Top Six Ways to Support your Microbiota

by Dr. Sarah Nyrose BSc ND

The microbiota – the composition of bacteria and fungi in our gastrointestinal system – plays an important role in our digestion and health.

O ur diet and lifestyle impact the health and composition of our gut microbiota. Here are our top six ways to support our beneficial bacteria and fungi through food and lifestyle:

1. Prebiotics: feeding your gut microbiota!

Bacteria thrive on prebiotics, which are carbohydrates that resist human digestion and are later fermented by intestinal microflora, specifically bifidobacteria and lactobacilli. While the term “prebiotic” is relatively new, foods high in prebiotics have been consumed since prehistoric times. 

When the bacteria break down these non-digestible fibres, they produce short chain fatty acids (SCFA), such as butyrate. SCFA’s nourish the cells of our gut lining, help regulate our immune system, reduce inflammation, promote the production of serotonin, and have potential anti-cancer properties.1

A varied diet that includes vegetables and grains with prebiotics can help maintain the health of your intestinal microflora. Foods high in prebiotics include:

  • Leeks
  • Asparagus

  • Garlic

  • Onions

  • Wheat

  • Oats


  • Chicory root
  • Jerusalem artichoke

  • Bananas

  • Apples
  • Burdock root

  • Leeks
  • Asparagus

  • Garlic

  • Onions

  • Wheat

  • Oats

  • Chicory root
  • Jerusalem artichoke

  • Bananas

  • Apples
  • Burdock root

2. Don’t skip the fibre.

It’s well known that a diet high in fibre is beneficial; it helps to reduce the risk of developing heart disease, diabetes, and arthritis. Fibre contains prebiotics, which feed the healthy bacteria, but it also acts to sweep out waste products, dead bacteria and toxins. Having daily bowel movements is an important part of regulating the gut microbiota and ensuring your body is getting rid of the waste. 

An adult should consume approximately 30–40 grams of fibre per day. Foods high in fibre include oats, pears, blackberries, legumes, nuts and seeds. To provide some perspective, a cup of oatmeal contains 4 grams of fibre, a cup of raspberries contains 8 grams of fibre, and a cup of black beans contains 15 grams of fibre. Check out our Seed Loaf to increase your morning fibre.

3. Polyphenols: the microbiota mediator.

Polyphenols are dietary compounds that are found in various fruits, vegetables, spices and beverages. Certain bacteria (Lactobacillus sp. and Bifidobacterium sp.) that line the gut break these compounds down into smaller metabolites. The polyphenols and their metabolites have been shown to modulate the gut microflora populations through selective antimicrobial action towards pathogenic bacteria.2

Food particularly high in polyphenols includes cloves, ground flaxseed, dark chocolate, berries, rosemary, basil, and coffee.

Fermented foods, such as sauerkraut, kimchi and kefir, contain live microorganisms and are an important dietary source of probiotics.

4. Include fermented foods in your diet. 

Fermented foods, such as sauerkraut, kimchi and kefir, contain live microorganisms and are an important dietary source of probiotics. The live microorganisms break down the food through fermentation, and in doing so, can enhance the nutritive and health properties of the food.3

5. Ditch the antibacterial soap; Avoid triclosan.

Unless you’re in a hospital, you should not be using antimicrobial/ antibacterial soap containing the chemical triclosan. Triclosan, which is too commonly found in numerous household items, such as toothpaste, soaps and cosmetics, is a microbicide- it kills bacteria. A study in 2016 looked at the impacts of Triclosan on the microbiome of adult zebrafish. They discovered that exposure to the microbicide altered the structure and diversity of the gut microbiota.Furthermore, the widespread use of Triclosan is contributing to microbial resistance. We want to reserve the use of these products for when they are really needed! 

 6. Only use antibiotics when you need them 

There are times when antibiotics are required and crucial to treat a bacterial infection. However, the inappropriate use of antibiotics is a global problem and is contributing to bacterial resistance to antibiotics. In addition, the unnecessary use of antibiotics can impact an individual’s microbiome, and allow for pathogenic bacteria to thrive. This is of particular importance for infants and children, when their microbiome is still impressionable and forming. 

If you need to take antibiotics, taking a broad-spectrum probiotic during and after the antibiotic course can help to prevent digestive side effects and protect the microbiome.5

  1. Slavin, J. (2013). Fiber and prebiotics: mechanisms and health benefits. Nutrients, 5(4), 1417-1435.
  2. Cardona, F., Andrés-Lacueva, C., Tulipani, S., Tinahones, F. J., & Queipo-Ortuño, M. I. (2013). Benefits of polyphenols on gut microbiota and implications in human health. The Journal of nutritional biochemistry, 24(8), 1415-1422
  3. Marco, M. L., Heeney, D., Binda, S., Cifelli, C. J., Cotter, P. D., Foligné, B., … & Smid, E. J. (2017). Health benefits of fermented foods: microbiota and beyond. Current opinion in biotechnology, 44, 94-102
  4. Gaulke, C. A., Barton, C. L., Proffitt, S., Tanguay, R. L., & Sharpton, T. J. (2016). Triclosan exposure is associated with rapid restructuring of the microbiome in adult zebrafish. PLoS One, 11(5), e0154632
  5. Rodgers, B., Kirley, K., & Mounsey, A. (2013). Prescribing an antibiotic? Pair it with probiotics. The Journal of Family Practice, 62(3), 148–150.

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