The Gut Microbiota of Fish - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 75

4 The Gut Microbiota of Fish

Jaime Romero 1 , Einar Ringø 2 and Daniel L. Merrifield 3
1 Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile,
Santiago, Chile
2 Norwegian College of Fishery Science, UiT The Arctic University of Norway,
Tromsø, Norway
3 School of Biological Sciences, Plymouth University, UK

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.

4.1 INTRODUCTION

In the classic description, the complex community of microorganisms inhabiting body sites in
which surfaces and cavities are open to the environment is termed the microbiota; previously
this was called the microflora or microbial biota. Moreover, the epithelial surfaces of fish and
all other vertebrates are colonized at birth by large numbers of microorganisms (microbiota)
that form commensal or mutual relationships with their hosts (Spor et al. 2011). The majority
of these microbes reside in the digestive tract, where they influence a broad range of host
biological processes. The vertebrate gut harbours a coevolved consortium of microbes that play
critical roles in the development and health of this organ. This microbial community can be
subcategorized into two major groups. One group simply passes through the lumen with food