Characterization of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16s rRNA gene

1. A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract play an important role in host performance, health and immunity. 2. High-throughput Illumina sequencing was performed for V3, V4, and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. 3. In the crop, <i>Firmicutes</i> (~78 %) and <i>Proteobacteria</i> (~16 %) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50 %), <i>Bacteroidetes</i> (~29 %) and <i>Actinobacteria</i> (~10 %) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. 4. For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.