A new view of the fish gut microbiome: Advances from next-generation sequencing

• Published in: Aquaculture 2015-11, Vol.448, p.464-475
• Main Authors: Ghanbari, Mahdi, Kneifel, Wolfgang, Domig, Konrad J.
• Format: Article
• Language: English
• Subjects: Aquaculture; Bacterial community membership; Diet; Fish; Fish microbiota; Gut microbiota; Knowledge; Microorganisms; Next-generation sequencing; Physiology
• ISSN: 0044-8486; 1873-5622
• DOI: 10.1016/j.aquaculture.2015.06.033

The fish gut microbiota contributes to digestion and can affect the nutrition, growth, reproduction, overall population dynamics and vulnerability of the host fish to disease; therefore, this microbial community is highly relevant for aquaculture practice. Recent advances in DNA sequencing technologies and bioinformatic analysis have allowed us to develop a broader understanding of the complex microbial communities associated with various habitats, including the fish gut microbiota. These recent advances have substantially improved our knowledge of bacterial community profiles in the fish intestinal microbiota in response to a variety of factors affecting the host, including variations in temperature, salinity, developmental stage, digestive physiology and feeding strategy. The goal of this review is to highlight the potential of next-generation sequencing platforms for analysing fish gut microbiota. Recent and promising results in this field are presented along with a focus on new perspectives and future research directions of fish gut microbial ecology. •NGS approaches have enabled researchers to gain a new view on the diversity of fish gut-associated microbiota.•Current NGS platforms, their principals and their importance for fish gut microbiota analysis are discussed.•A comprehensive review of the literature on the use of NGS methods for studying fish gut-associated microbiota is provided.