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The intestine and associated bacterial microbiota have a central role the physiology and homoeostasis of the host. The understanding of how farming conditions affect the intestine and associated microbiota of fish is the high importance to counteract the potential threats to health and welfare. Thus, this thesis aims to understand the role of stressful husbandry conditions on the intestine and associated microbiota of rainbow trout and Atlantic salmon. Within this context, the role of Pediococcus acidilactici as health promoter was also investigated Chapter 3 investigated the replacement of fishmeal by different plant protein ingredients in rainbow trout. The results of this chapter revealed that the effect of P. acidilactici on the microbiota of distal intestine in rainbow trout was dependent on the ingredients of the diet. The results also showed that the FM substitution induced major changes in the intestinal microbiota. Moreover, the modulation induced by plant-based diets on the microbiota varied according to the ingredients used. Chapter 4 studied the effect of dietary oxytetracycline in the distal intestinal microbiota of rainbow trout and the role of P. acidilactici to ameliorate the impact of antibiotic therapy. Experimental groups fed the diets with oxytetracycline had substantial changes in the distal intestinal microbiota including a decrease in the bacterial diversity. P. acidilactici did not ameliorate the effect of antibiotic therapy in the intestinal microbiota. Chapter 5 used Atlantic salmon during smoltification to study the changes in the microbiota of distal intestine and the role of P. acidilactici to promote intestinal health. The results showed that bacterial communities in the mucosa differed from the digesta. Seawater transfer and P. acidilactici had significant changes in the intestinal microbiota of both mucosa and digesta. However, the modulatory effect of both factors evaluated was larger in the mucosa-associated microbiota than in the digesta-associated microbiota. Furthermore, P. acidilactici induced a significant increase in antiviral-related genes. Chapter 6 investigated the replacement of fish oil by rapeseed oil alone or combined with P. acidilactici on the intestinal health and microbiota of two intestinal regions in Atlantic salmon. Replacement of fish oil by rapeseed oil alone or in combination with P. acidilactici supplementation did not induce major changes in the intestinal health and microbiota. The bacterial communities found were significantly different between the pyloric caeca and mid-intestine. In conclusion, this thesis contributes to new knowledge regarding the effect of dietary supplementation of P. acidilactici and the impact of different potential challenging factors in the health and intestinal microbiota of farmed salmonid species.

In the present study the impact on gut microbiology and indigenous gut histology of Atlantic salmon ( Salmo salar L.) was investigated following feeding of a control and a prebiotic (EWOS prebiosal ® ) diet and ex vivo exposure to saline or the probiotic bacterium Carnobacterium divergen s. The results showed that ex vivo exposure of C. divergens at 10 8 CFU ml -1 did not cause cell damage to the intestine tract of Atlantic salmon. Furthermore, prior provision of dietary prebiotic elevated the ability of C. divergens to adhere to the epithelium or mucus layer in the proximal intestine, where culturable heterotrophic bacterial levels (which were identified as C. divergens ) were elevated by 234% compared to the control. This effect was not apparent in the distal intestine. The ability of isolated carnobacteria from the ex vivo experiment to inhibit growth of two fish pathogenic bacteria ( Yersinia ruckeri and Aeromonas salmonicida ssp. salmonicida ) was assessed. Extracellular products from all 11 of the isolated carnobacteria strains, plus the type strain Carnobacterium inhibens CCUG 31728, inhibited the in vitro growth of Y. ruckeri . However, only extracellular products from C. divergens isolate 57 inhibited the growth of A. salmonicida ssp. salmonicida .