Microbiome that inhabits within the GIT tract contributes many health benefits to the host by regulating the immune homeostasis. Alterations of these gut microbial communities can cause immune dysregulation, resulting in autoimmune disorders. The mammalian intestine is colonized by trillions of microorganisms most of which are bacteria that have co-evolved with the host in a very symbiotic relationship. The gathering of microbial populations that resides on and within the host is commonly known as “microbiota”. A principle function of the microbiota is to protect the intestine against colonization by exogenous pathogens and potentially harmful indigenous microorganisms via several mechanisms, which include direct competition for limited nutrients and therefore the modulation of host immune responses. Understanding the interaction of the microbiota with pathogens and therefore the host might provide new insights into the pathogenesis of disease for preventing and treating intestinal and systemic disorders.

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