Date of Award

August 2020

Document Type


Degree Name

Master of Science (MS)


Biological Sciences

Committee Member

Christopher L. Parkinson

Committee Member

Anna M Seekatz

Committee Member

Barbara Campbell


The gut microbiota encompasses the microbial life present in animal digestive tracts, collectively termed the microbiome. These microbial communities are highly adapted to their environment and host, providing beneficial functions not encoded by the host genome. However, there is a lack of gut microbiome studies on wild, non-model organisms; because of the importance of microbiomes in host evolution, it is critical to understand how environment and host alike shape indigenous microbes in wild animal populations. Rattlesnakes (Crotalus and Sistrurus) provide a useful system to study microbiota differences due to their unique digestive process and locally adapted venoms, which function in prey capture/digestion and predator defense. Here, we use 16S rRNA gene sequencing to investigate factors that influence the microbiota of snakes (n=21) over time from five species in the genus Crotalus (the Mojave (C. scutulatus), Western-Diamondback (C. atrox), Prairie (C. viridis), Tiger (C. tigris), and Black-Tailed (C. molossus) Rattlesnakes). We compared the gut microbiota between species that possess different venom types to investigate whether venom type is playing a role in microbial selection. We also tracked changes in the gut microbiota over time from the wild to captivity and in response to digestion. Across species, the most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Fusobacteria, similar to previous reptile gut microbiome studies. Using beta diversity metrics, we observed that snakes harbored a gut microbiota that was more similar to themselves and their species than to geographic location. However, we observed 62 differentially abundant Operational Taxonomic Units (OTUs) between snakes with different venom types. Snakes also displayed higher levels of variation in the wild compared to during captivity, losing a substantial portion of OTUs (43%) post-captivity. This loss was sustained in captivity, where snakes gained new OTUs (42%). Post-feeding, we also observed a peak in species diversity. In conclusion, we found that the gut microbiome of southwestern rattlesnakes is distinguishable by different venom types, is more diverse in the wild than in captivity, and is influenced by digestion.



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