FIG 1.

The order Methanomassiliicoccales forms two large clades that loosely follow the source of isolation. Maximum-likelihood phylogeny of concatenated single-copy marker genes. The gray triangle corresponds to Thermoplasma acidophilum, Picrophilus oshimae, Ferroplasma acidarmanus, Acidiplasma aeolicum, and Cuniculiplasma divulgatum, which are outgroup taxa from class Thermoplasmata. Black circles indicate bootstrap values of >80 (of 1,000 bootstrap permutations), branch color represents the clade, and the scale bar represents the number of amino acid substitutions per site. Colored strips show the source of isolation of each of the included genomes and the general category to which the source belongs. Bar plots show the genome abundance enrichment in gut metagenome samples compared to environmental samples, calculated using DESeq2; dots indicate taxa with significant enrichment in either host or environmental biomes (adj. P < 0.05). Mmassiliicoccaceae, Methanomassiliicocceae; Mmassiliicoccus, Methanomassiliicoccus; Mplasma, Methanoplasma; Mmethylophilus, Methanomethylophilus; Mmassiliicoccales, Methanomassiliicoccales.