Food-bacteria interactions in the zebrafish gut

The gut microbiota form a diverse and complex ecosystem that influences its host's health, development, and nutrition. Zebrafish have proven to be a valuable model for studying gut microbes, partly due to their optical transparency at early developmental stages, allowing the assessment of physical properties of bacterial communities such as aggregation state and motility. However, interactions between food and gut bacteria remain poorly understood and challenging to study in zebrafish. To address this, we developed a UV irradiation method to reduce the bacterial load in rotifers, a micro-animal used as a food source for zebrafish. We measured the stability of bacterial communities over several days of food ingestion, finding significant species-specific variations. To investigate whether these variations are driven by differences in bacterial aggregation in the larval gut, we use light sheet fluorescence microscopy to visualize rotifers within the gut, characterize their effects on gut motility, and measure transit times. Additionally, we assess the impact of rotifers on bacterial behavior and abundance, focusing on strains that exhibit high and low aggregation within the gut.