How Your Gut Microbiome Can Prevent or Cause Diseases

The bacteria in our gut contribute are key regulators of health and disease… But what is the gut microbiome, and how does it impact us?


In 2016, an article in Harvard Health stated that “In many ways, your gut bacteria are as vast and mysterious as the Milky Way. About 100 trillion bacteria, both good and bad, live inside your digestive system. Collectively, they’re known as the gut microbiota. Science has begun to look more closely at how this enormous system of organisms influences — and even improves — health conditions, from heart disease to arthritis to cancer” (2). But what is this gut microbiome, and how much does it impact our health?

The gastrointestinal tract refers to the long tube through which food moves during the process of digestion, starting from the mouth, the oesophagus, the small and large intestine, and going all the way down to the anal sphincter. The gut, composed of the small and large intestines, represents the part of the gastrointestinal tract going from the pyloric sphincter of the stomach to the anus. Along the gut lives a rich and diverse ecosystem of microorganisms, known as the gut microbiome.


While few bacteria are present in the small intestine, the colon contains the highest microbial density on earth, with between 300 and 500 different species (4). To illustrate the importance of our rich ecosystem, Dr. Rob Knight — a microbial ecologist — stated during an interview for BBC that “you’re more microbes than you are human. Originally we thought that our cells were outnumbered 10 to one. That’s been refined much closer to a 1:1 ratio, so the current estimate is you’re about 43% human if you’re counting up all the cells” (5).

For long, we thought that the gut microbiome only played a role in the digestion of nutrients, but in the last decades, new and exciting research has unravelled its critical role of in our health. For example, our bacteria contribute to the production of vitamins such as vitamin K and vitamin B2, but also hormones such as serotonin, the “happy hormone” (6).

In 2013, a large-scale study published in Nature found that individuals with a smaller population of bacteria tend to be more obese and less healthy. Similarly, having high levels of specific bacterial strains correlate with health (7,8).

Those findings were so fascinating that researchers and the industry are now investigating the potential of probiotics, the healthy bacteria, to treat a wide range of conditions. We now know that probiotics can help alleviate irritable bowel syndrome (IBS), diarrhea and even lactose intolerance. In addition, exciting studies in vitro or in animals show that probiotics could promote weight loss and improve inflammation, blood lipids and organ damage and therefore, prevent metabolic diseases (9, 10, 11). But how do the bacteria in our gut harm, or protect us?

It’s useful to think of the gut microbiome as a distinct organ that communicates with the rest of the body through multiple pathways. For starters, our gut connects to the brain (the gut-brain axis) by a complex network of neurons known as the enteric nervous system, a system so important that gastroenterologists refer to it as the “second brain”. The importance of the enteric nervous system has been highlighted in an article published by the Cleveland Clinic, “We know that gastrointestinal problems can create anxiety and stress. We also know that anxiety and stress can make GI problems worse. Medical researchers who are studying depressive symptoms, Parkinson’s and Alzheimer’s disease, autism, amyotrophic lateral sclerosis, multiple sclerosis, pain, anxiety, and other ‘neuro’ conditions are beginning to look at what is going on in a person’s guts” (12).

Gut dysbiosis is a condition characterized by an overabundance of mainly gram-negative bacteria, such as E. Coli and Salmonella, which are not only harmful, but also more resistant to antibiotics due to structural differences. The membrane of gram-negative bacteria is distinct in part because it contains large molecules named lipopolysaccharides, that can leak from the bacterial wall and enter the circulation through the portal vein that connects the intestines with the liver (gut-liver axis). Our liver receives the blood from the stomach, spleen, pancreas, and intestines and is fundamental to clean up the blood from toxins and decide what should enter our systemic circulation and reach our other vital organs. However, in the long run, the toxins released during a prolonged gut dysbiosis attack and damage the liver and causes the development of non-alcoholic fatty liver disease and hepatocellular carcinoma, or liver cancer (13). Unfortunately, long-term abuse of our liver contributes to damaging other organs in our body, including our lungs, spleen, heart and blood vessels, and individuals diagnosed with liver disease most commonly dies from a dysfunction in their blood vessels that become stiffer, thicker and filled with fat and inflammation (14).


The good news is that while gut dysbiosis can damage our body, a healthy lifestyle promotes a large, diverse, and healthy population of bacteria with, which drastically improves our health, in part by reversing the damage to our liver. A healthy diet supports the good bacteria, such as the gram-positive genus Lactobacillus and Bifidobacterium, the two most prescribed probiotics on the market. A healthy gut microbiome produces powerful substances, such as short chain fatty acid — small compounds derived from the fermentation of dietary fibres in the colon — that are the favored sources of nutrients for colonocytes, but also improve blood pressure, blood lipids, inflammation as well as insulin resistance (7,16, 17, 18). With all that said, we now know that our good bacteria offer a wide range of benefits, but the challenge remains to find ways to change our gut microbiome. Until we find the optimal probiotic supplement, we should focus our attention on improving our diet and lifestyle habits. For our nutrition, a recent large-scale study investigating the gut microbiome of over 1000 individuals and published in Nature Medicine highlights the importance of eating unprocessed foods as well as healthy fruits, vegetables, fermented dairy products and coffee (19, 20).