The human gastrointestinal tract represents one of the largest organ between the host, environmental factors and antigens in the human body. In an average life time, around 60 tonnes of food pass through the human GI tract, along with an abundance of microorganisms from the environment which impose a huge threat on gut integrity. The collection of bacteria, archaea and eukarya colonising the GI tract is termed the 'gut microbiota' and has co-evolved with the host over thousands of years to form an intricate and mutually beneficial relationship.The gut microbiota enjoys a mutualistic relationship with the host, harvesting additional energy and nutrients from the diet and protecting the host from pathogens. The resident bacteria produce a wide range of metabolites and chemicals that influence host function and these include short-chain fatty acids such as butyrate, which is essential for the integrity of the colonic epithelium.

However, there is potential for these mechanisms to be disrupted as a result of an altered microbial composition, known as dysbiosis. Human Gut dysbiosis is linked to many pathologic conditions disturbing the energy metabolism; such as obesity and atherosclerosis. The microbiota in the human gut is mostly composed of bacterial phyla: Firmicutes and Bacteroidetes. Firmicutes bacteria are Gram-positive one. It plays a key role in the nutrition and metabolism of the host through SCFA synthesis. Through their metabolic products, Firmicutes bacteria are indirectly connected with other tissues and organs and regulate hunger and satiety. In contrast, Bacteroidetes bacteria are Gram negative and associated with immunomodulation. Increased or decreased Firmicutes / Bacteroidetes (F/B) ratio are associated with the development of obesity or irritable bowel disease (IBD). Short-chain fatty acids (SCFAs), the primary metabolite for colonocytes, are produced in the intestinal lumen by commensal anaerobic bacteria via carbohydrate fermentation. they play a role in preserving gut barrier functions, and have immunomodulatory and anti-inflammatory properties also it regulates the synthesis of the hunger-suppressing hormones leptin, peptide YY, and glucagon- like peptide 1. The gut microbiota can also affect appetite and satiety via vagus nerve activation or immune-neuroendocrine mechanisms. Irritable bowel syndrome (IBS) is a common gastrointestinal disorder characterized by chronic abdominal pain and changes in bowel habits without any known organic causes. Fecal SCFAs abnormalities have been reported in patients with IBS, implying that alterations in SCFAs might be related to IBS. The cause of IBS remains unknown, and no single treatment is found to be universally applicable to all patients with IBS. Among humans, positive correlations were reported between bacterial diversity, butyrate-producing bacteria and cardiorespiratory fitness (VO2max), and higher turnover of carbohydrates and proteins, and concentrations of short-chain fatty acids in athletes compared to sedentary controls. There is also growing evidence that physical activity status and exercise training may shape the gut microbiome.

Physical activity stimulates bacterial community richness by altering SCFAs-producing species, as well as favoring the colonization of health and athletic performance-promoting strains. The ability to promote a bacterial composition capable of protecting the intestinal mucosa also it was found that the effects on gut microbiome seem to gradually disappear when the physical activity is no longer practiced. Moderate aerobic exercise affects the intestinal system mainly through gut immune function gut barrier integrity through tight junction proteins expression and IgA production hypothalamic-pituitary-adrenal (HPA) axis stimulation which, in turn, affects enteric nervous system and intestinal transit time, as well as gut motility, intestinal pH and gut hormones release and bile acids metabolism within enterohepatic circulation. High intensity interval training (HIIT) encompasses exercise prescriptions that are tailored to individual needs and can be used in most any exercise setting. This ability to adapt makes HIIT a valuable tool in the exercise programming of patients with a chronic disease. HIIT has a positive effect on the Bacteroidetes/Firmicutes ratio and also increased the alpha diversity in gut microbiota.