Fig. 5

A ML phylogeny showing relationship among 82 species that represent 41 core genera of the human gut microbiome. Taxonomic nomenclature and classification follow NCBI, and for each phylum, updated names are shown with longstanding informal names shown in parentheses. Levels of bootstrap support lower than 90% are shown (500 replicates). For each genus, two representative species are included (names not shown — see Table S11 and Fig. S8A for details). B Dot plot showing levels of concordance for core genes and 16S hypervariable regions. Black dots show concordance with the species phylogeny and grey dots show concordance with the phylogeny representing a consensus of the topologies of each single-copy core gene phylogeny. The 440-bp section of the rpoB gene referred to in the text is shown with an asterisk. Gene and gene category labels and coloring follow Fig. 1