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Gut microbiota and dysbiosis
September 9, 2025
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The gut microbiota is an organ that, until now, has been ignored but is vital to our physical and mental health.
This group of microorganisms, mainly bacteria, viruses and fungi, live in our digestive tract and their functions are key in our body. It is an organ that we do not see or feel directly, but its balance, or lack of it, can influence everything from digestion and the immune system to mood, weight and risk of chronic disease.
1. What is the microbiota?
The gut microbiota is an ecosystem made up of all the microorganisms in the gut, especially in the colon. It is estimated that there are more than 40 trillion bacteria in our body, which can weigh between 1 and 2 kilos. We have more bacteria in our body than cells (30 trillion), most of them beneficial.
In general, beneficial or ‘good’ bacteria multiply frequently, leaving little room for harmful or ‘bad’ bacteria. Without the gut microbiota it would be very difficult to survive, because of the number of key functions they perform for the body.
Each person has a different composition of microbiota, which is formed from birth and is altered by our diet, lifestyle, the use of drugs and other environmental factors.

2. What happens if there is an imbalance?
When the so-called good bacteria decrease and the bad bacteria increase, dysbiosis occurs.
This complication is linked to a number of diseases such as:
- Inflammatory bowel disease (IBD): Crohn’s disease and ulcerative colitis.
- Irritable bowel syndrome (IBS).
- Obesity.
- Type 2 diabetes.
- Cardiovascular disorders.
- Depression and anxiety.
One example is the production of the substance TMAO (trimethylalanine-N-oxide), produced by certain micro-organisms when red meat or eggs are eaten. Excess of this substance can affect the accumulation of cholesterol in the arteries, thus increasing the risk of heart attack and chronic kidney disease.
3. How close are the gut and the brain?
It may seem that, because they have different functions, the gut and the brain have no relationship beyond the transmission of commands and information, but this is not the case. Both organs are linked by millions of neurons through the gut-brain axis.
The microbiota, in addition to digestion, also influences the production of neurotransmitters such as dopamine and serotonin, which are vital for regulating mood and sleep. In fact, up to 90% of serotonin is produced in the gut.
There is also believed to be a connection between the gut and memory and cognitive skills, hence the name ‘second brain’.
Research has found differences in the microbiota of people with anxiety, depression, chronic pain or autism compared to mentally healthy people. In addition, some probiotics may be beneficial in reducing mild depressive symptoms.

4. The relationship between the microbiota and the immune system
The immune system and microbiota are in constant communication. A healthy microbiota not only reinforces the intestinal barrier but also educates the immune system to act correctly.
In the case of dysbiosis, uncontrolled inflammations can occur, such as those that occur in autoimmune diseases. An imbalanced microbiota produces gas and chemicals that contribute to intestinal discomfort but can also increase the risk of leaky gut, allowing toxins into the bloodstream and triggering systemic inflammation.
5. Food and probiotics to improve microbiota
There are natural (and effective) ways to restore the balance of gut bacteria:
- With a diet rich in fiber: dominated by legumes, fruits, vegetables, oats and seeds, which feed the ‘good’ bacteria; and fermentable fiber, which produces fatty acids that protect the intestinal mucosa, prevent weight gain, diabetes and the risk of heart disease or cancer.
- Fermented foods: kefir, yoghurt, miso, kimchi, etc. provide natural probiotics.
- Prebiotics: the food of probiotics found in garlic, onions, bananas, leeks, asparagus, artichokes, soya, whole wheat and, in general, whole grains.
- Symbiotics: a combination of probiotics and prebiotics.
- Eat diets rich in plants and/or polyphenols.
- Reduce stress and get plenty of sleep.
- Moderate physical exercise.
- Take drugs such as antibiotics, proton pump inhibitors or anti-inflammatory drugs only when necessary.

Probiotics are supplements with live ‘good’ bacteria. Not all work the same, but most have been shown to be beneficial in improving irritable bowel symptoms, reducing intestinal inflammation, strengthening the immune system (including alleviating allergy or lactose intolerance symptoms) and preventing diarrhoea after antibiotic use. As everyone’s microbiota is different, its effect is not the same for everyone.
In short, to improve our energy, our immune system, our skin… it is important to listen to our gut.
References:
- Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), 1258–1270. https://doi.org/10.1016/j.cell.2012.01.035
- Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. Biochemical Journal, 474(11), 1823–1836. https://doi.org/10.1042/BCJ20160510
- Carding, S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health and Disease, 26(1), 26191. https://doi.org/10.3402/mehd.v26.26191
- Cryan, J. F., et al. (2019). The microbiota-gut-brain axis. Physiological Reviews, 99(4), 1877–2013. https://doi.org/10.1152/physrev.00018.2018
- Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ, 361, k2179. https://doi.org/10.1136/bmj.k2179
- Arboleya S, et al. Gut Bifidobacteria Populations in Human Health and Aging. Front Microbiol. 2016 Aug 19;7:1204.
- O’Mahony SM, et al. Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behav Brain Res. 2015 Jan 15;277:32-48.
- Cardona F, et al. Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem. 2013 Aug;24(8):1415-22.
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