Biogeography of the skin-associated microbiome across body regions of the Sierra Nevada yellow-legged frog (Rana sierrae)

Sonia Ghose, Evolution and Ecology, UC Davis, Davis, CA and Jonathan A. Eisen, Medical Microbiology and Immunology, University of California, Davis, Davis, CA; Evolution and Ecology, University of California, Davis, Davis, CA; Genome Center, University of California, Davis, Davis, CA

Background/Question/Methods
The Sierra Nevada yellow-legged frog, Rana sierrae, has been driven close to extinction in part by the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). Skin-associated microbes can inhibit Bd infection, and studies have shown that overall microbial community structure may result in distinct disease outcomes for the host. We know from other animal systems that there can be large variation in the microbiome associated with different body parts of the host organism and studies suggest that Bd infection in many frogs is primarily limited to the ventral abdomen, hind-legs, and hind-feet. For frogs, microbiome differences associated with body regions could be relevant to how Bd interacts with and infects different parts of the body. Here we address two main questions: (1) Is the microbiome heterogenous across distinct regions of the skin of R. sierrae individuals? and (2) Do differences in community structure correspond to body regions that Bd infects preferentially? We collected skin swabs from 10 body regions of R. sierrae individuals (n=13) at the San Francisco Zoo. We sequenced the bacterial 16S rRNA gene and identified amplicon sequence variants (ASVs) to look for differences in the microbiome composition across body regions.
Results/Conclusions
We found that the microbiome composition differed significantly across regions of the skin, and that this finding was largely driven by significant differences in the hind-feet and back compared to most other body regions. The two families in highest relative abundance on the skin were the Burkholderiaceae (Phylum Proteobacteria) and the Rubritaleaceae (Phylum Verrucomicrobia), and these families switched off as the dominant group depending on the region of the body. For example, the Rubritaleaceae was dominant on the back and snout, while the Burkholderiaceae was dominant on the abdomen, inner hind-limbs, and hind-feet. We also identified ASVs that showed logarithmic fold change in abundance between body regions. Preliminary results indicate that many of these ASVs are members of the Burkholderiaceae and Rubritaleacae, providing confirmation for the relative abundance results. Some members of the Burkholderiaceae are known to inhibit Bd through production of the anti-fungal metabolite violacein, and the dominance of this group on the ventral surfaces and feet supports our hypothesis that specialization of the microbiome may correspond to regions where Bd infects the skin. These findings may guide future investigations of Bd-frog-microbiome interactions and could inform conservation strategies that take microorganisms into account.