Conclusions
The community structure and composition of the microbiome varies depending on tissue type in the gastrointestinal and reproductive tracts of S. virgatus. While environmental factors have been known to cause regional variation in the gut microbiome, in this case there is evidence (Bunker et al., in review) that the difference is due to selection for cloacal microbes that increase host fitness, specifically via the transfer of antifungal microbes from mother to eggshells during oviposition. Additionally, although cloacal swabs and fecal samples are generally accepted methods of sampling the microbiome, neither was able to fully represent the entire community of the gut, and the two methods provided unique results. The cloacal swabs adequately sampled communities of cloacal and lower intestine tissues, whereas the fecal community sampled a distinct community not representative of any sampled gut tissue. We also found that fecal microbes do not seed the cloaca after defecation; while there were few differences between swabs taken before and after defecation overall, there was still evidence of possible fecal contamination of individual swabs. Care should be taken to account for this in future research. Studies that intend to use cloacal swabs or feces as a proxy for the gut microbiome must think carefully on whether these methods will accurately answer their question, or whether a specific, region-based study would be more appropriate. In this study, biologically relevant variation in the microbiome could have been masked due to sampling method.