Microbiome Wellbeing

Can your diet affect your microbiota?

Microbiome Wellbeing

Can your diet affect your microbiota?

You’re probably aware that a healthy diet helps fuel your body’s cells, tissues, and organs. But did you know bacteria and other microorganisms make up about half of your body and also need food?

The type and number of microbes you have depend in large part on your diet. These microbes, also called microbiota, are part of a vast microscopic ecosystem known as your microbiome. Keep reading to learn how your microbiota influences your health and how your diet can shape the microorganisms inside your body.

What is the microbiota?

Microbiota refers to the community of nearly 100 trillion microorganisms that live in your body, primarily your large intestine. Bacteria account for most, but viruses, fungi, protozoa, and yeasts are also in the mix.1,2 You might think of these microbes as harmful to your health, but a vast majority support your health in various ways. As such, they’re beneficial and even essential.

A normal microbiota supports digestion and helps harvest energy and nutrients from the foods you eat. Bacteria in your gut help break down indigestible fibre from plant foods like fruits, vegetables, grains, and legumes, by fermenting it. In doing so, they produce compounds called short-chain fatty acids (SFAs). These compounds have many health benefits, including nourishing the cells in your large intestine.1,2

In addition, your gut microbiota supports your immune system by:2

  • Crowding out harmful pathogens so they don’t multiply
  • Stimulating immune cells and producing antimicrobial proteins that help fight off foreign invaders
  • Strengthening your gut lining, preventing toxins from leaking into your bloodstream

Bacteria in your gut also produce essential vitamins like vitamin K, B12, and other B vitamins.

How your diet affects your microbiota

Your microbiota is as unique as your fingerprint. It’s shaped by factors like your genes, age, environment, medications (like antibiotics), and diet. Despite individual variations, normal microbiotas share similarities in the types and relative numbers of bacteria and other microbes. In healthy people, the gut microbiota is richly diverse. It has a balanced mix of microbes with more beneficial ones than harmful ones.1 However, your microbiota can change over time and become less diverse or imbalanced.

Diet is one of the most important factors that shape your microbiota because the foods you eat nourish trillions of microbes.3 Also, your diet is one of the few microbiota influencers you can control, so choosing the right foods is crucial.


Fibre is the part of plant foods the body can’t digest, but your gut bacteria thrive on it. Fibre stimulates the growth and activity of certain types of beneficial bacteria. Studies suggest that over time, eating a high-fibre diet changes the composition of microbes, promoting more richness and diversity in your microbiota.3 That diversity is an indicator of overall microbiota composition and a healthy gut.1, 4,5

Aim for at least 30 g of fibre daily to ensure a high-fibre diet. You can meet that goal by including a variety of these foods at each meal:

  • Colourful, fresh or frozen fruits and vegetables. They are all excellent choices, but your gut microbes are especially fond of underripe bananas, apples, artichokes, asparagus, onions, and garlic.
  • Whole cereal grains like oats, wheat bran, brown rice, barley, and quinoa.
  • Legumes like black, kidney, cannellini beans, lentils, and chickpeas.
  • Nuts and seeds like almonds, walnuts, pistachios, sunflower, chia, and flaxseeds.

Variety is key here because different microbes prefer different types of fibre.4 The greater variety of plant foods you eat, the more your microbiota benefits.

Foods with live and active cultures

Cultured and fermented foods contain many of the same species and strains of bacteria and yeasts found in a healthy microbiota. Eating and drinking more fermented and cultured foods can help boost your population of microbes.

When choosing fermented foods, check the food label to ensure the food contains “live and active cultures.” Fermented foods with live bacteria are most often in the refrigerator section of the grocery store and include:

  • Yoghurt
  • Kefir (fermented milk)
  • Sauerkraut
  • Kimchee
  • Fermented pickles or other vegetables
  • Kombucha (fermented tea)


A Western-style diet

A Western diet contains processed, packaged, fast foods, red meat, salty or sweetened snacks, and sugar or artificially sweetened beverages. These foods are low in fibre and high in added sugar, sodium, refined carbohydrates and fats, animal proteins, and various artificial ingredients and additives.

Western diets are linked with a less diverse microbiota.3,5,6 In contrast, vegetarian, vegan, or Mediterranean diet patterns promote more microbial diversity, especially when eaten over the long term.3,5,6 Still, even small, gradual changes can make a difference. Scientists note that positive microbiota shifts can happen within days after incorporating diet changes.1,3,4

Nutrition experts have known for a long time that these whole-food, plant-forward diets promote better health. It seems they also help nourish the trillions of tiny lives in your gut. When planning your meals and snacks, consider what your microbiota might like to eat too.



  1. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018 Jun 13;361:k2179. doi: 10.1136/bmj.k2179.https://www.bmj.com/content/361/bmj.k2179
  2. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7;21(29):8787-803. doi: 10.3748/wjg.v21.i29.8787.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528021/
  3. Sonnenburg JL, Bäckhed F. Diet-microbiota interactions as moderators of human metabolism. Nature. 2016 Jul 7;535(7610):56-64. doi: 10.1038/nature18846. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991619/
  4. Cronin P, Joyce SA, O’Toole PW, O’Connor EM. Dietary Fibre Modulates the Gut Microbiota. Nutrients. 2021 May 13;13(5):1655. doi: 10.3390/nu13051655. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8153313/
  5. Redondo-Useros N, Nova E, González-Zancada N, Díaz LE, Gómez-Martínez S, Marcos A. Microbiota and Lifestyle: A Special Focus on Diet. Nutrients. 2020 Jun 15;12(6):1776. doi: 10.3390/nu12061776. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353459/
  6. García-Monter C, Fraile-Martínez O, Gómez-Lahoz AM, Pekarek L, Castellanos AJ, Noguerales-Fraguas F, Coca S, Guijarro LG, García-Honduvilla N, Asúnsolo A, Sanchez-Trujillo L, Lahera G, Bujan J, Monserrat J, Álvarez-Mon M, Álvarez-Mon MA, Ortega MA. Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota-Immune System Interplay. Implications for Health and Disease. Nutrients. 2021 Feb 22;13(2):699.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7927055/


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