Fig. 4

Strain-level phylogenetic analysis of relevant microbial clades found both in NHPs and human microbiomes. a Ordination analysis using multidimensional scaling (MDS) on intra-FGB phylogenetic distances for the five most prevalent FGBs shared by NHPs and humans (Fig. 2c), showing both host-specific and shared clusters. b Phylogenetic tree of the ten most prevalent kSGBs, uSGBs, and pSGBs assigned to the Bacteroidetes phylum reported in Fig. 2a, with MAGs from wild NHPs in separate pSGB subtrees and captive NHPs clustering into SGBs shared with humans (uncollapsed tree in Additional file 2: Figure S2). c Phylogenetic tree of the Elusimicrobia phylum, with SGBs specifically associated with wild NHPs and others with humans and captive NHPs (uncollapsed tree in Additional file 2: Figure S4)