|Channel and hybrid catfish are the main aquaculture species in the USA. One of the most significant problems that catfish producers face is the presence of bacterial diseases throughout production. These diseases can cause high mortalities and consequently have an economic impact on the catfish industry. The microbiome is a complex group of microorganisms living in a symbiotic relationship with their host. A balanced microbiome is key to maintain fish health. If the fish microbial community structure is disrupted, it opens the door for opportunistic pathogens that directly affect the host’s health. Standard practices in aquaculture affect the fish physiology, which in turn affects the host symbiosis. In this dissertation, I aimed to characterize the microbiome in different tissues (gut, gill, and skin) of channel catfish (Ictalurus punctatus) and the gut microbiome in the zebrafish (Danio rerio) using metagenomic approaches to study the effect of standard aquaculture practices on freshwater fish microbial communities. I have described the structure of the bacterial microbiome in both the healthy state and diseased state, dysbiosis. In Chapter 2 of this dissertation, I characterized the development of the gut microbiome in channel catfish reared under standard industry practices. I identified critical time points during their development in which bacterial communities significantly changed from one ontogenic state to the next. Besides characterizing how their microbiome shifted and shaped overtime, I pinpointed the time after which the communities became stable. In Chapter 3 and 4, I focused on investigating the effect of antibiotis on the gut microbiome in zebrafish and catfish, respectively. As expected, antibiotic treatment induced a dysbiosis state in both hosts with an overall decreased in bacterial richness. Gut dysbiosis in zebrafish made the host more susceptible to opportunistic bacterial infections, an effect that was not observed in catfish. In Chapter 5, I assessed the effect of an external mechanical injury to the gut microbiome in channel catfish. I observed significant changes in the composition of the gut microbiome in injured fish, which suggest the presence of the ‘brain-gut’ axis in channel catfish previously described in mamals. Finally, in Chapter 6, I tested the effect of vaccines on the skin, gill, and gut microbiomes of channel catfish. No significant effect in those communities was found due to vaccination.