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

Autor: Duller S; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Vrbancic S; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Szydłowski Ł; Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland.; Sano Centre for Computational Medicine, Krakow, Poland., Mahnert A; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.; BioTechMed Graz, Graz, Austria., Blohs M; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Predl M; Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.; Doctoral School Microbiology and Environmental Science, University of Vienna, Vienna, Austria., Kumpitsch C; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.; BioTechMed Graz, Graz, Austria., Zrim V; Center for Medical Research, Medical University of Graz, Graz, Austria., Högenauer C; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria., Kosciolek T; Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland.; Sano Centre for Computational Medicine, Krakow, Poland.; Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland., Schmitz RA; Institute for General Microbiology, Christian Albrechts University, Kiel, Germany., Eberhard A; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Dragovan M; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Schmidberger L; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Zurabischvili T; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Weinberger V; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Moser AM; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria., Kolb D; Core Facility Ultrastructure Analysis, Medical University of Graz, Graz, Austria.; Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria., Pernitsch D; Core Facility Ultrastructure Analysis, Medical University of Graz, Graz, Austria., Mohammadzadeh R; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Kühnast T; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria., Rattei T; Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria., Moissl-Eichinger C; D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria. christine.moissl-eichinger@medunigraz.at.; BioTechMed Graz, Graz, Austria. christine.moissl-eichinger@medunigraz.at.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Aug 31; Vol. 15 (1), pp. 7593. Date of Electronic Publication: 2024 Aug 31.
DOI: 10.1038/s41467-024-52037-7
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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