Fish microbiota function in fish nutrition and health, but research has been hindered by difficulties in culturing these microorganisms. New molecular techniques, like DDGE (Denaturation gradient gel electrophoresis) and FISH (Fluorescence in situ Hybridization), have produced limited detailed quantitative results. Next-generation sequencing based metagenomics and microarray offers more promise. These high throughput methods can obtain the overall genetic information within a microorganism community and there is no need to cultivate the individual microbes in advance. Metagenomics combines the sequencing of 16S rRNA genes and genomes of the sampled microbiota. We provide an overview of recent research advances in fish metagenomics and related applications. Many studies have already been done on individual fish species, but it is necessary to obtain a comprehensive profile of the microbiota of all fish species using metagenomics sequencing.
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