Figure 1. Humanization of captive NHP gut microbiotas. (A) Plot shows the first and second Principal Coordinates of the Binary Sorensen-Dice dissimilarities among wild primates, captive primates, and humans. Shapes represent fecal samples collected from individual primates and are colored based on host species identity as indicated by the inset. Circles unite groups of shapes corresponding to wild, captive, or human samples. (B) Boxplots show maxima, minima, interquartile ranges, and medians of BSD dissimilarities between primates (wild or captive) and humans. Boxes are colored by primate species as in (A). Significant differences between means based on permutation tests are indicated by asterisks; *** p = 0.001.
Figure 2. Differential abundance of microbial genera between captive and wild NHP individuals. Volcano plots show the ANCOM test statistic (y-axis) and the centered logarithmic transformed (CLR) log-fold difference in relative abundance between captive and wild individuals for each microbial genus. Dots represent microbial genera colored by captive NHP population based on Figure 1, and each plot shows results for a single captive primate population: captive chimpanzee (USA2) (A), captive chimpanzee (USA1) (B), captive gorilla (C), captive douc (USA) (D), and captive douc (SGP) (E). Dashed line in each plot represents W statistic cutoff of 0.9. Statistics for all ASVs for each pair of captive and wild NHP populations are presented in Table S3. Venn diagrams (F and G) show overlap of the sets of differentially abundant microbial genera between pairs of captive NHP populations, represented by circles colored by captive NHP population as in Figure 1 and in the key. In (F), the number of genera shared by each pair of captive NHP populations is shown above lines connecting cartoons colored as in Figure 1. In (F) and (G), numbers in non-overlapping portions of circles represent differentially abundant microbial genera detected in both NHP populations but differentially abundant in only one NHP population. Numbers in overlapping portions of circles represent microbial genera that were differentially abundant in both NHP populations. Significance of overlap for each comparison is shown by asterisks: *** p -value < 0.001; NS not significant.
Figure 3. Host Specificity Scores reveal microbial genus-specific humanization of captive NHP gut microbiotas. Shown are examples of two microbial genera that display evidence of humanization (A) or retention from the wild (B) in captive chimpanzees. Boxplots show the maximum, minimum, interquartile range, and median of BSD dissimilarities between wild chimpanzees and captive chimpanzees or between humans and captive chimpanzees. The logarithm of the Host Specificity Score, calculated as the ratio of the means of boxplots within each panel, was <0 for Collinsella (A) and >0 for vadinCA11 (B), indicating humanization and retention from the wild, respectively. Boxes are colored by primate species as in Figure 1. Significant differences between means based on permutation tests are indicated with asterisks; *** p = 0.001.
Figure 4. Humanization of gut microbial genera in captive NHPs is reproducible and host-species specific. Plots show relationships of microbial genus-level Host Specificity Scores (HSSs) between pairs of captive NHP populations. Each point represents the HSSs of a bacterial genus in two captive NHP populations (rows and columns), and lines indicate best-fit linear regressions. Cartoons represent NHP species and are colored as in Figure 1. Tree connecting cartoons shows phylogenetic relationships among NHPs. Rows and columns correspond to NHP species, with each plot showing a regression between HSSs for a pair of NHP species. Box­­es are colored based on R2 of regression, with R2 > 0.8 colored dark red, 0.8> R2 > 0.1 colored light red, and R2 < 0.1 colored gray. R2, Spearman rho, and corresponding p- values are reported in the top left corner of each plot. Significance for non-zero slope of regression line (based on Pearson correlation) is indicated in the bottom right corner of each plot; NS not significant, *p < 0.05, ** p < 0.01, *** p< 0.001.