Your gut micro-organisms are essential for your health

Lactobacillus acidophilus

A large and dynamic bacterial community lives in your gut, and its interactions with your cells are essential for your health. In exchange for food, it influences your metabolism, promotes the growth of your gut cells and helps to protect against infections. However, this microbiota is a delicate ecosystem and if it is altered, it can affect your health.

Metabolic functions

Colonic micro-organisms metabolize non-digestible carbohydrates (e.g. cellulose, pectin, or gums) and transform them into short chain fatty acids, which are then absorbed by the colon and used as a source of energy. This system allows you to get up to 10% more energy from your food. However, the short-chain fatty acids are much more than just additional energy. They promote the growth of your gut cells, stimulate the absorption of minerals and water and have a beneficial influence on your glucose and fat metabolism.

The microbiota also metabolizes proteins to produce short chain fatty acids, but during this process potentially toxic substances such as ammonia and amines are formed as by-products.

It also provides you with vitamins, such as vitamin K and B12.

Immunity and infections

The surface of your guts is the main interface between your immunity and the external world, and the interactions between you and your colonic micro-organisms shape and develop your immune system. Our modern lifestyle, with its sterile, processed food and overconsumption of antibiotics, damages the microbiota and disrupts these interactions. As your immune system does not have the necessary bacterial contacts anymore, it becomes dumb and badly adapted to do its work correctly, which puts you at a higher risk of allergies and immune diseases.

Bacteria compete for food and for attachment sites on intestinal cells. A well-balanced microbiota will reduce the chances of infectious bacteria to find food, attach and multiply in your gut. It can also produce substances which can kill or neutralise pathogens.

Intestinal micro-organisms and chronic disease

An unhealthy microbiota is called dysbiosis. This can be due to a change in the relative amounts of the bacteria, a reduced diversity or a decrease in their activity. Scientists think that a dysbiosis puts you at a higher risk of diseases such as colon cancer, inflammatory bowel disease, obesity, metabolic syndrome or diabetes, as it is typically found in patients suffering from these conditions.

Causes of dysbiosis

Antibiotics, stress and dietary factors are the best known factors that can disrupt the normal microbiota.


Antibiotics do not only kill pathogens but also beneficial bacteria, and they have therefore a huge impact on the intestinal micro-organism. Their effect depends on their activity, dosage and length of administration. Recent studies have shown that the effect lasts much longer than previously believed. In one study it was seen up to 16 months.

Obviously, nobody takes antibiotics unless it is necessary, but more research is needed to find how and when to supplement them with live beneficial bacteria.


Studies have shown that physical and psychological stress can lead to a decline in the Lactobacillus population.

Stress also results in a decreased immunoglobulin A (Ig A) production. Ig A is crucial for our defence against pathogens and stressful events could therefore lead to an overgrowth of pathogens. Scientists also think that noradrenaline, a hormone which is typically secreted during stress, can promote the growth of some pathogens.

During competitions or periods of hard training, athletes suffer more often from infections than the general population. This might be partially due to stress. Recent studies suggest that yoghurt containing Lactobacillus might help to protect them.


A diet that contains too many processed and sterile products does not provide the microbiota with enough food to keep them healthy. Moreover, consumption of a high protein diet, such as the typical Western diet, increases the production of toxic bacterial metabolites, and eating too many simple sugars slows down the colon transit time. A slower transit time increases the bowels exposure to toxic products.

Probiotics and prebiotics

To make your microbiota stronger and healthier, you can increase the number of beneficial bacteria or stimulate the existing ones.

Probiotics are live micro-organisms that are beneficial for our health when taken in adequate amounts with food, usually as yoghurt. Lactobacillus and bifidobacillus are the most common types used.

As the gastrointestinal track is a harsh environment, many bacteria die before they reach a spot in the colon where they can develop. Scientists are therefore developing capsules to protect them during the journey.

Prebiotics are food ingredients that stimulate the growth and activity of beneficial micro-organisms. Jerusalem artichoke, soybeans and unrefined wheat contain large amounts of them, but you will find them in smaller quantities in thousands of plant-based foods. A healthy diet should provide you with enough prebiotics to keep your microbiota happy.

Probiotics and prebiotics could become important forms of treatment, but we need further research to know exactly which doses and combinations to take. In the meanwhile, it is good idea to prefer whole food over refined and processed products.

Disclaimer: This article is for general information only, and cannot be used to guide diagnosis or treatment. If you have any questions or concerns, you should talk to a qualified health provider.


K Brown, D DeCoffe, E Molcan et al. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 2012; 4(8):1095-1119.

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J A Hawrelak and S P Myers. The causes of intestinal dysbiosis: a review. Altern Med Rev 2004; 9(2): 180-197.

Y K Nakamura and S T Omaye. Metabolic diseases and pro-and prebiotics: mechanistic insights. Nutr Metab (Lond) 2012; 9: 60.

S Resta. Effects of probiotics and commensals on intestinal epithelial physiology: implications for nutrient handling. The Journal of Physiology 2009; 587:4168-4174.

K A Tappenden and A S Deutsch. The physiological relevance of the intestinal microbiota – contributions to human health. J Am Coll Nutr 2007; 26(6):6795-6835.


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