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).