The intestinal microbiome plays an important role in human physiology. Next-generation sequencing technologies, knockout and gnotobiotic mouse models, fecal transplant data and epidemiologic studies have accelerated our understanding of microbiome abnormalities seen in immune diseases and malignancies. Dysbiosis is the disturbed microbiome ecology secondary to external pressures such as host diseases, medications, diet and genetic conditions often leading to abnormalities of the host immune system. Specifically dysbiosis has been shown to lower circulating lymphocytes, and increase neutrophil to lymphocyte ratio, a finding which has been associated with a decreased survival in women with breast cancers. Dysbiosis also plays a role in the recycling of estrogens via the entero-hepatic circulation, increasing estrogenic potency in the host, which is another leading cause of breast malignancy. Non-modifiable factors such as age and genetic mutations disrupt the microbiome, but modifiable factors such as diet may also lead to profound disruptions as well. A better understanding of dietary factors and how they disrupt the microbiome may lead to beneficial nutritional interventions for breast cancer patients. 1. Introduction The human digestive tract is known to host trillions of microbes collectively called the intestinal microbiota [1–4]. A commensally, mutually beneficial relationship exists between the human host and these microbiota. The host’s digestive tract provides the nutrient niche for the microbiota, while the microbiota protects against pathogens, helps in the development of the immune system, aids in nutrient reclamation from food by fermenting indigestible fiber to short chain fatty acids, produces essential amino acids and vitamins, helps in the absorption of minerals, and aids the breakdown of dietary toxins and carcinogens [1–3, 5]. The intestinal microbiota also helps the growth and differentiation of enterocytes and colonocytes, thus maintaining the intestinal barrier against potential pathogens [6]. 2. Origin of Microbiome The intestinal microbiota is maternally inherited at birth as the newborn is delivered through the vaginal canal [7–9]. Later in development, factors both dependent on host choices such as diet and independent of host choices such as genetics and age modify the intestinal microbiota [10]. Insights into the dynamic structure of intestinal microbiota have become possible with the advent of next-generation sequencing technologies; such technologies are able to fully characterize the polymorphism of bacterial communities
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