Investigating the gut microbiome in farmed fish species during antibiotic treatment

Abstract

Antibiotics can disturb the gut microbiome of numerous vertebrate animals. However, the influence of commercially licensed antibiotics on the gut microbiome in some farmed fish species remains unclear. As the gut microbiome serves vital functions to support the physiology of the fish host, any alteration of this community may have detrimental consequences on the health and production of farmed fish. To this end, the aim of this PhD was to investigate the distal gut microbiome communities of two farmed fish species, in response to the commercially licensed antibiotic compound oxytetracycline. In addition, a secondary aim was to explore the changes in gut physiology in response to oxytetracycline and changes in the gut microbiome. Before addressing these research aims, the first study sought to determine whether titrating bacterial DNA concentration could reduce the inter-individual variability observed in the fish gut microbiome. Whilst titrating bacterial DNA did not reduce the individual variation observed in the distal gut microbiome between fish, this method of library generation improved gut microbiome characterisation through increased sequencing performance and reduced introduction of microbial DNA contamination. The next study explored the longitudinal changes in the microbiome and expression of key inflammatory cytokine genes within the distal guts of rainbow trout (Oncorhynchus mykiss), in response to and following oxytetracycline treatment. Findings from this study demonstrated that oxytetracycline rapidly stimulated community changes in the distal gut microbiome of rainbow trout, which continued after antibiotic treatment was terminated. Furthermore, these community changes led to a more diverse distal gut microbiome in treated fish following a two-week withdrawal period. Despite considerable changes in the gut microbiome, oxytetracycline treatment did not significantly affect the expression of key inflammatory cytokines within the distal gut of rainbow trout. A further study was conducted to investigate the effect of oxytetracycline on the gut health in Nile tilapia (Oreochromis niloticus). To achieve this, changes in the microbiome community within the distal gut of fish before and after antibiotic treatment was profiled, along with the abundance of antimicrobial resistance genes, and the expression of host genes related to immunity, metabolism and gut function. In this study, oxytetracycline was also found disrupt the distal gut microbiome of treated fish, but these community changes led to less diverse microbiome communities by the end of a two-week withdrawal period. Several bacterial taxa did however increase in sequence abundance in response to oxytetracycline, and had strong associations with several antimicrobial resistance genes. In addition, despite oxytetracycline not having a significant effect on the expression of marker genes related to gut physiology, antibiotic-induced microbiome changes were highly correlated with the expression of several immune-related genes.