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.