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Little is known about how the intestinal bacterial microbiota differs among different strains of chickens raised in an open sided house, predominantly those with lower growth rates, such as Indigenous chickens. Ninety-one-day-old chicks of each strain of chickens were raised in an open-sided house system and fed a conventional corn-soybean meal diet from Day 0–35 days of age. The objective of this study was to assess the relative abundance of bacteria microbiota identified in the intestinal tract of local Omani and Cobb 500 broiler chickens raised in an open-sided house system using 16S rDNA-based analysis. The results obtained showed the diversity of bacterial populations in different intestinal regions of two chicken strains. Bacilli were found in higher numbers and reached 98.8% of the bacteria in the duodenum on Day 5 in Cobb 500 versus 72.5% in the Omani chickens. Local Omani chickens had significantly higher numbers of Clostridia at an early age period. On Day 5 Clostridia comprised 13.1% of the bacteria in the duodenum of local Omani chickens, versus only 0.062% in the Cobb 500. The relative abundance of the bacterial microbiota differed significantly (p <0.05) across different intestinal segments of the two strains of chickens, suggesting that each region generated its bacterial community with different relative abundances.
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