Project description:Within the gut microbiome, Methanobrevibacter and Methanosphaera species are the prevailing methanogenic archaea. In general, these archaeal species interact widely with other members of the gut microbiome, subsequently facilitating the processes of digestion and fermentation within humans, thereby playing a significant role in the gut. Despite their significance, detailed characteristics and microbiome-host interactions remain largely unexplored. One potential mechanism for microbiome-host interaction and communication involves extracellular vesicles, which play a crucial role in both inter- and intra-kingdom interactions as well as intercellular communication. The production of extracellular vesicles has been confirmed for representatives of all three domains of life, eukaryotes, bacteria, and archaea. In this study, we report for the first time that human gut-derived archaea are capable of producing extracellular vesicles. Here, we present the ultrastructure, composition, proteome, and metabolome of these newly discovered archaeal extracellular vesicles (AEV) of M. smithii (strains ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae. Here, we describe their morphology, contents of archaeal extracellular vesicles (AEV) produced by the major methanogenic archaea of the human gut, namely Methanobrevibacter smithii (strains ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae. We also describe their interaction with human cell lines and ability to trigger immune responses. The findings show a high similarity of AEVs to their bacterial counterparts in size, morphology, and composition. Proteome and metabolome analysis demonstrate high similarities between vesicles derived from Methanobrevibacter species and are highly enriched in adhesin or adhesin-like proteins, suggesting an important role for archaeal-bacterial and archaeal-host interactions. Unless the specific role of AEVs could not be identified, their production itself suggests an intricate network of interdomain interactions shaping the dynamics of the human microbiome.

Project description:Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.

Project description:The human gut microbiota harbors methanogens represented by the dominant archaeon, Methanobrevibacter smithii, a polyphyletic group of acetogens, and sulfate-reducing bacteria. Defining their roles in the H2-economy of the gut has potential therapeutic importance for modulating the efficiency of fermentation of dietary components. We quantified methanogens in fecal samples from 40 healthy adult female monozygotic(MZ) and 28 dizygotic(DZ) twin pairs, analyzed bacterial 16S rRNA datasets generated from their fecal samples to identify taxa that co-occur with methanogens, sequenced the genomes of 20 M. smithii strains isolated from families of MZ and DZ twins, and performed RNA-Seq of a subset of strains to identify their responses to varied formate concentrations. The concordance rate for methanogen carriage was significantly higher for MZ versus DZ twin pairs. Co-occurrence analysis revealed 22 bacterial species-level taxa positively correlated with methanogens: all but two were members of the Clostridiales, with several being, or related to, known hydrogen-producing and -consuming bacteria. The M. smithii pan-genome contains 987 genes conserved in all strains, and 1860 variably represented genes. Strains from MZ and DZ twin pairs had a similar degree of shared genes and SNPs, and were significantly more similar than strains isolated from mothers or members of other families. The 101 adhesin-like proteins(ALPs) in the pan-genome (45±6/strain) exhibit strain-specific differences in expression and responsiveness to formate. We hypothesize that M. smithii strains use their different repertoires of ALPs to create diversity in their metabolic niches, by allowing them to establish syntrophic relationships with bacterial partners with differing metabolic capabilities and patterns of co-occurrence These strains were isolated from human feces, but they are in pure culture now. All the information about each species is associated with the genome accession number

			Action	DRS
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	ERR14224700_1.fastq.gz	Fastqsanger.gz
	ERR14224700_2.fastq.gz	Fastqsanger.gz

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Methanobrevibacter intestini from the human gut

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