HSSs reveal reproducible and host-species specific humanization of microbial genera in captive NHPs
Identifying differentially abundant ASVs and genera between matched wild and captive populations can reveal the effects of captivity on specific constituents of the NHP gut microbiota. However, these analyses alone do not provide information about the extent to which specific microbial clades within the captive NHP gut microbiota are humanized. Here, we define humanization of a microbial clade in a captive NHP population as the replacement of endogenous ASVs in the clade (i.e., ASVs found in wild NHP populations) by ASVs found in humans or the parallel absence from captive NHP populations and humans of ASVs in the clade found in wild conspecific NHP populations.
To assess the degree of humanization for each gut microbial clade in each captive NHP population, we tested whether the ASV-compositions of individual microbial genera in captive NHPs were more similar to those of the genera in humans (i.e., humanized) or to those of the genera in wild living conspecific individuals. These analyses allowed us to identify microbial genera in each captive NHP population whose endogenous host-species specific ASVs (i.e., ASVs private to wild conspecific hosts) displayed evidence of loss or of replacement by ASVs found in humans. We developed a statistic, Host Specificity Score (HSSs) (Materials and Methods), which can be calculated for any microbial clade or taxonomic rank of arbitrary phylogenetic depth. Here, we calculated these scores at the level of microbial genus, which was the finest-scale taxonomic resolution allowed by the 16S rDNA amplicon sequences in our dataset. Log-transformed HSSs are normally distributed around 0 and provide a quantitative ranking of the degree of humanization for all microbial genera in the gut microbiotas of a captive population, with lower scores indicating a greater degree of humanization. Log-transformed HSSs >0 indicate the ASV composition of the genus is more similar between captive primates and wild-living conspecifics than between captive primates and humans. Conversely, log-transformed HSSs <0 indicate that the ASV composition of the genus is more similar between captive primates and humans than between captive primates and wild-living conspecifics. Humanization of the ASV composition of a microbial genus in a captive NHP population, as indicated by a negative HSS, could be underlain by the loss of ASVs found in wild conspecific NHPs but not found in humans or the gain of ASVs found in humans but not found in wild conspecific NHPs.
Calculating HSSs for each microbial genus for each captive NHP population indicated that some genera in the captive NHP gut microbiota were humanized, whereas others were retained from the wild. An example of a bacterial genus that was humanized in captive chimpanzees in the United States (i.e., the genus Collinsella ) is shown in Figure 3A. An example of an archaeal genus that was retained from the wild in captive chimpanzees in the United States (i.e., the genusvadinCA11 ) is shown in Figure 3B. A list of all microbial genus-level HSSs for each captive NHP population are shown in Table S2.
Comparing HSSs between pairs of captive primate populations indicated that no microbial genus was humanized in every NHP population (Table S7). However, replicate captive populations of the same species displayed highly consistent genus-level patterns of gut microbiota humanization. The HSSs between two independent captive populations of chimpanzees were significant positively associated (R2= 0.82; p -value = 5.51e-24), as were the HSSs between two independent captive populations of doucs (R2 = 0.8;p -value = 8.46e-18). In addition, the HSS of chimpanzees were significantly associated with those of gorillas (R2 = 0.16; p -value = 0.000871 and R2 = 0.25;p -value = 1.05e-05), but not with those of doucs (Figure 4). Similar results, in which no genus displayed evidence of humanization in all captive NHP populations but replicate captive populations of the same NHP species displayed similar patterns of humanization of microbial genera, were observed in analyses of a related statistic, Microbiota Convergence Scores (MCSs) (Supplementary Materials and Methods, Figure S4, Table S8). Heatmaps of HSSs and MCSs of taxa found in all captive NHP populations are presented in Figure S5. Qualitatively similar results, in which HSSs and MCSs were significantly positively associated between conspecific captive NHP populations but tended to be not associated or negatively associated between heterospecific captive NHP populations, were observed in analyses based on data from the American Gut Project (McDonald et al., 2018) (Supplementary Materials and Methods; Table S9 and S10).