The indigenous microbiota (or microbiome) of fin-fish is of topical interest in fish health and nutrition research, as parallel studies in human and animal models have highlighted the importance of a balanced microbiota in maintaining host health. The microbiota is composed of an ecological community of commensal, symbiotic and pathogenic microorganisms and includes bacteria (which are the dominant microbes), archaea, viruses, protozoa and fungi. The fin-fish gut microbiota contributes to digestion, nutrient acquisition and the immune response, which can in turn affect growth, reproduction, development and vulnerability of the host to disease. Knowledge of the gut microbiome has been shown to be of relevance for the identification of both favourable and dysbiotic (or pathogenic) phenotypes and offers the prospect for downstream manipulation for optimising host health and nutrition and consequentially the productivity of farmed species.
In this study, the active components of the gut bacterial microbiome of wild Yellowtail Kingfish (YTK) were characterised and compared to the microbiome of the surrounding water and the gut of farmed YTK exhibiting signs of an underlying disease condition. The ability to manipulate the gut microbiome of farmed poor-performing YTK was then explored in a trial undertaken at the SARDI pool-farm facility (West Beach, South Australia, Australia) using antibiotics and faecal microbiota transplantation (FMT), with inoculum collected and prepared from ‘healthy’ farmed YTK donors (n=102 individuals).
Differences were observed in the bacterial assemblages of the surrounding water environment and the gut of wild and farmed YTK, highlighting that YTK can select, regulate and maintain their own environmentally-independent communities. Differences were also observed between the gut microbiome of wild and farmed YTK that were exhibiting signs of an underlying disease condition. This was characterised by reduced microbial species richness, diversity and evenness, and the occurrence of one or more dominant bacterial taxa, highlighting a shift towards a dysbiotic state with potential loss of functionality.
Following antibiotic treatment and FMT, using inoculum prepared from ‘healthy’ on-farm YTK donors and administered via gavage, an increase in bacterial taxonomic diversity and species evenness was observed two days post inoculum in some poor-performing YTK recipients, attributed to an increase in bacterial phyla and decrease in the abundance of potential opportunistic pathogens. Differences were also observed at 8 days post inoculum, followed by a reversion to the ‘normal’ state at 15 days post inoculum. These results suggest that the gut microbiome of poor-performing YTK can be modulated to potentially improve health outcomes, but requires further investigation and optimisation of the approach to allow for more longer-term favourable health outcomes.