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.