Natural essential oils in aquaculture. How essential oils affect the stress factors and intestinal microbiota of rainbow trout (Oncorhynchus mykiss)?

Maintaining animal health trough a healthy diet is one of the most important factors in fish farming. Gastrointestinal disorders, can impact importantly the survival, growth, and health of farmed rainbow trout. Essential oils are well-known as antioxidant, anti-microbial and anti-inflammatory molecules. In this experiment we evaluated the effects of essential oils supplementation in fish diet on the gut microbiota of farmed trout. We fed an equal number of fish (from an “all female” stock), in three independent rearing tanks: the control group received the standard diet, in the two other groups standard diet was supplemented with 0.02% and 0.03% GrowNat™/MixOil™. A total of 58 fecal samples were collected at seven different times (T0-T6) for a total of 32 weeks. The fecal microbiota was investigated by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and 16S rRNA gene pyrosequencing (454 FLX Roche). Hierarchical clustering analysis of the ARDRA band profiles shows a clear separation between control and treated samples in particular on T6 indicating a possible effect of the supplementation in modulating gut microbiota. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed differences between treated and untreated fish. Finally our results show the potential of this animal model to study the host–microbiota interactions, using a metagenomics approach to evaluate the interaction of environment, genetics, and microbiota in health and disease.