Comparative analysis of metagenomic DNA extraction methods from gut microbiota of zebrafish (Danio rerio) for downstream next-generation sequencing

ABSTRACT

Zebrafish (Danio rerio) being a well-established model system can provide significant understanding about interactions between gut microbiota and host system. Gut bacterial diversity may be unraveled only by analyzing metagenomic DNA from diverse higher organisms which helps to identify gut microbes beneficial to the host. Isolation and standardization of metagenomic DNA from zebrafish gut are an inconsequential, but demanding process, as most microbes in the gastrointestinal tract are unculturable. A variety of commercial kits and modified protocols is used for bacterial metagenomic DNA extraction. However, only few methods are reported for the effective isolation of community DNA from zebrafish. The present work portrays an augmented method for gut metagenomic DNA isolation from zebrafish gut, focused on obtaining effective yield and purity. Three methods using kit were evaluated, of which the modified kit method was an affordable and feasible method for isolation of metagenomic DNA from zebrafish. The modified protocol can be used for isolating quality DNA which is an important parameter for downstream applications such as polymerase chain reaction, cloning, next-generation sequencing, and others.