Complex assemblages of microorganisms are associated with the digestive tract of vertebrates contributing 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, mammals constitute less than ten percent of vertebrate species and information on similar associations in more diverse and ancient vertebrate lineages such as fish is limited. The 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 gastrointestinal parts of 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 European sea bass Dicentrarchus labrax, an economically important carnivorous farmed species. Microbial communities of the three main parts of the gastrointestinal tract, pyloric caeca, foregut and hindgut, were characterized by sequencing of the 16S rRNA genes. The results show a unique and stable spatial distribution of the microbiome composition across the gastrointestinal tract, which is resilient to perturbation of diet and antibiotic treatment. These findings, suggesting ecological niches across the fish gastrointestinal tract and their functional meaning, will be discussed in the context of host-microbiome interactions.
