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1 Yildirim et al
1Supplemental Information 2
3Supplementary Text S1
4 Our dataset included specimens from captive and wild species, including two
5groups of blood-line related vervets (three to eight generations removed): one group is
6maintained at the Wake Forest Primate Center (WFPC) and one group is free-ranging in
7St. Kitts, respectively. The vervets housed at WFPC were fed a typical American diet
8(TAD, lab diet 5LOP; Supplementary Figure S7) over a six-month period prior to
9sampling. This gave us the unique opportunity to establish links among diet, captivity,
10and vaginal microbiome composition. Despite these significant differences in diet and
11environment, no significant difference was observed between these two groups with
12regard to phylogenetic distribution (ANOSIM R=0.007, p=0.36; Figure 4A and 4B),
13taxonomic composition (Figure 2), or species richness (Table S1).
14 We compared the number of shared or unique OTUs among captive and wild
15representatives of vervets and baboons, excluding those reads that were observed less
16than three times overall. 212 OTUs were shared among vervet representatives, more
17than were unique to either group (wild specific = 97; captive specific = 210). Further,
18after normalizing OTU abundances to read depth, there were no significant differences
19in the relative abundances of any OTU between captives and wild vervets (p>0.01).
20Captive and wild baboons shared a similar number of phyla (n=242) as seen with the
21vervets but, in contrast, substantially more OTUs were unique to each group (wild
22specific = 1343; captive specific = 705). Based on abundance, however, only five OTUs
23were found to be significantly different between captive and wild baboons (p <0.01).
24These results were not influenced by sampling depth, as no significant difference was
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25observed between captives and wilds for any baboon (p>0.01). Comparisons of the wild
26and captive baboon representatives were confounded by species-distinctions and
27substantially greater geographical separation (both latitudinal and longitudinal) relative
28to the vervets.
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66 67Figure S1 68
69 70 71Supplementary Figure S1. A heatmap of the relative abundance of 16S rRNA gene sequences displayed at the 72taxonomic phylum level. The column z-score indicates differences between primate samples in terms of the relative 73abundances of bacterial phylotypes associated with the primate samples; white color indicates relative abundance of 74phylotypes having column average. Blue color tones represent relative abundances up to 4 standard deviation less than 75the average abundance, thus these phylotypes are significantly underrepresented in the sample; and red color tones 76representing relative abundances up to 4 standard deviation above the column average, ie, these phylotypes are 77significantly enriched in the sample. Samples and bacterial phylotypes were clustered using average linkage hierarchical 78clustering of a distance matrix based on Bray-Curtis distance.
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79 80Figure S2 81 82
83 84 85Supplementary Figure S2. Clustering of pairwise binary Jaccard similarities of genus level abundance 86distributions between samples. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method was used in 87cluster analysis. Genus level percent abundances in Asymptomatic BV (ABV) and symptomatic BV (SBV) samples were 88recently published (Ravel et al. 2013); species level assignments were binned in genus level taxonomic hierarchy (genus 89level relative abundances can be found in supplementary Tables S5) 90
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91Figure S3 92
93 94 95Supplementary Figure S3. Clustering of pairwise binary Bray-Curtis similarities of genus level abundance 96distributions between samples. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method was used in 97cluster analysis. Genus level percent abundances in Asymptomatic BV (ABV) and symptomatic BV (SBV) samples were 98recently published (Ravel et al. 2013); species level assignments were binned in genus level taxonomic hierarchy (genus 99level relative abundances can be found in supplementary Tables S5 100
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101 102Figure S4 103
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106 107Supplementary Figure S4. Kernel density plot of Pearson Correlations of phylogenetic 108distance matrices obtained from primate host and vaginal microbiome (>450,000 109iterations). 110
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118Figures S5A-S5J
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149 157 150 158 162 159 163 160 164 161 165 166 167 168 169 170Supplementary Figure S5A to 5J. Effect of socio-ecological factors on diversity of 171vaginal microbiome estimated by Shannon index. Sex related factors such as female 172promiscuity, mating group size and male testes mass significantly contribute to 173increasing diversity (p < 4.356x10-05, p < 2.976x10-06, p < 4.4x10-04, respectively). In 174contrast, group size and gestation time were found to be associated with decreased 175diversity (p < 2x10-2, and p < 7.7x10-3, respectively). A- Baculum length; B- Body size; 176C- Gestation time; D-Group size; E- Home range; F- Mating group size; G-Neonatal 177size; H- Promiscuity, I- Swelling; J- Testes mass 178 179 180 181 182 183 184 185 186
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187 188 189 190 191 192Figure S6 193 194
195 196 197 198Supplementary Figure S6. Variation in beta diversity among NHPs and humans 199(measured as the average Bray-Curtis dissimilarity from individual samples to their 200group centroid). Bw-Yellow Baboons, Bc-Olive Baboons (captive), Ch-Chimpanzees, 201Hm-Humans, Lm-Lemurs, Hw-Black howler monkeys, Mb-Mangabeys (captive), RC- 202Red Colobus, Vc-Vervets captive, Vw-Vervets wild 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
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220Figure S7.
221 222 223 224Supplementary Figure S7. Ingredients in Typical American Diet (TAD) used to feed 225captive primates. The diet mimics a typical American diet by containing a mixture of 226animal- and plant-derived protein sources, unsaturated and saturated vegetable and 227animal-derived lipids, and as a mixture of simple and complex carbohydrates. 228 229
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