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.