Multidisciplinary

Significance Gastrointestinal symbionts of organisms are important in the breakdown of food for the host, particularly for herbivores requiring exogenous enzymes to digest complex polysaccharides in their diet. However, their role in the digestion of algae in marine piscine herbivores remains unresolved. Here, we show that the diversity of food sources available to herbivorous surgeonfishes is directly linked with the genetic makeup of their enteric microbiota. Importantly, the genomic blueprint of dominant enteric symbionts belonging to diverse Epulopiscium clades differs according to the host diet. Thus, the acquisition of a unique enteric microbiota specialized to their diets likely shapes the nutritional ecology of piscine herbivores, in turn facilitating the coexistence of a high diversity of marine species within coral reefs.