D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland.
Nat Commun. 2024 Aug 31;15(1):7593. doi: 10.1038/s41467-024-52037-7.
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.
古菌是人类微生物组的重要组成部分，但由于可培养代表物的稀缺，它们在胃肠道 (GIT) 中的研究受到限制。我们的研究提出了一种从人类粪便样本中靶向富集和分离产甲烷古菌的方法。该程序结合了甲烷呼气测试、计算机代谢建模、培养基优化、FACS、稀释系列以及通过纳米孔技术进行的基因组测序。其他分析包括共培养的细菌组、古菌基因组的比较基因组学、功能比较以及基于结构的未知差异特征的蛋白质功能预测。从 16 个粪便样本中的 14 个成功建立了稳定的古菌培养物，获得了 9 株以前未培养的菌株，其中 8 株不存在于最近的古菌基因组目录中。对来自个体供体的 Methanobrevibacter smithii 和 Candidatus Methanobrevibacter intestini 菌株的比较基因组学和功能评估揭示了可能与胃肠道疾病相关的特征。我们的工作拓宽了 GIT 研究中可用的古菌代表物，并深入了解了 Candidatus Methanobrevibacter intestini 基因组在关键微生物组环境中的适应性。
