Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken

The ever-increasing demands for chicken protein by humans highlighted the implications of studying the effects of gut microbiome composition and diversity on this respect. The present study explored the bacterial community profile and its correlation with the different age stages of chicken. Egyptian local chicken were fed on a routine commercial diet and fecal samples were collected at different age points for microbiome analyses. Bacterial profiles of the chicken gut microbiome were investigated using 16S rRNA gene amplicon sequencing and a metagenomics DADA2 pipeline was used for data processing and analysis. The results showed significant diversity among all samples. Alpha diversity and the relative abundance of bacterial taxa first decreased then recovered with time. This was clear with Firmicutes genera that showed a depletion in their abundance followed by a subsequent recovery to the initial levels. However, Actinobacteria increased significantly over time. At the genus level, Lactobacillus and Corynebacterium declined in abundance, while Pediococcus displayed an increase in abundance with time. Similar dynamic patterns were exhibited at different taxonomic bacterial affiliates. While the initial decrease in bacterial diversity may be attributed to the effect of antibiotics, the subsequent attempt of the microbiome to restore its balance, composition and diversity may be driven by the influence of growth-promoting supplements in the diet. In addition, good management of the bacterial changes with chicken age might affect the poultry industry, consumers' health and even environmental health in a positive way.