Gut Microbiota Diversity and Growth Performance in the Three Genotypes (Normal Feathered, Frizzled Feathered and Naked Neck) of Improved Nigerian Indigenous Chickens in Uyo

Abstract

This study investigated the gut microbiota composition and growth performance of three genotypes of improved Nigerian indigenous chickens; Normal Feathered (NF), Frizzled Feathered (FF), and Naked Neck (NN) raised under intensive management conditions. A total of 200 day-old FUNAAB-Alpha chicks were reared for eight weeks at the University of Uyo Teaching and Research Farm. Growth parameters, including body weight and linear body measurements, were recorded weekly. Cecal samples were collected from 12 birds (four per genotype) for microbial analysis using 16S rRNA gene sequencing on a PacBio platform. Bioinformatics analysis was performed with QIIME2, SILVA databases, and PICRUSt2 to identify taxa, assess diversity indices, and predict functional roles. Results revealed that Bacteroidota and Firmicutes dominated the gut microbiota across genotypes, with Lactobacillus johnsonii and Lactobacillus crispatus emerging as key species. Notably, the Naked Neck genotype exhibited superior growth performance, with significantly higher body weight at weeks 6 and 8 (p<0.05). Sex significantly influenced growth, with males consistently outperforming females. The findings suggest that host genotype and sex significantly shape gut microbial composition and growth traits in Nigerian indigenous chickens. These insights provide a foundation for improving poultry productivity through genotype selection and microbiome-informed management strategies