GSE25408
The pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii
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 Overall design: 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. Strains of Methanobrevibacter smithii were grown in vitro (modified MBC media) to mid-log phase, at 37°C in serum bottles pressurized with 80% hydrogen, 20% CO2 gasses at 30psi. Cells were harvested by centrifugation, and DNA was isolated by phenol-chloroform and ethanol precipitation.