Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

Abstract

During attempts to obtain novel, human-associated species of the domainArchaea, a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA andmcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10Tproduced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10Tcould not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10Tgrew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10Tand several uncultured, methanogenicArchaeathat had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘CandidatusAciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T(83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10Tbelongs to a novel order that is distinct from theThermoplasmatales. The novel strain also appeared to be distinct fromMethanosphaera stadtmanaeDSM 3091T(72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10Trepresents a novel species of a new genus for which the nameMethanomassiliicoccus luminyensisgen. nov., sp. nov. is proposed. The type strain of the type species is B10T( = DSM 24529T = CSUR P135T).