Fig. 2

Methanomassiliicoccales taxon defined based on whole-genome identity pairwise comparisons. A A maximum likelihood tree based on 243 Methanomassiliicoccales genomes, including 33 MAGs and two cultured strains from this study, was inferred from a concatenated set of 118 archaeal marker proteins. The gray triangle corresponds to the five outgroup taxa from the order Thermoplasmatales. Support values > 80% are shown as black dots. Stars on the clade represent the genomes reconstructed in this study and publicly available cultured genomes, whereas unmarked clades represent MAGs retrieved from previous studies. Colored strips on the two outermost rims show the biome type to which the isolation belongs and the animal source of the host-associated genomes. Two layers of the concentric bar plot indicate the genome size (G.S.) and the corresponding assembled completeness (Com.). B Amino acid identity (AAI) values and 16S rRNA gene sequence pairwise comparisons showing acknowledged genus (AAI > 65%) and species (AAI > 95% or 16S rRNA gene sequence identity > 97%) cutoff values. C Acronyms represent the 22 Methanomassiliicoccales genera (G. 1 to G. 22) identified in this study. Clades in the phylogenomic tree were collapsed according to the taxonomic level. Colored clades represent three previously named genera. Genera were divided into the environmental and gastrointestinal clades. Box plots showing divergences in the AAI index and genome size between genomes assigned to these genera. The composition of the biome category in each genus is displayed in a histogram