Your Gut Microbiome – Miraculous and Mysterious – Part 4

 Encouraging a Robust Gut Microbiome with Diet


Epidemiological and clinical trials have shown that food choices can reduce the risk of chronic diseases. Healthy diets focus on minimally processed foods naturally high in fiber such as fruits, vegetables, legumes and whole grains. Sadly, most people in the modern industrialized world eat very low levels of these foods. The resulting lack of fiber reduces the production of short-chain fatty acids by gut bacteria and, since these products play a major role in the decreased risk for conditions such as cardiovascular disease, cancer and gastrointestinal problems, the result is higher incidence of chronic diseases. Research points out that human beings and their gut microbiota evolved together over millions of years of consuming primarily plants, a diet that is very different from that of today. This mismatch may provide an explanation for the increase in chronic diseases with which we are now dealing.



In 2011 researchers analyzed the gut microbes of people across many countries and continents and observed clusters of similar bacterial species which enabled them to place every human being into one of three distinct “enterotypes” (balanced symbiotic states between microbes and their host). These enterotypes were found to be unrelated to the host’s age, gender or body weight although diet was a strong influencer (1).
The three enterotypes were….
1 High levels of species from the Bacteroides phylum of bacteria
2 Fewer Bacteroides species but many species from the Prevotella phylum of bacteria
3 High levels of Ruminococcus phylum species

A few months later, different researchers pointed out that people could be placed in just two enterotype groups based on their food choices (2).
These two enterotype groups were…
1 Mainly species from the Bacteroides phylum of bacteria. This group was associated with a long-term diet high in protein and animal fat.
2 Mainly species from the Prevotella phylum of bacteria. This group was associated with a long-term diet high in carbohydrates

More recently, researchers have dispensed with the idea that microbes in the gut cluster with similar species. Instead, they have concluded that there is actually a gradient of functionality and species types present in any given microbiome. They note that key functions of the gut bacteria can be performed by multiple species so that important metabolic processes remain unaffected by changes in bacterial composition within the whole microbiome (3,4).

In any case, it is clear that the bacterial species in any specific microbiome is largely influenced by diet and lifestyle factors. This helps us to delineate the steps we can take in our own lives to encourage the healthiest microbiome possible.

NOTE: Bacteroides species of bacteria can be “good bacteria” or “bad bacteria”, depending on their situation. Bacteroides species are prevalent in the human gut, comprising about 25% of all gut bacterial species. They are passed from mother to child during a normal vaginal birth and so become part of the human gut microbiota very early in life. Both Bacteroides and Prevotella prefer to work on plant material. Thus species of both these groups increase in number with a vegetarian or vegan diet although such diets generally encourage a greater abundance of Prevotella species than Bacteroides species. Bacteroides species have a complex but mostly beneficial relationship with the host, as long as they remain within the gut. Within the intestine, Bacteroides have many benefits including the breaking down of complex fibers, regulation of the immune system and preventing colonization of the gastrointestinal tract with disease-causing bacteria. When they escape the gut however, they become dangerous and can cause infections at many body sites including the abdomen, brain, liver, pelvis, and lungs as well as in the bloodstream. (5,6)



Characteristics of human gut bacterial communities change dramatically with different dietary patterns. Analysis of microbial gut communities shows a stepwise drop in species diversity as dietary patterns go from herbivore to omnivore to carnivore. (7).

Diets high in protein and saturated fat (from animal-sourced foods) encourage an inflammatory gut environment consisting of high numbers of Bacteroides species. Such diets are associated with lower diversity of the gut microbiome and higher risk of obesity and inflammatory bowel diseases. Animal-based diets result in lower production of short-chain fatty acids by the gut bacteria. This is partly because dietary factors from animal-sourced foods have the potential to harm a microbiome. For example, iron from red meat can enhance the ability of a disease-causing bacteria to damage the host and increase the permeability of the gut barrier, allowing foreign substances to enter the bloodstream. (8,9).

