Understanding your microbiome’s digestion potential

Author: Christine Stewart

05 December 2018 Education Nutrition
Middle age couple cooking healthy food together in the kitchen for better gut microbiome health

Many of us are learning our gut microbiome plays a fundamental role in our health and wellbeing. But did you know, we also need to nourish the microbes in our gut? It seems what we eat not only affects our health, but also the health of our gut bugs!

Whether climbing mountains, walking the dog or sitting at your desk, we all need nourishment to keep our bodies functioning. The food we eat every day contains a wide variety of nutrients, including protein, fat, carbohydrate, vitamins, and minerals. Your small intestine cleverly breaks down these nutrients into small particles so they can be easily absorbed and used for a variety of bodily functions.

But what nutrients do our gut microbes need?

It turns out that like us, our gut bugs need protein and carbohydrates in order to thrive. Gut bacteria consume a particular type of carbohydrate that our bodies can’t break down – fibre1! Dietary fibre is the structural part of plants which are resilient to our digestive juices2. Technically speaking, it is the bonds between the carbohydrate molecules that cannot be broken down by the enzymes available in the small intestine, so the dietary fibre reaches our large intestine relatively untouched3. This is where our friendly gut bacteria step in.

Gut bacteria consume a particular type of carbohydrate that our bodies can’t break down – fibre1!

Deep inside your gut, masses of bacteria are working tirelessly to split the glue that holds fibre together. They do this by releasing special enzymes, breaking fibre into simpler components and unleashing the energy potential inside. This process is called fermentation4,5. An end-product of fermentation is the creation of short-chain fatty acids (SCFA’s) such as butyrate, propionate and acetate6. Butyrate is the preferred fuel source for the cells lining our gut and helps to keep the integrity of this layer intact. It’s also thought to have anti-inflammatory properties in our gut7.

Butyrate is the preferred fuel source for the cells lining our gut and helps to keep the integrity of this layer intact. It’s also thought to have anti-inflammatory properties in our gut7.

Traditionally, fibre has been classified according to its ability to dissolve in water;

  1. Soluble fibre is thought to dissolve in water, forming a gel-like substance that is easily fermented by gut bacteria. Soluble fibre is mainly found in plant cells. Good sources are oats, barley, legumes and citrus fruits.5
  2. Insoluble fibre refers to the structural parts of plant cell walls which are more resistant to fermentation5. Good sources include bran, beans, legumes and vegetables.

We now understand that solubility of fibre in water is not the ideal way to understand the fermentability of fibre. We are now more likely to focus on ‘prebiotic’ fibres which are defined as selectively fermented fibres which support beneficial changes within the microbiome4.

Common types of prebiotic fibres include:

  • Resistant starches are fermentable starches that avoid digestion in the small intestine and act as a prebiotic fibre. Many popular gut health diets, such as the CSIRO Healthy Gut Diet, focus on increasing the amount of resistant starch in the diet. Good sources include cooked and cooled rice and potatoes, whole legumes and green bananas8.
  • Fructans are some of the most well researched prebiotic fibres. All fructans are basically long chains of fructose molecules but small chains (2 – 9 molecules) are known as FOS (fructooligosaccharides) while longer chain lengths are called Inulin. Fructans are found in the same grains as gluten (wheat, barley and rye) as well as various fruits and vegetables such as garlic, onion or watermelon. People with Irritable Bowel Syndrome may find that fructans exacerbate their symptoms9.
  • Pectin is a structural component found within the cell walls of plants most famously used as the ‘gelling’ agent in jam. Pectin has been shown to promote the growth of beneficial species of bacteria, such as Bifidobacterium longum and Lactobacillus gasseri10 and is generally well tolerated even by people with Irritable Bowel Syndrome. Foods naturally rich in pectin include apples, plums and lemons8.

So, what happens if we don’t eat enough fibre to keep our gut microbes well fed? They seek out alternative energy sources such as protein or the mucus protecting our gut lining. While the human gut naturally contains microbes that prefer to break down protein into smaller particles (amino acids) for energy, the metabolites produced from this type of fermentation can be more inflammatory than those produced from fibre fermentation.

There is still so much to learn about our gut bugs and how they can contribute to health. But one thing is clear; eating a diet rich in plant-based foods provides the fibre needed to have a positive influence on your gut microbiome! So do yourself (and your microbes) a favour and put more fruit, vegetables, whole grains, nuts, seeds, legumes and pulses on your plate!


  1. National Health and Medical Research Council (NHMRC). (2006) Nutrient Reference Values for Australia and New Zealand. Commonwealth of Australia. Available at https://www.nrv.gov.au/nutrients/dietary-fibre
  2. Food Standards Australia and New Zealand. (2006). Standard 1.1.2 - Definitions used throughout the Code. Canberra: FSANZ. Available at http://www.foodstandards.gov.au/code/Documents/1.1.2%20Definitions%20v159.pdf
  3. DeVries, J. W. (2003). On defining dietary fibre. Proceedings of the Nutrition Society, 62(1), 37-43. https://doi.org/10.1079/PNS2002234
  4. Slavin, J. (2013). Fiber and prebiotics: mechanisms and health benefits. Nutrients, 5(4), 1417-1435. https://doi.org/10.3390/nu5041417
  5. Williams, B., Grant, L., Gidley, M., & Mikkelsen, D. (2017). Gut fermentation of dietary fibres: physico-chemistry of plant cell walls and implications for health. International journal of molecular sciences, 18(10), 2203. https://doi.org/10.3390/ijms18102203
  6. Ríos-Covián, D., Ruas-Madiedo, P., Margolles, A., Gueimonde, M., de los Reyes-Gavilán, C. G., & Salazar, N. (2016). Intestinal short chain fatty acids and their link with diet and human health. Frontiers in microbiology, 7, 185. https://doi.org/10.3389/fmicb.2016.00185
  7. Cushing, K., Alvarado, D. M., & Ciorba, M. A. (2015). Butyrate and mucosal inflammation: new scientific evidence supports clinical observation. Clinical and translational gastroenterology, 6(8), e108. https://doi.org/10.1038/ctg.2015.34
  8. Stephen, A. M., Champ, M. M. J., Cloran, S. J., Fleith, M., Van Lieshout, L., Mejborn, H., & Burley, V. J. (2017). Dietary fibre in Europe: current state of knowledge on definitions, sources, recommendations, intakes and relationships to health. Nutrition research reviews, 30(2), 149-190. https://doi.org/10.1017/S095442241700004X
  9. Wilson, B., & Whelan, K. (2017). Prebiotic inulin‐type fructans and galacto‐oligosaccharides: definition, specificity, function, and application in gastrointestinal disorders. Journal of gastroenterology and hepatology, 32, 64-68. https://doi.org/10.1111/jgh.13700
  10. Shinohara, K., Ohashi, Y., Kawasumi, K., Terada, A., & Fujisawa, T. (2010). Effect of apple intake on fecal microbiota and metabolites in humans. Anaerobe, 16(5), 510-515.https://doi.org/10.1016/j.anaerobe.2010.03.005