Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces

Microbial diversity and community function are related, and both can be highly specialized in different regions of the gut. The cloacal microbiome of Sceloporus virgatus lizards has low diversity, suggesting a specialized function, and is known to transfer antifungal microbes to eggshells during oviposition. We hypothesize that the cloacal microbiome is distinct from other parts of the digestive and reproductive systems. Here, we compare the microbiome of tissue samples from the cloaca, lower intestine, upper intestine, and oviduct. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these tissues, and whether feces might “seed” the cloacal microbiome. We found that the upper intestine and oviduct had unique microbial communities, while the lower intestine and cloaca had similar communities with lower diversity indicative of regional specialization. The cloacal community, in particular, showed extreme specializ...