Gut Microbiome Composition Differs Extensively Between Indian Indigenous Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-specific as Well as Across-breed Core Microbiomes Are Found

Abstract

Background: With increasing concern on antimicrobial resistance and given the key role of gut microbiome to the host’s nutrition, productivity, development and function of immune system and competitive exclusion of pathogens, characterization of the chicken gut microbiota of different breeds or lines holds high potential for providing clues for developing alternative to antibiotic growth promoters and reducing pathogen load. Methods: In this study, we analyse and compare the gut microbiome of indigenous Indian Nicobari, Ghagus and Aseel chicken breeds originated in Nicobari island, coastal area and Indian mainland, respectively and a global commercial broiler VenCobb400 line reared without antimicrobials using 16S rDNA V3-V4 hypervariable amplicon sequencing.Results: The dominant gut microbial Phyla were Bacteroidetes and Firmicutes in native breeds whereas in VenCobb 400 the phylum Firmicutes was most dominant. Bacteroidetes/Firmicutes ratio in Ghagus and Nicobari were similar but differed from that of Aseel. The Aseel, VenCobb 400, Ghagus and Nicobari breed or line presented 3461, 857, 1911 and 1767 distance (97% cutoff) based operational taxonomic units (OTUs) with > 2 members. Alpha diversity analysis indicated higher diversity as well as richness in indigenous breeds than in the broiler line. Beta diversity analysis indicated significant difference (P<0.001) in community structure between different breeds or line and clear separation of clusters at different taxonomic levels based on breeds or line. Differential abundance analysis using edgeR detected 88 phylotype OTUs with significant (P<0.05) difference in abundance between groups. Linear discriminant analysis effect size (LEfSe) revealed 82 breed or line specific phylotype OTU level biomarkers. Five phylotype OTUs occurred as core microbiome across all breeds or line representing 13% of total prokaryote count. Seven phylotype OTUs were core microbiome across the three native breeds representing 49.3% of total prokaryotic sequences of native breeds. Correlation analysis indicated existence of complex microbial networks in all breeds or line.Conclusion: The study indicated highest overlap in microbial community composition between the coastal breed (Ghagus) and the island breed (Nicobari) among indigenous breeds and very low overlap between the broiler line and all indigenous breeds. Despite extensive variation, breed specific as well as across breed or line core microbiomes were found. This study provides new insight into the comparative community structure of microbiome of chickens of 4 breeds or line of different genetic background or geographical origin and may facilitate development of breed specific feed additives and alternative to antibiotic growth promoters.