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What is the Gut Microbiome?

Your gut is your gastrointestinal (GI) system or digestive system and includes your stomach, small intestine, and large intestine (colon). It digests and absorbs nutrients from food and utilizes those nutrients to fuel and maintain your body. About 200 different species of bacteria, viruses, and fungi reside in your colon. The bacteria and other microorganisms in your gut are known as your gut microbiome. The bacteria help to break down food, converting it into nutrients your body can utilize.

Certain types of microorganisms in your gut may be harmful to your health, but many are beneficial and necessary for a healthy body. In the gut microbiome, the “good” bacteria do more than just help with digestion. They help keep your “bad” bacteria under control. They multiply from time to time to devoid the unhealthy bacteria of space from growing. Fiber-rich foods, for instance, are crucial for fiber-eating bacteria that are linked with a healthy gut microbiome. On the other hand, ultra-processed foods can encourage harmful bacteria to grow and upset the gut’s delicate balance. A healthy balance of bacteria in your gut is vital to achieve equilibrium and optimal gut health.

How Can You Improve Gut Microbiome for Sport Performance and Why is it Important?

Our gut microbiome influences our overall health and well-being, and in the case of athletes and active individuals it conditions their performance. An unbalanced gut microbiome contributes to several gastrointestinal issues, such as abdominal distension, nutritional deficiencies, excessive fermentation, intestinal permeability, and even a sense of increased fatigue after exercising and global inflammation of the body, which affects muscle recovery capacity. Hence, following a healthy and balanced diet is crucial to promote a healthy gut microbiome which could influence athletic performance. The key to achieving this is the process of fermentation by bacteria of certain fiber-rich foods in the colon and the subsequent production of short-chain fatty acids (SCFAs). These SCFAs can be oxidized in muscle, which contributes to making muscle glucose more available. They also promote muscle mass preservation, insulin sensitivity, and increased blood flow, which are all key factors, from both an overall health and performance point of view. Particularly, it has been noted that the bacterial species that make a type of SCFA, known as butyrate, have a significant positive effect on both performance and muscle recovery.

How Does Gut Microbiome Impact Diabetes?

Diabetes is a chronic metabolic disorder characterized by hyperglycemia or the presence of high sugar (glucose) levels in the blood. The level of glucose in the blood is regulated by the hormone insulin, which is produced by the pancreas. Diabetes occurs when either the pancreas does not produce sufficient insulin or when the body cannot effectively utilize the insulin it produces. Type 2 diabetes mellitus is the most common type of diabetes.

A number of studies have shown that gut microbiome plays a significant role in type 2 diabetes mellitus. The gut microbiome is involved in managing glucose and insulin sensitivity. Symptoms of diabetic patients can be improved by altering the gut microbiome, which helps to reverse the impaired glucose tolerance and fasting glucose in prediabetes. One type of bacteria noted in the gut may be instrumental in the development of type 2 diabetes, while another may protect from the disorder, according to early results from an ongoing, prospective study. The study found individuals with elevated levels of a bacterium called Coprococcus tended to have greater insulin sensitivity, while those whose gut microbiomes had elevated levels of the bacterium Flavonifractor tended to have reduced insulin sensitivity.

How Does Gut Microbiome Contribute to Fatty Liver Disease?

Fatty liver disease is a condition caused by excess fat buildup in the liver cells. Fatty liver is of two types:

  • Non-alcoholic Fatty Liver Disease (NAFLD): The buildup of fat in the liver is not associated with the consumption of alcohol. 
  • Alcoholic Fatty Liver Disease: The buildup of fat in the liver is associated with excess alcohol consumption.

An imbalance in the gut microbiome has been connected to the development of fatty liver disease. Poor dietary habits can modify the composition of the gut microbiome leading to gut microbiome dysbiosis. Dysbiosis or gut microbiome imbalance can especially occur when a diet is high in fructose sugars, saturated fats, and animal products. Different species of bacteria in the gut metabolize nutrients differently, activating different pathways that contribute to the buildup of fat within the liver and activating inflammatory cascades that promote liver damage. Short-chain fatty acid production, conversion of choline into methylamines, modification of bile acids (BA) into secondary BA, and ethanol production, all of which are mediated by gut bacteria, are also known to be aggravating factors for NAFLD.

How Does Gut Microbiome Affect Crohn’s Disease or Ulcerative Colitis?

Crohn’s disease and ulcerative colitis are a type of inflammatory bowel disease or IBD. IBD refers to a group of intestinal disorders that cause chronic inflammation of the gastrointestinal (GI) tract or digestive tract. In Crohn’s disease, inflammation may occur in any region of the small intestine. However, the inflammation usually affects the final part of the small intestine. In ulcerative colitis, inflammation occurs in the innermost lining of the large intestine.

Studies have indicated that dysbiosis or negative alterations in the composition of the gut microbiome can lead to Crohn’s disease and ulcerative colitis. Individuals with Crohn’s tend to have lower levels of Faecalibacterium prausnitzii, beneficial bacteria that protect the gut from inflammation. Researchers also found dysbiosis resulting in high levels of adhesion-invasive Escherichia coli that can attach to the gut lining causing inflammation. Studies also indicate that lower levels of several beneficial types of bacteria such as Lactobacillus may increase the risk of a flare in patients with ulcerative colitis and Crohn’s disease.

What are the Tests Available to Measure Gut Microbiome?

Gut microbiome tests are tests employed to evaluate the level of microorganisms in your GI tract. These tests can provide an idea of the types and amounts of microorganisms in your gut. Research indicates that these microorganisms may play a role in chronic conditions, such as inflammatory bowel disease (IBD), type 2 diabetes, cardiovascular disease, and colorectal cancer. Gut microbiome tests commonly use stool samples to examine gut flora and measure gut health. Healthcare professionals will collect a stool sample from you and analyze the sample under laboratory conditions. The sample helps to find out which microbes live in your gut, their types, species, and their beneficial and harmful effects. Information from this test helps your physician tailor a personalized dietary regimen to enhance your gut health.

How Does a Hydrogen Breath Test Help in Checking Small Intestinal Bacterial Overgrowth?

The hydrogen breath test is a simple, non-invasive medical test that measures the level of hydrogen or methane gas that you exhale after drinking a mixture of water and glucose. A rapid hike in exhaled methane or hydrogen may indicate bacterial overgrowth in your small intestine. The test is usually used to confirm or rule out common digestive issues, such as SIBO (small intestine bacterial overgrowth) and lactose intolerance. The test can help your physician confirm the diagnosis of SIBO when beneficial bacteria from your large intestine have moved into your small intestine, where they do not belong. In a healthy digestive system, the carbohydrates and sugars that you consume are predigested before they reach the bacteria in your large intestine. If they have not been completely digested by then, the anaerobic gut bacteria in the colon will digest them, converting them into gas. This gas in your colon is absorbed into your blood and carried into your lungs, where it is expelled through your breath. That is how your breath can indicate what is going on in your gut.


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Dr. Gyawali is exclusively available at

Mubadala Health – Jumeirah, Dubai

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I was referred to Dr Gyawali for a manometry test. He carefully studied my medical history. and realised that my previous doctor had repeatedly missed a significant diagnosis. He immediately referred me on to the necessary specialists for urgent treatment. I cannot thank him enough..

Patient at Queen's Hospital

29th February 2020