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,Christine Moissl-Eichinger 

Archaea play a crucial role in the human microbiome, yet their study in the gastrointestinal tract (GIT) remains limited due to a lack of cultured strains. This study introduces a method for enriching and isolating methanogenic archaea from human fecal samples using methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and Nanopore sequencing. The approach also involves analyzing co-cultured bacteria, comparative genomics, functional analysis, and protein structure-based function prediction. Stable archaeal cultures were established from 14 of 16 fecal samples, yielding nine previously uncultivated strains, eight of which were absent from a recent archaeome genome catalog. Genomic comparisons of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini revealed traits potentially linked to gastrointestinal diseases. This work expands available archaeal strains for GIT research and provides new insights into the adaptability of Candidatus Methanobrevibacter intestini in the human microbiome.

DOI: 10.1038/s41467-024-52037-7

Keywords: ArchaeaGastrointestinal tract (GIT)Human microbiomeMethanogenic archaeaMethane breath testingFACSNanopore sequencingMethanobrevibacter smithiiCandidatus Methanobrevibacter intestiniComparative genomicsFunctional analysisMicrobiome adaptability