Reproducible shifts of microbial ASVs and genera to captivity in replicate conspecific NHP populations
We observed significant overlap in the microbial ASVs and genera that displayed significant shifts in relative abundance from the wild, based on ANCOM analyses, between replicate captive NHP populations of the same species (i.e., conspecific populations) (Table S5). Of the 627 ASVs detected in both replicate captive populations of chimpanzees (USA1 and USA2), 102 and 153 were significantly overrepresented or underrepresented in USA1 and USA2 chimpanzees, respectively, relative to their matched wild populations (each captive chimpanzee population was matched with a different wild chimpanzee population, Materials and Methods). Of these ASVs displaying significantly different relative abundances between captive and wild chimpanzees, 53 displayed significant differences in both captive populations of chimpanzees (USA1 and USA2) (2.1-fold more than random expectation, hypergeometricp -value = 1.429e-11). Similarly, of the 573 ASVs detected in both replicate captive populations of doucs (USA and SGP), 61 and 66 were significantly overrepresented or underrepresented in USA and SGP doucs, respectively, relative to their matched wild population. Of these ASVs displaying significantly different relative abundances between captive and wild doucs, 53 displayed significant differences in both captive populations of doucs (USA and SGP) (6.8-fold more than random expectation, hypergeometric p -value = 5.43e-43). In contrast, this degree of overlap between ASVs displaying significantly different abundances between captivity and the wild was not observed between heterospecific captive NHP populations. For example, of the 64 ASVs shared by USA1 chimpanzees and SGP doucs, 10 and 15 were significantly overrepresented or underrepresented in chimpanzees and doucs, respectively, relative to their matched wild populations. Of these ASVs, only 3 displayed significant differences in both USA1 chimpanzees and SGP doucs (1.3-fold more than expected, hypergeometric p -value = 0.215).
We also observed significant overlap between the sets of microbial genera that were differentially abundant between captivity and the wild in replicate captive conspecific NHP populations (Figure 2; Table S6). Of the 126 microbial genera detected in both replicate captive populations of chimpanzees (USA1 and USA2), 23 and 22 were significantly overrepresented or underrepresented in USA1 and USA2 chimpanzees, respectively, relative to their matched wild populations. Of these genera, 7 displayed significant differences in both captive populations of chimpanzees (USA1 and USA2) (4.2-fold more than random expectation, hypergeometric p -value = 0.0355) (Figure 2F). Similarly, of the 82 genera detected in both replicate captive populations of doucs (USA and SGP), 16 and 12 were significantly overrepresented or underrepresented in USA and SGP doucs, respectively, relative to their matched wild population. Of these genera, 5 displayed significant differences in both captive populations of doucs (USA and SGP) (6.8-fold more than random expectation, hypergeometric p -value = 5.95e-5) (Figure 2F). In contrast, this degree of overlap between genera displaying significantly different abundances between captivity and the wild was not observed between heterospecific captive NHP populations. For example, of the 67 genera shared by USA1 chimpanzees and SGP doucs, 15 and 11 were significantly overrepresented or underrepresented in chimpanzees and doucs, respectively, relative to their matched wild populations. Of these genera, only 3 displayed significant differences in both USA1 chimpanzees and SGP doucs (1.2-fold more than expected, hypergeometric p -value = 0.234) (Figure 2G).
In addition to hypergeometric tests for significant overlap of ANCOM results between pairs of captive NHP populations, we also conducted regression analyses to test whether W statistics of ASVs and genera we associated between pairs of captive NHP populations. These analyses revealed qualitatively similar results to the hypergeometric tests. Specifically, ASV and genus W statistics tended to display significant positive relationships between pairs of conspecific NHP populations, but less significant and more variable relationships between pairs of heterospecific NHP populations (Table S5, Table S6).