The Ultimate Three Food Habits for a Healthy Microbiota

Over the past few years, what we used to call our good gut bacteria or intestinal flora has been the object of growing scientific investigations and public interest. It is now widely accepted that a healthy microbiome is one of the key-element to our overall health and the use of probiotics supplements and fermented foods have become common practice. However, we might not be so familiar with the best practices when it comes to feeding our microbiota and maintaining a healthy microbiome. Let’s explore some simple ways to achieve that!

Getting acquainted with our wonderful microbiom

Did you know that the human gastrointestinal (GI) tract contains an abundant and diverse microbial community that gathers an incredible 100 trillion microorganisms? In fact, the density of bacterial cells in our colon has been estimated at 1011 to 1012 per milliliter, which makes this organ one of the most densely populated microbial habitats known on earth!

Each person is provided with a unique gut microbiota profile which perform various essential functions in our body. For a start, our gut microbiome encodes over three million genes. In comparison, the human genome consists of approximately 23, 000 genes. Our gut bacteria are also involved in nutrient metabolism, the maintenance of structural integrity of our gut mucosal barrier, the modulation of our immune system and protecting us against several pathogens.

1. Diversity is the Key

Everyone’s gut microbiota is characterized by a specific combination of hundreds of bacterial species. This unique blend is shaped in early life and is affected by external factors such as antibiotic use, body mass index (BMI) level, exercise frequency, lifestyle, and cultural and dietary habits. The richer and more diverse the microbiota, the greater the number of health benefits to which they may contribute and the more able they are to withstand external threats. Each species plays a different role in health and requires different nutrients for growth. Thus, by our dietary choices, we are selecting substrates for some species and providing a competitive advantage over other GI microbiota.

Eating a diverse range of whole foods is important to sustain a diverse microbiota. Unfortunately, dietary diversity has been lost during the past 50 and this decreased agrobiodiversity is occurring at an incredible rate. According to the Food and Agricultural Organization of the United Nations, 75% of plant genetic diversity has been lost, as farmers worldwide are abandoning their multiple local varieties for genetically uniform, high-yielding varieties. Today, 75% of the world’s food is generated from only 12 plants and five animal species. One of the important contributors to the loss of foods variety in our diet is our ever-expanding appetite for cheap, highly processed foods. Besides the obvious deadly combination of saturated fat, calories, sugar, chemicals and lack of fiber that they harbor, ultra-processed foods are mostly composed of only four ingredients namely corn, wheat, soy and meat. We have to make a conscious effort to eat a varied and diverse diet of healthy, natural foods in order to sustain an equally diverse and healthy microbiome.

2. Increase Your Fiber Intake

Plant-based foods such as fruit, vegetables, legumes, grains and nuts contain dietary fiber. Among these fibers, inulin, fructooligosaccharide (FOS) and galactooligosaccharides (GOS) are considered prebiotic. Prebiotics are food component resistant to gastric acidity, hydrolysis by digestive enzymes, and which bypass absorption in the upper intestine to the colon where they are metabolised by the microbiota. Prebiotic consumption has been associated with growth of Bifidobacterium, Lactobacillus and lactic acid bacteria. The biotransformation of these prebiotics by our microbiota also result in the production of short-chain fatty acids (SCFAs), including acetate, propionate and butyrate. SCFA have a range of effects. They participate in the regulation of barrier function and an improper inflammatory response in the gut while also being involved in the regulation of metabolic health and mitigating risks of cardiovascular events.

Obtaining more fiber through our diet is definitely the best option because supplements don’t provide the vitamins, minerals and other nutrients that fiber-rich foods do. However, it can be challenging to eat enough fiber, especially for people on restricted diets such as gluten-free and low-carbs or ketogenic diets. Fiber products can be a useful alternative as long as we ensure they are free of sugar or aspartame and artificial colours.

3. Consume Fermented Foods Daily

Fermentation is an ancient technique of preserving food and is still used in the production of items such as wine, cheese, sauerkraut, yogurt, and kombucha. The process of fermenting usually involves microorganisms such as bacteria or yeasts which convert the sugars in food and beverages to organic acids or alcohol. They act as a natural preservative and provide fermented foods a distinct tartness and zest. Fermented foods are often more nutritious than their unfermented form. Fermentation also promotes the growth of beneficial bacteria, such as lactobacilli. As a result, fermented foods have been associated with a range of health benefits, ranging from better digestion to stronger immunity.

Fermented foods are found in almost every culture so incorporating them into our diet can be a fun way to discover a new type of cuisine! It is always advisable to increase them gradually due to their high probiotic content which can responsible for minor gastric discomfort. It’s also important to note that not all fermented foods are created equal: some products may contain high levels of added sugar, salt, and fat. A good way to obtain healthier and more economical fermented foods is to start fermenting them at home. The extra effort is usually worthwhile since a healthy amount of fermented foods can benefit the microbiota by enhancing its function and reducing the abundance of bad bacteria in the intestines. But remember that even when it comes to fermented foods, variety is still the key.

In Conclusion

Adopting a diet containing a good variety of unprocessed or low-processed foods, rich in fibers and containing fermented items is not only beneficial for our microbiota but also for our overall health. Interestingly, this is a type of diet often found in traditional cultures and rural areas. The adoption of an ultra-processed diet promoted and sustained by big corporations has had detrimental effects on our beneficial gut bacteria, our health and our environment. It is time that we reconnect with our food heritage and rediscover the pleasure of cooking, the great taste of natural, unaltered ingredients and the magic of collaborating with organisms to create fermented foods that are good for them and for us!


Rinninella E, Raoul P, Cintoni M, et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms. 2019;7(1):14. Published 2019 Jan 10 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351938/
Heiman, M. Greenway, F. A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism. Volume 5, Issue 5, May 2016, Pages 317-320. https://www.sciencedirect.com/science/article/pii/S2212877816000387
iii Leeming, E. Johnson, A. et al. Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration Nutrients 2019, 11(12), 2862; https://www.mdpi.com/2072-6643/11/12/2862/htm
iv Leeming, E. Johnson, A. et al. Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration Nutrients 2019, 11(12), 2862; https://www.mdpi.com/2072-6643/11/12/2862/htm

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