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Fish-microbe interactions play an important role in the feed digestion, nutrient absorption, immune system development and disease susceptibility of the host. Therefore, a healthy and stable gut microbiota contributes to the growth and overall health status of the host. To improve the microbial management in aquaculture, it is important to know the main the factors governing fish gut microbiota development and to understand to which extent the induced changes in gut microbiota composition affect fish performance.The aim of this thesis was to modulate fish gut microbiota by culturing the fish under different rearing conditions and by dietary supplementation of feed additives, with the expectation to improve the growth of the fish and gut microbiota homeostasis.The recent development and challenges faced by the aquaculture industry are summarized in Chapter 1. To improve the productivity and sustainability of aquaculture, the importance of environment-microbes-host interactions is highlighted. Furthermore, the factors mainly affecting fish gut microbiota composition and dynamics are reviewed, providing potential strategies to modulate fish gut microbiota. Besides, the analytical method of gut microbiota and the model species used are described. This chapter ends with an overview of the experimental work done during the thesis.In Chapter 2, the effect of different rearing conditions on the initial colonisation of the fish gut microbiota was investigated. To do so, Nile tilapia embryos were incubated and the hatched larva were cultured for 26 days in a flow-through system (FTS) or a recirculating aquaculture system (RAS) or RAS with dietary probiotic Bacillus subtilis supplementation. FTS showed significantly lower survival than those in RAS and RASB, while no differences were observed in fish growth and the apparent feed conversion ratio between treatments. Different treatments resulted in different gut microbiota compositions, which strongly correlated with the survival rate and standard body length at harvest.in Chapter 3, the effect of in-situ biofloc (LW) and dietary supplementation of ex-situ live (LF) or dead biofloc (DF) on fish gut microbiota composition and growth performance was compared to a biofloc-free control treatment. We identified a core gut prokaryotic community among all treatments. The relative abundance of the core community was significantly influenced by LW treatment, while the DF or LF treatments only caused minor changes on taxa not belonging to the core gut microbiota. The distinct microbial community in the biofloc water was associated with the modulatory effect of LW on tilapia gut microbiota. A growth-promoting effect on tilapia was observed from the LW treatment, while DF and LF treatments had no effect on fish growth performance as compared to the control treatment. Our study highlights the probiotic effect of in-situ biofloc water, in contrast to processed biofloc which showed little nutritional or probiotic effect. Chapter 4 was designed to verify how dietary supplementation with probiotics and enzymes influence the nutrient digestibility and volatile fatty acid (VFA) content along the gastrointestinal tract and the microbial composition in the distal gut of juvenile Nile tilapia. We showed an increase in VFA content with probiotic supplementation in the proximal gut, and a decrease in lactate content with enzymes along the gut. Besides, enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. These results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability. Enzymes and probiotics supplementation had no effect on the gut microbial diversity of Nile tilapia, but enhanced microbial interactions according to network analysis. Such results, together with increased abundance of beneficial gut microbes such as Lactobacillus and Bacillus species, indicate positive impacts on fish gut health and contribute to a more stable microbial environment.In Chapter 5, we tested the legacy effect of early life rearing history on the gut microbiota succession. For this, we performed a 4-month study, during which Nile tilapia larvae were exposed during the first two weeks of life to different microbial environments (i.e. flow-through system and biofloc system), and thereafter, fish were reared during two consecutive 2-month periods, per period in a different RAS environment. In accordance with the results from chapters 2 and 3, we show that the early life rearing environment can have significant effects on fish performance, with the biofloc system leading to healthier gut microbiota compositions and better fish growth. We observed a temporal effect on the gut microbiota development with compositions gradually converging when fish were transferred to shared environments. Long-term effects on growth, nutrient digestibility, nitrogen and energy balances were not observed during later life. Despite that, interestingly, we show that early life exposure to different environments had a long-term effect on the gut microbial interactions, with more complex networks coming from fish exposed to the biofloc system during early life.In Chapter 6 the main results of this thesis are discussed and recommendations on the microbial management in aquaculture as well as future perspectives on fish microbiome research are presented. By comparing all the results from this thesis, we show that the gut microbiota of Nile tilapia is strongly affected by the rearing conditions during early life stage, with RAS and BFS resulting in a more stable gut microbiota, while FTS exhibiting large individual variation in gut microbiota composition. A microbial rich environment (BFS) or supplementation with probiotics can result in more species interactions in the gut microbiome and a better fish performance. A meta-analysis on all the gut microbiota data from all experiments shows a temporal effect and highlights the importance of fish age when comparing gut microbiota of Nile tilapia.Overall, this thesis highlights the significant impact of the early life rearing environment in aquaculture and its long-term effect on microbiome development and microbial interactions. We show high plasticity of fish gut microbiota during early life, which is ultimately shaped by the environment and dietary additives (e.g. probiotics and enzymes), resulting in distinct fish survival, growth and nutrient digestibility. The research provides strategies to manipulate the fish gut microbiota composition. Immunological and fish health research are suggested to further improve our understanding of the role of microbiota in aquaculture rearing systems. |
