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Expanding the cultivated human archaeome by targeted isolation of novel Methanobrevibacter strains from fecal samples
Open accessPreprint — published as 10.1038/s41467-024-52037-7 · Paper page
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 targeted cultivation method enriching methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modelling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyses include 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 were 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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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Moissl-Eichinger, C., Duller, S., Vrbancic, S., Szydłowski, Ł., Mahnert, A., Blohs, M., Predl, M., Kumpitsch, C., Zrim, V., Högenauer, C., Kosciolek, T., Schmitz, R., Eberhard, A., Dragovan, M., Schmidberger, L., Zurabischvili, T., Weinberger, V., Moser, A., Kolb, D., Pernitsch, D., Mohammadzadeh, R., Kuehnast, T., & Rattei, T.
- Affiliations
- Medical University of Graz
- Medical University of Graz (AT)
- Jagiellonian University (PL)
- University of Vienna (AT)
- Silesian University of Technology
- Christian-Albrechts-Universität zu Kiel (DE)
- ORCID
- Venue
- Nature Communications
- Published
- 2024-04-19
- Volume
- 15
- Issue
- 1
- Pages
- 7593-7593
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC11366006
- OpenAlex
- W4402087069
- Cited by
- 21
- References
- 1
- Citations by year
- 2026: 12 · 2025: 9
- FWCI
- 2.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- 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 (DOC 69, P30796, COE7, SFB-F83, P 32697)
- Universität Wien
- Karl-Franzens-Universität Graz
- Medizinische Universität Graz
- 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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