A primer on metagenomics and next-generation sequencing in fish gut microbiome research

The fish gut is a complex ecosystem populated by an exceedingly diverse and assorted group of microbes, influenced by various factors such as habitat salinity, temperature, trophic level, taxonomy, feeding habits as well as host selective pressures within the gut. The gut microbiota is involved in several physiological functions of the host such as digestion, metabolism, reproduction, development, and immune response and is often heralded as an 'extra organ'. Earlier studies employed culture-dependent techniques for the study of fish gut microflora. The establishment of great plate anomaly and technological strides in culture-independent techniques, particularly in the omics technologies such as metagenomics and next-generation sequencing techniques have led to a better understanding of the confederation of microorganisms with their respective hosts. This article reviews the applications of and prospects of metagenomics and amplicon and shotgun sequencing approaches in fish gut microbiota research.

Automated summary

The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.