DIETARY AND STRUCTURAL SHIFTS IN FISH GUT MICROBIOME

The digestive tract of vertebrate is associated with complex assemblages of microorganisms which are believed to contribute to their host’s functioning. Current information on gut microbiota composition and function is derived primarily from mammals, where it has revealed associations between microbial composition and host diet, anatomy and phylogeny. However, information on similar associations in fish, which is the most diverse and ancient vertebrate lineages, is limited. Few studies have shown that dietary ingredients can potentially select for different microbes within the gastrointestinal tract. In addition, fish gastrointestinal tract exhibits regional specialization along the rostral–caudal axis similar to the mammalian gut. Thus, it may be expected that the bacterial taxonomic composition of the various parts in fish would also be different. In the present work, next-generation sequencing was used in order to describe the bacterial community composition along the gastrointestinal tract of the carnivorous European sea bass Dicentrarchus labrax. Fish were administered with diets containing different levels of macronutrients (protein and fat). Microbial communities of the three main parts of the gastrointestinal tract, pyloric caeca, midgut and hindgut, were characterized by sequencing of the 16S rRNA genes. The results show a unique spatial distribution of the microbiome composition across the gastrointestinal tract, which is reinforced by diet. These findings, suggesting ecological niches across the fish gastrointestinal tract and their functional meaning, will be discussed in the context of host-microbiome interactions.