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.