The community structure of the fish intestinal microbiome

We have known for over a century that the gut microbiome of animals is a complex ecosystem of microorganisms. Indeed, the gut contains a diverse community of bacteria, archaea, fungi, and viruses that play a crucial role in maintaining the health and well-being of animals, including fish, through interactions with the host and each other. Studying the gut microbiome of fish has become gradually more common, due largely to advances in technology. Specifically, amplicon and metagenomic sequencing have become increasingly available and provide molecular identification of the inhabitants of the gut. Prior to this advance, identifying components of this ecosystem was dependent on labor intensive traditional microbiology techniques that were unable to identify the vast majority of unculturable microorganisms. However, with advanced sequencing nearly all gut microbes can be identified, making the in-depth exploration of community structure possible. Characterization of the gut microbiome has had a revelatory effect on publications, with a plethora of articles providing species-specific information regarding the identity of gut microbes. This research has also revealed that the gut microbiome is dynamic with community structure influenced by external factors such as diet and the environment as well as internal regulation by the host. In this article, we will discuss the structure of the gut microbiome of fish, focusing on its composition across fish taxa and the various factors that impact its makeup. Then we will briefly touch on the application of microbiome community knowledge.