Validity of fecal sampling for characterizing temporal variation in threespine stickleback's gut microbiota

Diverse microbial communities associated with the guts of their hosts are crucial for many aspects of their hosts physiology, ecology, and evolution. The gut microbiota has been characterized for a broad range of species across the animal kingdom. Yet, for many host species we still dont have a good understanding of whether non-lethal sampling (e.g., fecal matter) can accurately capture the diversity of gut-associated bacterial communities, as estimated from lethal sampling of intestinal tissue. We further lack knowledge on whether such non-lethal sampling methods are suitable for studying temporal gut microbiota dynamics. Here, we addressed these questions in threespine stickleback fish, a model system in evolutionary ecology, by comparing bacterial communities based on 16S rRNA gene sequencing from intestinal tissue and feces. Despite some differences in community composition between the two sample types, we show that bacterial communities of feces and intestinal tissue largely overlap. Further, we were able to detect consistent and significant changes of fecal bacterial communities associated with an experimental diet shift. These results suggest that fecal sampling represents an adequate non-lethal method to characterize the gut microbiota of threespine stickleback. This allows for studying temporal gut microbiota dynamics at the individual level, which increases opportunities for future experimental gut microbiota research.