Host Specificity Scores and Microbiota Convergence Scores
We developed a statistic, the Host Specificity Score (HSS), to assess
microbial genus-specific patterns of humanization in captive NHP gut
microbiotas. This statistic was defined for a microbial genus in a
captive NHP population as the mean binary Sorensen-Dice dissimilarity of
the ASV composition of the genus between the captive NHP population and
humans divided by the mean binary Sorensen-Dice dissimilarity of the ASV
composition of the genus between the captive NHP population and a
conspecific wild-living population. HSSs of >1 indicate
that the ASV composition of the microbial clade is more similar between
captive NHPs and wild-living conspecifics than between captive NHPs and
humans. In contrast, a score of <1 indicates that the ASV
composition of the microbial clade is more similar between captive NHPs
and humans than between captive NHPs and wild-living conspecifics.
In order to calculate HSSs, we split the ASV table containing all
samples by microbial genus and calculated genus-level mean binary
Sorensen-Dice (BSD) dissimilarities between captive NHPs and wild
conspecifics as well as between captive NHPs and humans. ASVs without
taxonomic assignments and microbial genera detected by fewer than 5
reads were excluded from downstream analyses. Asin the ANCOM analyses
described above, captive chimpanzees retired from the New Iberia
Research Center (USA2) were paired with wild chimpanzees from Tanzania
(TZA) and zoo captive chimpanzees (USA1) were paired with wild
chimpanzees from the DRC (DRC). The HSS for each genus was calculated
and log-transformed for regression analyses.
In addition to HSSs, we also calculated for each microbial genus in each
captive NHP population a Microbiota Convergence Score (MCS). This index
measures the degree to which the ASV composition of the genus in a
captive NHP has converged with the ASV composition of the genus in
humans relative to the ASV composition of the genus in the wild
conspecific NHP population. Descriptions of these analyses are presented
in the Supplemental Materials and Methods. For both HSSs and MCSs,
heatmaps were calculated in R using heatmap.2 with the parameter
scale=“col” and default settings. In addition to analyses based on the
Yatsunenko et al. (2012) dataset, we also calculated per genus HSSs and
MCSs for each captive NHP population using an American Gut dataset
(McDonald et al., 2018) (Supplementary Materials and Methods). All
scripts used to calculate HSSs and MCSs are publically available at
github.com/CUMoellerLab/Houtz_etal_2021-NHP_microbiome.