Abstract

Animals harbour a complex microbial community, consisting of bacteria, yeast, viruses, archaeans and protozoans, in their gastrointestinal (GI) tract. These microbes influence various host functions including development, digestion, nutrition, disease resistance and immunity. One important aim of GI microbiota studies therefore is to give a scientific basis for developing effective strategies for manipulating GI microbial communities to promote the host health and improve productivity. This chapter reviews the current knowledge on the microbiota composition in several fish species, emphasizing the compilation of results reported regarding the most frequently observed bacterial genera and phyla in marine and freshwater species. This also includes descriptions of the microbiota in early stages of development, the influence of environmental and host factors on the establishment of the bacterial populations that become part of the gut microbiota, and the importance of these microbial communities on host health, development and nutrition.