Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken
Elnaggar, A., Abdelmoteleb, M., El-Shishtawy, H., Osman, Y. (2024). Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken. EKB Journal Management System, 70(3), 1-9. doi: 10.21608/mjb.2024.447106
Ammar M. Elnaggar; Mohamed Abdelmoteleb; Hisham M. El-Shishtawy; Yehia A. Osman. "Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken". EKB Journal Management System, 70, 3, 2024, 1-9. doi: 10.21608/mjb.2024.447106
Elnaggar, A., Abdelmoteleb, M., El-Shishtawy, H., Osman, Y. (2024). 'Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken', EKB Journal Management System, 70(3), pp. 1-9. doi: 10.21608/mjb.2024.447106
Elnaggar, A., Abdelmoteleb, M., El-Shishtawy, H., Osman, Y. Bioinformatics Analyses of the 16S rRNA Gene Evaluated the Fluctuation of Bacterial Diversity in the Gut Microbiome of Local Egyptian Chicken. EKB Journal Management System, 2024; 70(3): 1-9. doi: 10.21608/mjb.2024.447106

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

Mansoura Journal of Biology
Volume 70, Issue 3, September 2024, Pages 1-9    PDF (1.03 M)
Document Type: Original Article
DOI: 10.21608/mjb.2024.447106
Authors
Ammar M. Elnaggar* 1; Mohamed Abdelmoteleb1; Hisham M. El-Shishtawy2; Yehia A. Osman1
1Botany Department, Faculty of Science, Mansoura University, Mansoura - 35516, Egypt
2Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center, Egypt)
Abstract
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.
Keywords
Microbiome; Chicken; Metagenomics; 16S rRNA; Diversity
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