zrim, Christoph Högenauer, Tomasz Kosciolek, Ruth A. Schmitz, Anna Eberhard, Melanie Dragovan, Laura Schmidberger, Tamara Zurabischvili, Viktoria Weinberger, Adrian Mathias Moser, Dagmar Kolb, Dominique Pernitsch, Rokhsareh Mohammadzadeh, Torben Kühnast, Thomas Rattei and Christine Moissl-Eichinger ()
Additional contact information
Stefanie Duller: Medical University of Graz
Simone Vrbancic: Medical University of Graz
Łukasz Szydłowski: Jagiellonian University in Krakow
Alexander Mahnert: Medical University of Graz
Marcus Blohs: Medical University of Graz
Michael Predl: University of Vienna
Christina Kumpitsch: Medical University of Graz
Verena Zrim: Medical University of Graz
Christoph Högenauer: Medical University of Graz
Tomasz Kosciolek: Jagiellonian University in Krakow
Ruth A. Schmitz: Christian Albrechts University
Anna Eberhard: Medical University of Graz
Melanie Dragovan: Medical University of Graz
Laura Schmidberger: Medical University of Graz
Tamara Zurabischvili: Medical University of Graz
Viktoria Weinberger: Medical University of Graz
Adrian Mathias Moser: Medical University of Graz
Dagmar Kolb: Medical University of Graz
Dominique Pernitsch: Medical University of Graz
Rokhsareh Mohammadzadeh: Medical University of Graz
Torben Kühnast: Medical University of Graz
Thomas Rattei: University of Vienna
Christine Moissl-Eichinger: Medical University of Graz

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-52037-7

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