الفهرس 
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Abstract
The term “microbiota” is defined as the collection of micro-organisms in a distinct location, such as the human gut. The term “microbiome” generally refers to the collective genes contained within the microbiota, which in the case of the human gut includes three million unique genes that are mostly from bacteria of relatively few of the known bacterial phyla the two most prominent being the Firmicutes and the Bacteroidetes.
The „normal‟ gut microbiota is dominated by anaerobic bacteria, which outnumber aerobic and facultative anaerobic bacteria by 100- to 1,000-fold. In total, the intestinal microbiota consists of approximately 500–1,000 species that, interestingly, belong to only a few of the known bacterial phyla.
By far the most abundant phyla in the human gut are Firmicutes and Bacteriodetes, but other species present are members of the phyla Proteobacteria, Verrumicrobia, Actinobacteria, Fusobacteria and Cyanobacteria.
In the adult intestine, a total of about 1014 bacterial cells are present, which is ten times the number of human cells in the body. Their combined genomes (known as the microbiome) contain more than 5 mil-lion genes, thus outnumbering the host‟s genetic potential by two orders of magnitude. This large arsenal of gene products provides a diverse range of biochemical and metabolic activities to complement host physiology. In fact, the metabolic capacity of the gut microbiota equals that of the liver, and the intestinal microbiota can therefore be considered as an additional organ. These bacteria are essential for several aspects of host biology.
They facilitate the metabolism of otherwise indigestible polysaccharides and produce essential vitamins; they are required for the development and differentiation of the host‟s intestinal epithelium and immune system; they confer protection against invasion by opportunistic pathogens; and they have a key role in maintaining tissue homeostasis.
The primary defensive mechanisms include the production of mucus and other secretions, regulation of paracellular permeability and synthesis of antimicrobial peptides by Paneth cells. Moreover, the epithelium and gut-associated lymphoid tissue (GALT) develop complex interactions and immune responses to different stimuli, which involve the production of cytokines, chemokines and activation of different effector T cells. Altogether this ensures pathogen elimination and avoids over-reactions that can lead to tissue damage and pathologic inflammatory conditions.
Among the beneficial activities of the gut flora on human host, many are related to cancer protection: control of the intestinal epithelial cell differentiation and proliferation; growth and development of the epithelial barrier ; apical tightening of the tight junctions; protection against pathogenic species; development/modulation of gut-associated lymphoid tissue (including host innate immune system, with the important roles of NOD-like receptors and Toll-like receptors – TLRs); fermentation of non-digestible carbohydrates to produce short-chain fatty acids – SCFA; biliary acids metabolism; xenobiotics and dietary carcinogens degradation.
Microbes residing within the gastrointestinal tract are collectively referred to as gut-microbiota or microflora and are essential in many metabolic activities such as fermentation of unused energy substrates, and production of vitamins, biotin, and vitamin K for the host.
There is a link between the gut microbiota and chronic GI diseases, including irritable bowel syndrome (IBS) and IBD, systemic diseases such as type 2 diabetes (T2D) and obesity, as well as the onset of colorectal cancer (CRC).
Early results in animal models of multiple sclerosis and rheumatoid arthritis also suggest a pronounced influence of the gut microbiota. In animal models, these autoimmune diseases do not develop in germ-free mice. In the case of multiple sclerosis models, the disease phenotype is restored when germ-free mice are colonized by specific bacterial taxa.
These autoimmune diseases all result from inappropriate action of the adaptive immune system mediated by the gut microbiota. Introduction of bacterial polysaccharides from the commensal Bacteroides fragilis protects against the development of these autoimmune diseases.
The use of probiotics and prebiotics to improve the interactions between gut microbes and host metabolism in obesity and other metabolic diseases has been extensively investigated. Probiotics are live microorganisms that, when used as food supplements, beneficially affect the host by improving intestinal microbial balance and changing the composition of the colonic microbiota.
Specific bacterial species such as Bifidobacterium spp. have been shown to improve glucose homeostasis, reduce weight gain and fat mass, and restore glucose mediated insulin secretion in mice fed a high-fat diet.