Diversity of intestinal bacterial microbiota of indigenous and commercial strains of chickens using 16s rDNA-based analysis

The objective of this study was to assess the relative abundance of bacteria microflora in different segments of the gastrointestinal tract (duodenum, jejunum, ilium, and cecum) of indigenous (local Omani) and commercial (Cobb 500) chicken strains. Birds were raised under an intensive management system fed a nonmedicated corn-soybean meal diet from Day 0–35 days of age. Using 16S rDNA-based analysis the study showed that in both breeds of birds Bacilli were the most abundant class of bacteria in the duodenum, jejunum, and ileum. Local Omani chickens had significantly higher numbers of Clostridia at most time periods. Actinobacteria were found in higher numbers and reached 54.9% of the bacteria in the jejunum at Day 35 in Cobb 500 versus only 5.42% in the Omani chickens. The bacterial microbiota relative abundance differed significantly (p < 0.05) across different intestinal segments of the two strains, suggesting that each region developed its own bacterial community and the relative abundances of these were quite different.