Abstract
Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.
Highlights
Chickens are a cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year [1]
The 16s rRNA gene amplicon sequencing results were deposited in the Sequence Read Archive of the National Centre for Biotechnology Information (NCBI)
We carried out the first comprehensive analysis of the chicken gut microbiome of the Nicobari and Ghagus breeds of Indian native chickens originating in biodiverse hotspots, such as Nicobari Island and coastal India, respectively
Summary
Chickens are a cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year [1]. Poultry represents one of the most efficient form of animal protein with highly efficient feed conversion. Global human population growth, urbanization, and income levels are contributing to the huge increase in demand for protein and, livestock and poultry. Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition. Feed efficiency and faster growth are crucial goals in the highly competitive poultry production system. Maintaining a healthy gut is an important prerequisite to attain these goals.
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