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

Abstract

Microbial diversity and community function are related, and can be highly specialized in different gut regions. The cloacal microbiome of Sceloporus virgatus provides antifungal protection to eggshells during oviposition – a specialized function that suggests a specialized microbial composition. Here, we describe the S. virgatus cloacal microbiome from tissue and swab samples, and compare it to tissue samples from the gastrointestinal (GI) tract and oviduct, adding to the growing body of evidence of microbiome localization in reptiles. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these microbial communities and whether feces might “seed” the cloacal microbiome or impact the accuracy of cloacal swab sampling. We found that different regions of the gut had unique microbial community structures. The cloacal community, in particular, showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues, but fecal samples had much higher diversity and a distinct composition (62% Firmicutes and 39% Lachnospiraceae) relative to all gut regions. Finally, we found that feces and cloacal swabs recover different communities, but cloacal swabs may be contaminated with fecal matter if taken immediately after defecation. These results serve as a caution against the assumption that fecal samples provide an accurate representation of the gut, and that although cloacal swabs can reflect a portion of the lower GI tract microbiome, they may also result in a mixed community of gut and fecal microbes.