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

Author

Listed:
  • Stefanie Duller

    (Medical University of Graz)

  • Simone Vrbancic

    (Medical University of Graz)

  • Łukasz Szydłowski

    (Jagiellonian University in Krakow
    Sano Centre for Computational Medicine)

  • Alexander Mahnert

    (Medical University of Graz
    BioTechMed Graz)

  • Marcus Blohs

    (Medical University of Graz)

  • Michael Predl

    (University of Vienna
    University of Vienna)

  • Christina Kumpitsch

    (Medical University of Graz
    BioTechMed Graz)

  • Verena Zrim

    (Medical University of Graz)

  • Christoph Högenauer

    (Medical University of Graz)

  • Tomasz Kosciolek

    (Jagiellonian University in Krakow
    Sano Centre for Computational Medicine
    Silesian University of Technology)

  • 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
    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
    BioTechMed Graz)

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.

Suggested Citation

  • Stefanie Duller & Simone Vrbancic & Łukasz Szydłowski & Alexander Mahnert & Marcus Blohs & Michael Predl & Christina Kumpitsch & Verena Zrim & Christoph Högenauer & Tomasz Kosciolek & Ruth A. Schmitz , 2024. "Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52037-7
    DOI: 10.1038/s41467-024-52037-7
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