Fig. 4
Phylogeny of S24-7 species and novel isolates within the family. a Phylogenomic placement of the Muribaculaceae family within the phylum Bacteroidetes was conducted using PhyloPhlAn [57]. Representative genomes within Bacteroidetes were used to place the Muribaculaceae isolates and MGS genomes generated in the present study; Fibrobacter succinogenes was used as out-group. The tree is drawn to scale with branch lengths measuring the number of amino acid substitutions per site. Local support values were calculated using the Shimodaira-Hasegawa test with 1000 resamples; only those values < 100% are shown. For the sake of clarity, clades with a branch length to nodes < 2 have been collapsed with the size of the triangle being proportional to the number of genomes within the corresponding clade (see Additional file 4: Figure S2 for the original, not collapsed tree structure within Muribaculaceae). Clades are named based on the internal genomes taxonomy, with corresponding numbers of genomes indicated in brackets. b Tree based on 16S rRNA gene sequences showing the phylogenetic position of cultured species within Muribaculaceae compared with members of most closely related families. The evolutionary history was inferred using the Neighbor-Joining method [53]. The optimal tree with the sum of branch length 2.97236459 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) are shown next to the branches (values equal to 100% are not shown) [15]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method [64] and are in the units of the number of base substitutions per site. The analysis involved 64 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 1518 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [28]