Analysis of the gut microbiota of healthy CARI-Nirbheek (Aseel cross) Chickens: A metagenomic approaches

Abstract

Rising specialized knowledge of the chicken gastrointestinal tract microbiota through culture-independent metagenomic analysis has improved the understanding of the dynamics of bacterial diversity and their involvement in chicken metabolism and health. A metagenomics study was performed with the gut of healthy country chicken scientifically known as CARI- Nirbheek Species. Nucleotide composition analysis of 16S rRNA metagenomics studies was performed using MySeq Illumina Sequencer. In this study, the Polymerase Chain Reaction focused on V3-V4 16S rRNA ribosomal gene. The primary analysis was performed employing Next-generation sequencing data, elimination of short along with chimeric sequences, clustering into OTUs (operational taxonomic units), and biodiversity assessment by calculating ACE, Chao1, and Shannon indices. According to the identity level, 97% show these sequences were dissected through to 393 operational taxonomic units (OTUs). The sequencing findings for the 16S rRNA gene amplicon have been posted in the NCBI biological database at Sequence Read Archive (Accession number: PRJNA761012). The results revealed Firmicutes as the predominant phyla, which accounted for 50% of the gut microbiota, followed by Cyanobacterial (26%), Proteobacteria (17%), and Archaea, which only accounted for 0.14%. Among the isolates from the chicken gut, the predominant genera were Clostridium, Turicibacter, Enterococcus, and Camphylobacter. Species such as Shigella, Bulledia, Atopium were lower in cecal microbiota. Based on our results, Clostridium sp was found to be the most abundant genera in CARI-Nirbheek chicken. In-depth studies on the function and synergies of the gut microbiota could help the research community to develop specific probiotics to achieve the expected breeding goals.

Keywords

• Chicken gut
• Metagenomic analysis
• Aseel cross
• Country breed
• Microbial diversity