Host Specificity Scores and Microbiota Convergence Scores
We developed a statistic, the Host Specificity Score (HSS), to assess microbial genus-specific patterns of humanization in captive NHP gut microbiotas. This statistic was defined for a microbial genus in a captive NHP population as the mean binary Sorensen-Dice dissimilarity of the ASV composition of the genus between the captive NHP population and humans divided by the mean binary Sorensen-Dice dissimilarity of the ASV composition of the genus between the captive NHP population and a conspecific wild-living population. HSSs of >1 indicate that the ASV composition of the microbial clade is more similar between captive NHPs and wild-living conspecifics than between captive NHPs and humans. In contrast, a score of <1 indicates that the ASV composition of the microbial clade is more similar between captive NHPs and humans than between captive NHPs and wild-living conspecifics.
In order to calculate HSSs, we split the ASV table containing all samples by microbial genus and calculated genus-level mean binary Sorensen-Dice (BSD) dissimilarities between captive NHPs and wild conspecifics as well as between captive NHPs and humans. ASVs without taxonomic assignments and microbial genera detected by fewer than 5 reads were excluded from downstream analyses. Asin the ANCOM analyses described above, captive chimpanzees retired from the New Iberia Research Center (USA2) were paired with wild chimpanzees from Tanzania (TZA) and zoo captive chimpanzees (USA1) were paired with wild chimpanzees from the DRC (DRC). The HSS for each genus was calculated and log-transformed for regression analyses.
In addition to HSSs, we also calculated for each microbial genus in each captive NHP population a Microbiota Convergence Score (MCS). This index measures the degree to which the ASV composition of the genus in a captive NHP has converged with the ASV composition of the genus in humans relative to the ASV composition of the genus in the wild conspecific NHP population. Descriptions of these analyses are presented in the Supplemental Materials and Methods. For both HSSs and MCSs, heatmaps were calculated in R using heatmap.2 with the parameter scale=“col” and default settings. In addition to analyses based on the Yatsunenko et al. (2012) dataset, we also calculated per genus HSSs and MCSs for each captive NHP population using an American Gut dataset (McDonald et al., 2018) (Supplementary Materials and Methods). All scripts used to calculate HSSs and MCSs are publically available at github.com/CUMoellerLab/Houtz_etal_2021-NHP_microbiome.