Abstract

Metagenomics is the culture independent analysis of microbial diversity in an ecosystem and it can be used to find out the gut microbial diversity of chicken. Native chicken is characterised by good genetic resistance and they are adapted to extensive system of   management. NGS (Next generation sequencing) analysis of intestinal micro biome using primers targeting V₃, V₄ and V₄-V₆ region of 16S rRNA helped in revealing the microbial diversity of native chicken CARI Nirbheek (a native chicken breed having the blood of indigenous breed Aseel). Firmicutes was the dominant bacterial phylum and bacilli were the dominant class. Lactobacillus was the dominant genus followed by Bifidobacterium. Lactobacillus helveticus and Lactobacillus delbrueckii were the dominant bacterial strains having probiotic properties which may help in increasing the genetic resistance and growth in extensive management. Metagenomics studies using NGS helps in exploring the intestinal microbial diversity and identifying the bacterial strains which helps in increasing the genetic resistance and growth of native chicken under backyard rearing.

Keywords : Metagenomics, Illumina, MGRAST, Firmicutes and CARI Nirbheek