Fig. 2

Diversity of bacteria recovered. a Multilocus phylogenetic reconstruction from 706 isolate assemblies using Phylophlan and the Amphora2 universal single-copy marker gene set. Colors and labels on the inner ring indicate family-level taxonomic assignment from GTDB-tk. Heatmaps in middle rings indicate log10 estimated coverage per isolate genome from CoverM within metagenomes of wild P. paniscus, P. troglodytes schweinfurthii, and Pan troglodytes troglodytes. Each gray outer ring indicates presence (black) or absence (gray) of a putative plasmid cluster within bacterial isolates. b Pairwise Average Nucleotide Diversity among strains within each 95% genome-wide ANI cluster show different patterns of within- “species” diversity revealed by whole-genome screening. Highlighted strains indicated by circled number and colored clade on tree in a. Heatmap color values indicate log pairwise nucleotide diversity between each pair of isolates in a cluster. Color bars at the left and annotations at the right show the host species identity of the sample from which the isolate was recovered. Color bars at the top show the host individual