Diets high in whole unprocessed carbohydrates and fiber (from plant foods, especially whole grains, fruits, vegetables and legumes) encourage anti-inflammatory bacterial species such as those from the Prevotella phylum that are proficient at producing short-chain fatty acids. People eating a plant-based diet harbour significantly lower numbers of inflammatory Bacteroides species compared to those eating a more omnivorous diet that is lower in fiber and higher in animal protein and saturated fat. Increased dietary fiber from plant-sourced foods increases gut bacteria diversity and reduces inflammation. Additionally, fiber and polyphenols from plants can inhibit the growth of disease-causing bacteria and increase beneficial bacteria such as bifidobacteria and lactobacilli. (5,8,9,10,11).

Prebiotic foods are foods that contain undigestible fiber compounds that pass largely unchanged through the upper part of the gastrointestinal tract to feed the microbes of the lower intestine. However, they are set apart from other high fiber foods in that they stimulate the growth, composition and/or activity of intestinal bacteria thus conferring a beneficial physiological effect on the host (12). Examples of some of the healthiest prebiotic foods are onions, leeks, garlic, asparagus, spinach, beans, oats, whole-wheat, bananas, chicory root and Jerusalem artichokes.
Fructo-oligosaccharides (FOS) occur naturally in these foods. They have been found to stimulate the growth of non-pathogenic intestinal microbiota and can decrease blood levels of cholesterol (14).
A double blind, randomized, crossover study illustrated that eating whole grains can increase numbers of beneficial bifidobacteria and lactobacilli species and decrease total cholesterol levels (15).
Studies on oatmeal porridge also elucidate its positive effect on gut microbial functions (16).

Short-term dietary changes have an immediate influence on the gut bacteria population. A 2014 study fed subjects either an all plant-based diet of grains, beans, fruits and vegetables or an all animal-product diet of meats, eggs and cheeses for only three days and observed dramatic shifts in the species present in the gut microbiome. The microbiome resulting from the plant-based diet contained higher numbers of bacteria associated with good gut health while the microbiome resulting from the animal-based diet contained bile-tolerant organisms that are associated with inflammation and disease (17).

Vegetarian or Vegan? It is clear that diets emphasizing foods from plants are a strong factor for a microbiome high in healthy bacteria. But does a fully plant-based vegan diet promote a healthier microbiome than a vegetarian diet? A 2014 review looked at this question and found that the gut microbiomes of vegans, vegetarians and omnivores follow a continuum. Though microbiomes of vegetarians are healthier than those of omnivores, vegan microbiomes outshine the others. (5)

1 Vegan microbiomes contain fewer disease-causing microorganisms and a greater abundance of protective species which likely play a role in reduced risks of chronic diseases such as cardiovascular disease, colon cancer, diabetes and obesity.
2 Vegan gut microbiomes show reduced levels of inflammation compared to both vegetarian and omnivorous microbiomes.
3 Vegans lack the gut microorganisms that can convert dietary carnitine and choline into TMAO, a molecule that promotes the build up of atherosclerotic plaques in blood vessels and is linked to higher incidence of cardiovascular disease.
4 People eating a vegan diet have a lower risk of hypothyroid disease. This is attributed to both a reduction in inflammatory enzymes and high dietary fiber, both of which affect intestinal bacterial metabolism.
5 Diet-induced changes in the microbiome from eating a vegan diet can reduce disease activity in patients with rheumatoid arthritis.

GEOGRAPHICAL AND CULTURAL FACTORS come into this as well and, here again, dietary patterns play a major role. Traditional societies such as those of rural Africa and the Guahibo Amerindians from South America have a much greater abundance of Prevotella species in their microbiome compared to people in industrialized societies. Traditional diets are based on plants such as corn and cassava.
The gastrointestinal tracts of children in rural Africa show significantly higher levels of short-chain fatty acids and increased microbial diversity compared to those of children in Western Europe.
North Americans and Western Europeans who are eating diets rich in animal protein have a preponderance of inflammatory Bacteroides species in their gut microbiomes. (18)


Still to come…

In the last part of this article we’ll look at other ways to influence the health of your microbiome.




1 Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R. et al. Enterotypes of the human gut microbiome. Nature. 2011 May 12;473(7346):174-180

2 Wu, G.D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y..-U., Keilbaugh, S.A. et al. Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes. Science. 2011 Oct 7; 334(6052): 105–108.

