The functional role of the fish microbiome

Abstract

Aquaculture is the fastest growing sector of agriculture, currently producing more than half of all seafood. Within Australia, yellowtail kingfish (Seriola lalandi) is an emerging fish species farmed in temperate waters. While the production of this species is in constant growth, the development of this industry is not without hurdles. For instance, diseases associated with the mucosal surfaces of the fish (e.g. gut enteritis - an inflammation of the gastrointestinal tract) are a recurrent issue in the production of this species. However, the underlying mechanisms inducing this gut inflammation remain poorly understood. New research has elucidated the importance of microbial communities in mucosal surfaces (microbiota) that may play a key role in this disease. These mucosal surfaces (comprising the gut, skin, gill and olfactory organs) support important functions for the host including digestion and nutrient uptake, osmoregulation and recycling waste products, provide the first line of defence against potential pathogens, and form a barrier – along with the host microbiota. Most fish mucosal diseases are linked to the disruption of these microbial communities, which no longer supports the wellfunctioning of these mucosal surfaces and therefore influence fish health. Within this thesis, I synthesise our current understanding of the fish microbiota, in particular in a health and disease context (Chapter I). I also explain how this wealth of information can be of particular value for the aquaculture industry by proposing new prospects to improve the fish resilience to disease. Using the yellowtail kingfish as species model, I explore both changes in the fish microbiota across the gut and skin mucosal surfaces and the evolution of the fish immune response during gut enteritis (Chapter II). By doing so, I also investigate important host-microbiota interactions to further understand the interplay between the fish immune system and its microbiota during disease. Of particular note, I found significant gene expression changes (e.g. upregulation of cytokines related genes) and microbiota perturbations (e.g. loss of diversity) in the skin of fish at the early state of the disease, revealing the sensitivity of this mucosal tissue in response to a gut disease. In Chapter III, I explored the impacts of novel treatment options by modulating the fish microbiota using faecal microbiota transplantation (FMT) in conjunction or in replacement of antibiotic treatment to re-establish a more balanced and healthy fish gut microbiota. This also shed light on the process of microbial repopulation following antibiotic exposure, a feature well under studied though paramount for the successful recovery of the host. In this study, antibiotics greatly influenced the fish gut microbiota and was marked by a significant decrease in diversity, accompanied by an increase in the relative abundance of an uncultured Mycoplasmataceae sp. in the antibiotic treated fish. The effect of the FMT treatment appeared to vary substantially between individuals, and was associated with stark differences in bacterial diversity, suggesting that modulation of the gut microbiota can only be induced in some individuals and for a short time period. In the final Chapter, I develop a new laboratory protocol using PMA to assess microbial viability in the fish gut microbiota. Such information is particularly relevant when investigating the influence of the microbiota in health and disease to better characterise the activity and likely role of these microbial communities, a feature currently overlooked with the gold standard 16S metabarcoding approach. Using this approach, I found that PMA treatment reduced the microbial diversity and richness from both digesta and mucosal gut samples, as well as induced a loss of important bacterial members considered as beneficial (e.g. lactic acid bacteria). In essence, my research aimed to explore the involvement of the fish microbiota in the health and fitness of the host and improve our understanding of host-microbiota interactions. Such knowledge would ultimately allow us to better modulate the fish microbiota and develop new treatment options. Overall, my thesis contributes to fish health research by providing context and perspective of the fish microbiota. Even though much more effort is needed, I aimed at producing translational research by demonstrating the importance of such studies for the aquaculture industry to potentially enhance fish resilience to infection/disease and ultimately improve current production systems.