Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment

The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers’ health. •Analysis of microbiota from the entire hindgut, specifically focusing on segments that are widely recognised as crucial for gut health and function was done.•The FUNAAB Alpha chicken breed gut microbiota was primarily composed of sequences from the phyla Bacteroidetes, Actinobacteria, and Firmicutes.•The Firmicutes/Bacteroidetes ratio exhibited similarities between the normal and frizzle feathers genotypes, and was significantly differed from those in naked neck chickens.•Bacterial species with prebiotic and probiotic properties, such as Lactobacillus spp., were present in significantly higher proportions in the frizzle feather and naked neck genotypes.