Fig. 1

The cotton rat microbiome as examined with 16S rRNA gene sequencing. a Study design includes 10 male cotton rats from both S. fulviventer and S. hispidus. Feces were taken across a 111-day period, while sample swabs of nose, ear, skin were taken at day 95. b Site richness (Obs. OTUs) and c alpha diversity (Shannon index) metrics at the OTU level indicate that the S. fulviventer microbiome was significantly richer and more diverse across all sites. Other alpha-diversity metrics (Chao1, Simpson) are shown in Figure S2. d Ordination of samples (Bray-Curtis dissimilarities, OTU level) reveals distinct microbiota compositions between feces and external sites regardless of species. Color and shape of each point indicate the species and body site sampled. e-f Zoomed-in beta-diversity relationships between e fecal microbiomes and f external microbiomes. The color of each point is matched to each individual cotton rat. Statistical testing was performed using PERMANOVA between species. Each site was plotted separately in Figure S3. ns = P > 0.05, * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001