The human gut microbiota is a complex, dynamic, and spatially heterogeneous ecosystem inhabited by a myriad of microorganisms interacting with each other and with the human host, including bacteria, fungi, and viruses. In health conditions gut microbiota is symbiotic with the host and maintains normal physiological processes in a dynamic equilibrium state. Microbiome refers to the collective genomes of the micro-organisms in a particular environment, and microbiota is the community of micro-organisms themselves. Approximately 100 trillion micro-organisms (most of them bacteria, but also viruses, fungi, and protozoa) exist in the human gastrointestinal tract. The distribution of this microflora is uneven, with highest concentrations in the colon. Bacterial colonization of human gut by environmental microbes, beginning immediately after birth, becomes more complex with increasing age, with a high degree of variability among human individuals. The gastrointestinal tract is the main site where environmental microorganisms and antigens interact with the host, through intensive cross-talks. Gut microbiota is essential for intestinal development, homeostasis and protection against pathogenic challenge; moreover, gut microbes are involved in metabolic reactions, with harvest of energy ingested but not digested by the host; they have also trophic effects on the intestinal epithelium, by favouring the development of intestinal microvilli, and play a fundamental role in the maturation of the host’s innate and adaptive immune responses. Sugars like table sugar and lactose are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases.
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