Meeting Abstract
Gut microbial communities play critical roles in the biological functions of their host, such as mediating nutrient absorption, digesting food components the host cannot, and offering protection against enteric pathogens. Extensive research on gut microbial communities has been conducted on mammals, including humans and rodents, but much less work has been done in birds. Furthermore, much of the research on host-microbe interactions make use of fecal samples and rectal swabs as a proxy for intestinal samples, which can be difficult to obtain directly. However, little is known regarding overlap between the microbial communities of the gut, feces, and swabs, which limits interpretability of results based on swabs and fecal samples. To address this gap in knowledge, we compared the microbiota from five sample types – proventriculus, small intestines, large intestines, cloacal swabs, and feces – across individual Zebra Finches (Taeniopygia guttata) housed in constant conditions with a standardized diet. We compared diversity and community composition through 16S rRNA sequencing. Our results show that microbial communities from both cloacal swabs and feces were distinct from proventriculus and small intestinal samples, but indistinguishable from large intestinal samples, indicating that these non-lethal samples may be useful proxies for large intestinal communities. Additionally, cloacal swabs were better than fecal samples in capturing individual variation, suggesting cloacal swabs may be particularly useful in experiments with a repeated measures design. Gaining insight into noninvasive sampling techniques for passerines has implications for studies of gut microbial diversity and abundance in wild bird populations. Further, reliable non-lethal sampling is necessary for experiments where repeated sampling is required.
