Sustained changes in digestive physiology and microbiome across sequential generations of zebrafish fed different diets

Alterations to ratios of protein and fiber in an organism's diet have been shown to structurally and functionally alter its individual digestive physiology. However, it is unclear how these dietary changes may affect phenotypic changes across generations. We utilized feeding trials, morphological analyses, enzyme activities, and 16S rRNA sequencing of the gut microbiome of zebrafish (Danio rerio) to determine how variations to fiber and protein concentrations, kept consistent across sequential generations, affect phenotypic changes. Our results show that Parental (P) and first generation (F1) fish did not differ from each other in terms of their intestine length, intestine mass, enzyme activity levels, and microbial community composition for any of the three experimental diets (high-protein/low-fiber, moderate-protein/fiber, and low-protein/high-fiber). However, each of the three experimental diets for the P and F1 fish, as well as the ancestral diet fish, did have distinct microbial community structure from one another. This indicates that there is a strong dietary effect on digestive physiology and gut microbial community and that these effects are consistent when the diet is kept homogenous across generations. •Effects of diet on gut structure and function persist among generations.•Microbiome changes were also consistent with diet.•Overall microbiome changes still constrained by starting community.•Largest microbiome changes were the abundance of species already present.•Some rare species' abundance increased with diet treatments.