3 Gorvitovskaia, A., Holmes, S.P., Huse, S.M. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4, 15 (2016) doi:10.1186/s40168-016-0160-7.

4 Knights, D., Ward, T.L., McKinlay, C.E., Miller, H., Gonzalez, A., McDonald, D., Knight R. Rethinking “Enterotypes”. Cell Host and Microbe. October, 2014; 16(4): 433-437.

5 Glick-Bauer, M., Yeh, M.C. The health advantage of a vegan diet: exploring the gut microbiota connection. Nutrients. 2014 Oct 31;6(11):4822-4838.

6 Wexler, H.M. Bacteroides: the Good, the Bad, and the Nitty-Gritty. Clin Microbiol Rev. 2007 Oct; 20(4): 593–621.

7 Wong, J., Comelli, E.M., Kendall, C.W.C., Sievenpiper, J., Noronha, J.,Jenkins, D.J.A. Dietary Fiber, Soluble and Insoluble, Carbohydrates, Fructose, and Lipids. From the book: The Microbiota in Gastrointestinal Pathophysiology. 2017; Pages 187-200. DOI:10.1016/B978-0-12-804024-9.00022-7.

8 Puupponen-Pimiä, R., Aura, M., Oksman-Caldentey, K.-M., Myllärinen, P. et al. Development of functional ingredients for gut health. Trends in Food Science & Technology. 2002; 18(1):3-11.

9 A Zhang, Y.-J., Li, S., Gan, R.-Y., Zhou, T., Xu, D.-P., Li, H.-B. Impacts of Gut Bacteria on Human Health and Diseases. Int J Mol Sci. 2015 Apr; 16(4): 7493–7519.
10 Klimenko, N.S., Tyakht, A.V., Popenko, A.S., Vasiliev, A.S., Altukhov, I.A., Ischenko, D.S., et al. Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project. Nutrients. 2018 May; 10(5): 576.

11 Tuohy, K.M., Conterno, L., Gasperotti, M., Viola, R. Up-regulating the human intestinal microbiome using whole plant foods, polyphenols, and/or fiber. J Agric Food Chem. 2012 Sep 12;60(36):8776-8782.

12 Holscher, H.D. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017; 8(2): 172-184.


14 Sabater-Molina, M., Larqué, E., Torrella, F., Zamora, S. Dietary fructooligosaccharides and potential benefits on health. J Physiol Biochem. 2009 Sep;65(3):315-328.

15 Costabile, A., Klinder, A., Fava, F., Napolitano, A., Fogliano, V., Leonard, C., Gibson, G.R., Tuohy, K.M. Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br J Nutr. 2008 Jan;99(1):110-120.
16 Valeur, J., Puaschitz, N.G., Midtvedt, T., Berstad, A. Oatmeal porridge: impact on microflora-associated characteristics in healthy subjects. Brit J Nutr. January 2016: 115(1); 62-67.

17 David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-563.

18 Wong, J.M.W. Gut microbiota and cardiometabolic outcomes: influence of dietary patterns and their associated components. Am J Clin Nutr. July 2014; 100(suppl-1): 369S–377S.

Promoting a healthy adventurous lifestyle powered by plants and the strength of scientific evidence.

My name is Debra Harley (BScPhm) and I welcome you to my retirement project, this website. Over the course of a life many lessons are learned, altering deeply-rooted ideas and creating new passions.


  1. Ruth Russell on April 24, 2020 at 2:03 pm

    Thanks Deb. I always like to read the articles you post. I’m still not either a vegetarian or a vegan but because of your influence we have made
    some changes to our diets for the better. We are buying much less meat and dairy products. For the first time in many years I am starting a little vegetable & herb garden in my yard…. Smalls steps add up to big steps… Many thanks for your info and encouragement.

    • Deb on April 26, 2020 at 9:45 pm

      Hi Ruth, I am so happy to hear about your steps towards changing your diet. You’re going in the right direction and the farther you go, the easier it will be to keep on. Now is a good time to start. These strange times give us even more reasons to look after our health!

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