Profiling of bacterial community’s dynamics inhibiting the intestinal tract of broiler chickens growing in naturally ventilated house

Abstract

An experiment was conducted to evaluate the relative abundance of gastrointestinal microbial structures in different gut sections of Cobb500 broiler chickens reared in naturally ventilated houses and fed a standard diet for 35 days under the ambient environment of Oman. In this research, sequences from 1,179,068 16S rDNA analyses were grouped into 253 operational taxonomic units with a sequence similarity threshold of 97%. These units revealed the presence of seven phyla and twenty-six families. Firmicutes were found to be the dominant phylum in the duodenum (96.4%), jejunum (88.8%), ileum (96.8%), and cecum (96.8%). In contrast, Tenericutes and Thermi were the least prevalent phyla across these gut regions, accounting for between 0.01% and 0.12% of the total sequences. Actinobacteria, Bacteroidetes, and Cyanobacteria showed higher prevalence in the cecum (accounted for 6.59%, 7.42%, and 7.50%, respectively) than in duodenum, jejunum, and ileum. Lactobacillaceae were notably observed as the predominant family in the four gut segments, accounting for 73.87% in the duodenum, 43.30% in the jejunum, 77.81% in the ileum, and 46.30% in the caecum, collectively comprising a substantial portion of the sequencing data. Lachnospiraceae and Ruminococcaceae emerged as dominant families, comprising 28.61% and 30.8% of the sequencing data across all four intestinal sections, respectively. Statistical analysis of the 16S rDNA libraries showed that each section of the intestine contains a unique bacterial community with an increase in bacterial diversity parallel to age increase. The study's findings reveal the temporal dynamics of the chicken's gut microbiota in a naturally ventilated housing environment. The results obtained provide a unique perspective on the diversity of bacterial communities, highlighting significant differences in microbial composition across different segments of the intestine and offering practical insights for the management of broiler chicken health.