Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov

Abstract

The methanogenic strain Mx-05^T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05^T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H₂ as an electron donor. H₂/CO₂, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05^T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05^T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L^-1 NaCl (optimum 0.12 mol.L^-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H₄MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05^T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05^T (JCM 31474T).

Keywords: Methanomassiliicoccales; archaea; human gut microbiota; methanogens.

Figure 1

Proportional abundance of bacteria and archaea in enrichment cultures using either H₂/methanol (a) or H₂/trimethylamine (b) two years after the beginning of the enrichment culture. Percentage values next to the bacterial names correspond to the sequence identity they display to the closest species.

Figure 2

Methanomassiliicoccales maximum likelihood tree built with an LG+F+R10 model from 41 concatenated protein sequences. The tree is rooted on ‘Candidatus Sysuiplasmatales’ [38], with 10,325 positions after trimming. Values on the tree indicate the bootstrap supports > 70%. The tree was formatted with Itol [45]. Isolated species are indicated in bold.

Figure 3

Cryo-electron microscopy pictures of strain Mx-05^T showing the whole cell (a) and details (b). Black arrows (b) indicate potential adhesin-like proteins on the surface of the cell.