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.