Using gnotobiotic living food to study gut bacterial stability in zebrafish

The dynamics of gut microbial communities influence the health of humans and animals. Community composition is known to fluctuate strongly, but the factors that set the relevant timescales remain minimally studied due to the difficulty of generating controllable experimental systems, especially in which the role of food ingestion can be separated from the role of microbial input. To address this, we have developed a protocol to eliminate the innate bacteria in the micro-animal rotifers and use them as a nutrient source for zebrafish larvae, a model vertebrate organism. The method consists of UV light cycles to reduce the native bacterial population, keeping a fraction of motile rotifers that fish can capture. We examine and quantify the effect of rotifer ingestion on the population of a commensal bacterium, Enterobacter (EN), finding a decline with a timescale of days. We further examine the impacts of feeding on gut communities composed of up to five bacterial species. The use of bacteria-depleted rotifers enables studies of a range of physiological properties, such as fish size, intestinal transport mechanics, and overall metabolic activity, under conditions that can separate the impacts of feeding and bacterial presence.