Investigation into the function and evolution of the human microbiome, our ‘old friends’ helping us unlock the nutritional benefits from a wider range of food sources, is leading to a revolutionary new understanding of the nutritional benefits of a high fiber diet.

Plant fiber is a natural, abundant and versatile material, found within the cell wall of all plants on earth! Historically, fiber has been used to produce clothing, shelter, paper, fire and food. All of these have been vital to the progression of humanity since the dawn of agriculture. But plant fiber as food has arguably had the largest influence on the evolution of our species.


Today, the benefits of a high fiber diet are emphasized by all major international health agencies (Stephen et al., 2017). Experts advocate for this lifestyle choice as an important approach in the management and prevention of numerous diseases, including obesity, type 2 diabetes, heart disease and inflammatory diseases (Rook et al., 2017). Dietary fiber is recognized as the preferred food source for a healthy microbiota (Johnson et al., 2018), with the following food sources helping to increase your dietary fiber intake:

  • Fruits – such as bananas, oranges, pears, apples and berries – and especially the skin of kiwifruit, apples, grapes and tomatoes

  • Dark vegetables – carrots, beets, broccoli, spinach, artichokes and potatoes

  • Beans and legumes

  • Whole grain bread

  • Dark grains – brown rice over white rice

  • Unsalted nuts and seeds – almonds, pistachios, or pumpkin and sunflower seeds

As researchers begin to uncover the crucial role our microbiota has on health and disease, they are also developing a better understanding of the benefits of high fiber diets, or the consequences of not maintaining a balanced diet with recommended levels of fiber intake.

The Modern vs. Historical Diet

It’s no secret that the Western world’s high fat, highly refined diet has a negative impact on health. However, recent studies are quantifying the effects that our increasingly unhealthy diets are having on our health.

A 2010 study by De Filippo and colleagues in Italy compared the fecal microbiota of children living either in Europe or in the rural African village of Burkina Faso. The isolated nature of this village allowed for it to be used as a parallel to an early human settlement at the birth of agriculture. While European children ate a diet typical for the developed world, African children had a diet high in fiber but low in fat and animal protein, consisting primarily of cereals (millet and sorghum grain), legumes (black-eyed peas) and vegetables.

(Left) A rural village in Burkina Faso. (Center) A typical diet of African children consisting of ground millet and sorghum. (Right) Grinding of millet and sorghum on a grinding stone to make a thick porridge. Adapted from De Filippo et al., 2010.

The results showed that gut microbiota differed significantly based on diet, with African children having bacteria capable of breaking down plant fibers (prevotella and xylanibacter) that were completely absent in the European population.

The researchers hypothesized that the reduction in microbiota richness they observed in European compared with African children “could indicate how the consumption of sugar, animal fat, and calorie-dense foods in industrialized countries is rapidly limiting the adaptive potential of the microbiota.”

Nutritious millet porridge topped with chocolate pieces, hazelnuts, almond slices and cherry. Credit: NoirChocolate.
Nutritious millet porridge topped with chocolate pieces, hazelnuts, almond slices and cherry. Credit: NoirChocolate.

A diverse, healthy microbiome

In the same way that genetic diversity in a population is beneficial for disease resistance, diverse microbiota in your gut protects its host against pathogenic bacteria in the following ways:

(1) Metabolite production

A healthy microbiota produces specific antimicrobial by-products that deter pathogenic bacteria. A healthy microbiota also secretes immunoprotective molecules.

(2) Occupation of ecological niches

Our body is like a cinema with the seats taken up by good bacteria. When we excessively clean ourselves with soaps and shampoo, we free up the ‘seats’ in the healthy microbiome, increasing the chance that they’re taken up by bad bacteria (pathogens).

(3) Nutrient competition

A healthy microbiota breaks down resistant food sources, such as plant fiber, to access an untapped energy source and allow “good” microbes in our gut to out-survive pathogenic bacteria that have allocated their resources towards infection (Rook et al., 2017).

The link between a fiber-rich diet and the maintenance of a diverse, balanced microbiota was explained in a 2016 study by Desai et al. Typically, the food sources of a healthy microbiota are the energy-rich plant fibers that pass through the stomach undigested and reach the small intestine. However, when fiber is absent from the diet, gut bacteria are forced to switch to an alternative energy source – the glycoprotein-rich mucus layer of the gut wall. This is a problem, because this layer functions as the gut’s first line of defense against invasive pathogens. The diminishment of this layer of the gut wall increases the host’s susceptibility to infection.

A subset of gut microbes have adapted to use the mucus layer of the gut wall as an energy source. In the absence of fiber in the diet, these microbes proliferate and out-compete beneficial fiber-digesting bacteria. Once the mucus layer of the gut wall has been depleted, the gut microbiota becomes highly unstable, allowing pathogenic bacteria to more easily penetrate this defensive barrier. This can lead to the lethal inflammatory bowel disease ulcerative colitis (Desai et al., 2016).

Read more: Fiber Is Good For You. Now Scientists May Know Why, by Carl Zimmer, New York Times

Human gut anatomy showing organization at cellular and molecular level mechanism, and interaction with bacteria in the human gut.

Looking after your gut health

So, what can you do to maintain your microbiome health?

First, there is mounting evidence that events in early life can have a long-term impact on your microbiome-related health. Mothers pass their microbiota to their children during natural childbirth and breastfeeding. These events represent opportunities for mothers to “inoculate” their children with beneficial bacteria while they are still developing the complex “organ” that is the microbiome (Mueller et al., 2015). For this reason, women should avoid unnecessary perinatal antibiotics.

However, as an adult, there are steps you can take immediately after reading this article to improve your gut microbiota. Lifestyle choices such as maintaining a balanced, high fiber diet and avoiding highly refined foods are your best bets. Simple measures are to swap white bread for multigrain, use beans or legumes as the primary protein source in your next meal, or choose a sweet fruit or vegetable instead of candy to snack on. In the end, remember the magic number for your daily dietary fiber intake: 25g per day!

A high fiber raw banana “ice cream” desert, topped with blueberries, strawberries and mint. Credit: Aiselin82.


Rook, G., Bäckhed, F., Levin, B.R., McFall-Ngai, M.J., McLean, A.R., 2017. Evolution, human-microbe interactions, and life history plasticity. Lancet 390, 521–530.

Johnson, K.L., Gidley, M.J., Bacic, A., Doblin, M.S., 2018. Cell wall biomechanics: a tractable challenge in manipulating plant cell walls ‘fit for purpose’! Curr. Opin. Biotechnol. 49, 163–171.

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J.B., Massart, S., Collini, S., Pieraccini, G., Lionetti, P., 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. 107, 14691–14696.

Agha, R., Gross, A., Rohrlack, T., Wolinska, J., 2018. Adaptation of a Chytrid Parasite to Its Cyanobacterial Host Is Hampered by Host Intraspecific Diversity. Front. Microbiol.

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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. Nutr. Res. Rev. 30, 149–190.

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