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

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Duller, Stefanie, Vrbancic, Simone, Szydłowski, Łukasz, Mahnert, Alexander, Blohs, Marcus, Predl, Michael, Kumpitsch, Christina, Zrim, Verena, Högenauer, Christoph, Kosciolek, Tomasz, Schmitz, Ruth A., Eberhard, Anna, Dragovan, Melanie, Schmidberger, Laura, Zurabischvili, Tamara, Weinberger, Viktoria, Moser, Adrian Mathias, Kolb, Dagmar, Pernitsch, Dominique, Mohammadzadeh, Rokhsareh, Kühnast, Torben, Rattei, Thomas, Moissl-Eichinger, Christine·2024·Nature Communications
DOI 10.1038/s41467-024-52037-7PMC PMC11366006

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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.

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Metadata

Authors
Duller, S., Vrbancic, S., Szydłowski, Ł., Mahnert, A., Blohs, M., Predl, M., Kumpitsch, C., Zrim, V., Högenauer, C., Kosciolek, T., Schmitz, R. A., Eberhard, A., Dragovan, M., Schmidberger, L., Zurabischvili, T., Weinberger, V., Moser, A. M., Kolb, D., Pernitsch, D., Mohammadzadeh, R., Kühnast, T., Rattei, T., & Moissl-Eichinger, C.
Affiliations
  • Medical University of Graz (AT)
  • Jagiellonian University (PL)
  • University of Vienna (AT)
  • Christian-Albrechts-Universität zu Kiel (DE)
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-08-31
Volume
15
Issue
1
Pages
7593-7593
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-52037-7
PMC
PMC11366006
OpenAlex
W4402087069
Cited by
21
References
5
Citations by year
2026: 12 · 2025: 9
FWCI
2.83
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Homo Politicus (Academy of Humanities and Economics in Lodz) (submittedVersion, cc-by-nc-nd)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Austrian Science Fund (P 30796, SFB F-83, COE 7)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Anaerobic Digestion and Biogas Production
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
Keywords
Methanobrevibacter, gut archaea, fecal samples, target enrichment, Methanobrevibacter smithii, methane breath test, in silico metabolic modeling, co-culture, comparative genomics, protein function prediction, gastrointestinal diseases, human gut microbiome
MeSH terms
Gastrointestinal Microbiome, Adult, Feces, Female, Humans, Male, Methane, Phylogeny, Genome, Archaeal, Methanobrevibacter, Gastrointestinal Tract

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