Figure 4. Phylogenetical analysis of mouse gut microbiota.

(A) Maximum-likelihood phylogenetic tree of 16 species identified in this study. The tree was generated in MEGA6⁵⁵. Reference sequences were obtained from the GreenGene (13_8) database. The clustering of the sequences was tested by a bootstrap approach with 1,000 repeats, and bootstrap values below 70 were clipped. The red box indicates the species separated from their genus. (B) Detected variants between two 16S rRNA gene sequences of the separated species are represented as a vertical line on the 16S rDNA sequences. Variants were defined as nucleotide present in less than 50% of aligned position frequencies. The black and red arrows indicate the binding positions of primer sets for the amplification of V3–V4 regions and nearly full-length regions on 16S rDNA sequences, respectively.