Taxonomy and diversity analyses
Taxonomy was assigned to ASVs by fitting a naive-Bayes classifier trained on the Greengenes v.13_8 99% OTUs reference using the sk-learn classifier. A phylogenetic tree was constructed by inserting the sequences into the Greengenes 13_8 reference tree using the QIIME2 plugin q2-fragment-insertion, which uses the SEPP insertion method. Shannon entropy and Chao1 alpha diversity indices were calculated for each sample. The Shannon index measures richness and evenness, whereas Chao1 measures the abundance weighted ASV richness within a microbiota. To examine the sharing of ASVs between captive and wild NHPs and humans, the binary Sorensen-Dice dissimilarly was calculated for each pair of samples (Dice 1945). Binary Sorensen-Dice dissimilarities were calculated as one minus the quotient of the total number of ASVs shared between two samples by the sum of the total number of ASVs in each sample.