The digestive systems of aquatic and terrestrial invertebrates and vertebrates host different categories of microorganisms known as the gut microbiota or microbiome. This includes bacteria, fungi, protozoa, and viruses. The term “microbiota” refers to the community of these microorganisms, while “microbiome” represents the collection of their genomes in a given environment. These microorganisms engage in a symbiotic relationship with their host, playing critical roles in digestion and immune function. Moreover, the gut microbiota helps preserve the integrity of the intestinal lining, metabolizes dietary components and xenobiotics, influences behavior via the gut-brain axis, and regulates immune responses.