Sex predicts gut microbiota variations in wild yellow baboons

Microbiota research in wildlife has mainly focused on the investigation of extrinsic (e.g., diet, habitat) rather than intrinsic factors (e.g., sex, genetic background) affecting variation in host gut communities. However, since male and female mammals often differ in dietary requirements, sex is likely to play a major role in gut microbiota variation. Here, we analyzed the bacterial and fungal communities of 34 faecal samples of the sexually dimorphic yellow baboon (Papio cynocephalus) living in two contrasting forest types (intact/protected vs. fragmented/disturbed) in the Udzungwa Mountains of Tanzania. Sex was determined for each sample (19 females and 15 males) using the marker genes SRY and DDX3X; these results were then combined with those from two amplicon-sequencing datasets focusing on bacterial (V3-V4 region of the 16S rRNA gene) and fungal (ITS1-ITS2) communities from the same samples. We found that females had gut microbiotas with a higher bacterial richness [Kruskal test; Shannon (alpha diversity): P = 0.010] and different composition [ANOVA; weighted Unifrac (beta diversity): P = 0.030] compared to males. Furthermore, forest type had a greater impact on females than males, such that the gut microbiotas of females from the two forests differed significantly in fungal composition [pairwise adonis test; Bray-Curtis: P = 0.02] and bacterial richness [pairwise Wilcoxon Rank Sum test; Shannon: P = 0.023], while those of males did not. Our results suggest that intrinsic biological factors should be carefully considered when investigating wild animal microbiodiversity, and that such intraspecific variation could impact the outcome of conservation actions.