Abstract
The gastrointestinal tract (GIT) of chickens is rich of complex and diverse microbiota that is important to immune system development, pathogen exclusion, and digestion and absorption of nutrients. The 16S rRNA sequencing is an effective method for studying the ecological and biological functions of the chicken GIT microbiota. The current study aimed to assess the composition and diversity of gut microbiome of healthy broiler chicken in comparison to those infected with Salmonella. A total of 100 Broiler chickens’ whole cecal samples were randomly collected, which divided into 50 healthy broiler chicken (HBC) and 50 diseased broiler chicken (DBC), The bacteriological examination of samples revealed that 4/100 (4 %) of the examined samples were identified as S. enterica species Salmonella typhimurium represented 75% while Salmonella enterditis showed 25%. All the isolates were confirmed to be Salmonella using a primer targeting invA gene. A total of 2 whole cecal samples from each group were subjected to 16S rRNA sequencing with bioinformatics analysis to investigate the composition and the diversity of chicken microbiome. The results showed a significant abundance and diversity in the microbiota composition of HBC when compared with that of DBC. It reflected decreased numbers of beneficial bacterial agents in DBC which increased its liability to acquire infection. Salmonella altered the microbiome composition of infected chickens and using advanced molecular techniques will help to investigate the microbial composition in a collective manner that helps in keeping birds healthy to promote productivity and incomes.

Key words: Salmonella infection, Broiler cecal microbiome,16S rRNA sequencing, Bioinformatic analysis.