A diverse microbiota is found throughout the gastrointestinal tract (GIT) of chickens, most predominant in the cecum (Mead, 1997; Videnska et al., 2014). The gut microbiota plays an essential role in nutrition, detoxification of certain compounds, growth performance and protection against pathogenic bacteria. The microbiota is crucial to strengthen the immune system, thereby affecting growth, health, and wellbeing of chicken. Generally, the gut microbiota modulates host responses to limit the colonization of pathogens (Rehman et al., 2007). There is little information about the diversity and function of the gut microbiota in chickens, its impact on the host and the impact of certain pathogens.