Discussion
Comparing multiple well-sampled wild and captive populations of
chimpanzees, gorillas, and doucs with humans allowed us to test for
reproducible effects of captivity on specific microbial lineages in the
gut microbiotas of non-human primate (NHP) species. Our results indicate
that captivity humanizes the primate gut microbiota, but that the
microbial taxa underlying this process of humanization vary
substantially and consistently among NHP species. No microbial ASV or
genus was significantly overrepresented or underrepresented in all
captive NHP populations relative to wild conspecific populations (Tables
S5, Table S6). Similarly, no microbial genus displayed evidence of
humanization, defined by Host-Specificity Scores (HSSs), in every
captive NHP population (Table S7). In contrast, we observed striking
consistency of the effects of captivity on gut microbiota constituents
between replicate captive NHP populations of the sample species. The
same ASVs and genera reproducibly shifted in relative abundance in
replicate captive conspecific NHP populations relative to matched wild
NHP populations (Table S5, Table S6, Figure 2). Similarly, most
microbial genera displayed reproducible signatures of humanization in
replicate captive conspecific NHP populations: the HSSs of one captive
population predicted >80% of the variation in HSSs in the
other captive population in both NHP species for which replicate captive
populations have been sampled (i.e., chimpanzees and doucs) (Figure 4,
Figure S4). The consistency of per-genus measures of humanization in
replicate conspecific captive NHP populations was also observed in
analyses based on human gut microbiota data from the American Gut
Project (Supplementary Materials and Methods; Table S9-S10). Previous
results have shown that the gut microbiotas of monkeys are humanized in
captivity (Clayton et al., 2016); our results demonstrate that this
humanization also occurs in captive ape populations. In addition, our
results indicate that the humanization of the gut microbiota is
underlain by distinct sets of microbial lineages in captive NHP
populations of different species, but that the sets of microbial
lineages that are humanized by captivity can be predicted with high
accuracy by the species identity of the NHP population.
Interestingly, certain microbial taxa showed consistent patterns of
humanization between replicate captive NHP populations of the same
species but opposite patterns between replicate captive NHP populations
of different species. For example, Oribacterium andRoseburia , genera within the Lachnospiraceae, showed evidence of
humanization, based on HSSs, in both captive douc populations, but these
genera were robust to humanization in both captive chimpanzee
populations (Table S8, Figure S5).
The observations that different NHP species display discordant but
reproducible patterns of humanization of gut microbial lineages in
captivity raises questions about the mechanisms underlying this pattern.
One explanation is that each NHP species contains a distinct set of
microbial lineages that are better adapted to the gut environment of
their respective host species relative to the congeneric microbial
lineages found in humans. For example, microbial genera whose ASVs were
retained from the wild in captive NHP populations (i.e., genera
displaying a log-transformed HSS > 0) represent microbial
lineages that may, in captive NHPs, outcompete microbial lineages found
in humans. Discordance of per-genus HSSs between NHP species could arise
if the microbial lineages that outcompete congeneric lineages derived
from humans belong to different genera in different NHP species. In
addition, differences in diet may affect the process of gut microbiota
humanization in captivity, leading to discordance between species but
reproducibility within species. For example, previous work has shown
that global patterns of gut microbiota composition (i.e., alpha and beta
diversity) are more affected by captivity in folivorous NHP species than
in less dietary specialized NHP species (Frankel et al., 2019). Under
this scenario, differences in the degree of dietary shifts experienced
in captivity could lead to different effects on individual microbial
lineages and genus-level patterns of humanization between NHP species.
Our results highlight the importance of population-level sampling of
captive NHPs in order to identify specific gut microbial lineages most
affected by captivity. Studies of fewer numbers of captive individuals
per NHP species have statistical power to detect differences in alpha
and beta diversity between captive and wild gut microbiotas and have
yielded important insights into the effects of captivity on the gut
microbiota (Uenishi et al. 2007; Nakamura et al. 2011; Clayton et al.
2016; McKenzie et al. 2017; McKenzie et al. 2017; Tsukayama et al. 2018;
Frankel et al. 2019; Hale et al. 2019; Lee et al. 2019; Frankel et al.
2019; Campbell et al. 2020; Narat et al. 2020). However, identifying
individual microbial lineages or clades (e.g., ASVs or genera) that
display significantly different relative abundances between populations
requires sampling sufficient numbers of individuals to overcome high
false-discovery rates inherent in multiple testing. Our results suggest
that future studies focused on identifying specific microbial lineages
in the gut microbiota that are affected by captivity should when
possible prioritize replication at the level of host individual.
The statistics that we developed (HSSs and MCSs) provide quantitative
means to identify the specific clades of microbial lineages that display
the strongest evidence of humanization in captive hosts. HSSs and MCSs
can be applied to any microbial clade or taxonomic rank as well as any
captive population for which microbiota data from wild conspecifics are
available. In addition to captive populations, these statistics could
also be applied to identify humanized gut microbial taxa in animals
associated with humans in other contexts, such as urban settings or
other habitat disruptions that may affect the gut microbiota (e.g.,
Amato et al. 2013). In the case of captive NHPs, the identification of
individual microbial taxa that are repeatably humanized has important
implications for managing the health of captive hosts. Humanized
microbial taxa represent candidate contributors to gastrointestinal
dysbiosis in captive NHP populations, in particular if they are
reproducibly humanized in individuals that develop gastrointestinal
dysfunction (Amato et al. 2016). For example, the genusCollinsella was repeatably humanized in replicate captive
chimpanzee populations, and overrepresentation of this genus in the gut
microbiota has been associated with reduced fiber intake, insulin
resistance, and rheumatoid arthritis in human populations (Chen et al.
2016; Gomez-Arango et al., 2018; Mena-Vázquez et al. 2020). Similarly,Clostridium lineages were repeatably humanized in replicate
captive chimpanzee populations, and lineages from this genus are the
most common causes of gastrointestinal infections in humans (Smits et
al. 2016). The gut microbial lineages that are reproducibly humanized in
captive populations represent high priority for targeted culturing from
wild NHP populations. Culturing and biobanking representatives of these
microbial lineages from wild NHPs could provide opportunities to restore
the gut microbiotas of captive NHP populations.