Characterisation of the gut microflora in rainbow trout fry (Oncorhynchus mykiss) using deep-sequencing

For many years it has been known that the bacterial microflora in the gut of warm-blooded animals exists in harmony with the host and exert various beneficial effects on the health by their metabolic activities. Hence, the gut microbiota has a high importance for the animal. In many studies from e.g. humans and the pig mapping of the bacterial flora from the gut have shown dominance by some specific bacterial groups, and this bacterial profile is termed as a ‘core microbiota’. For lower vertebrates like fish mapping of the bacterial flora in the gastrointestinal system is to date a relatively new research field and previous studies have mainly been done on bacterial species that can be cultured or by classical molecular techniques like T-RFLP and DGGE. In the last recent years deep-sequencing techniques have enabled sequencing and mapping of entire microbial communities from for instance an environmental sample or a tissue / fecal sample from an animal. These metagenomic studies have provided new and deeper insight into the microbial ecology and the influence of the microbiota in warm-blooded animals.
In this study next-generation sequencing of the 16S rDNA gene on the Illumina HiSeq platform was used to examine the composition of the microbial flora in the gut of rainbow trout (Oncorhynchus mykiss) fry. The fish were examined before and after first-feeding and after administration by commercial probiotic lactobacilli to the feed.