Diet & Lifestyle

The Microbiome Diet: 5 Ways to Improve Gut Health Through Diet

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The Microbiome Diet: 5 Ways to Improve Gut Health T...

Last Updated: October 2, 2020

Did you know that changing your diet can result in a shift of the microbial composition of your gut in as little as 24 hours? (13) Gut health has become a popular topic due to the numerous ways in which it impacts overall health and disease states. You can actively promote better gut health by consuming a diet that supports the health of your gut microbiota, the live microorganisms that reside in your digestive tract. In turn, your microbiota is involved in many important body functions, such as modulating immune function, protecting against infections, and producing certain nutrients. (7)

Continue reading to learn about the gut microbiome, the impact of different dietary components, and how to improve gut health with dietary habits.

Young girl holding a bowl of vegetables and smiling.

The best diet for gut health includes prebiotic fiber, polyphenols from plants, and probiotics which may benefit the gut microbiome.

What is the gut microbiome?

While the community of microorganisms inhabiting the gastrointestinal (GI) tract is known as gut microbiota, the gut microbiome refers to the collective genetic material and functions of the microorganisms populating the GI tract. (9)(15) A symbiotic relationship exists between the gut microbiota and its host. Microbes in the digestive tract are often described as “commensal”, which means they obtain food or other benefits from their host without causing harm. In turn, these microbes also provide a number of health benefits to the host. (7)

Poor microbiome health can be marked by lower bacterial diversity and microbial imbalance, known as dysbiosis. (15) Impaired microbiome health has been associated with increased disease risk in many health conditions, including:

The National Institutes of Health (NIH) funded The Human Microbiome Project (HMP), a two-phase research project which sought to understand the microbial composition of healthy microbiota in humans based on genetic sequencing data. Interestingly, the HMP found that healthy individuals have a large variability in the composition of microbial strains. Phase two of the study, the integrated Human Microbiome Project (iHMP), included measures of microbial functional activity, such as metabolite production by the participants and their microbiome, as well as functional changes in the participants, which provide further insight into the connection between microbiota and disease. (4)(8)

Impact of dietary components on the microbiome

Various aspects of the diet can impact the gut microbiota by stimulating the growth of certain strains of bacteria, (7) affecting overall microbial diversity, (13) and influencing their production of bioactive metabolites. Metabolites produced by bacteria include vitamins, amino acids, and short-chain fatty acids. (1) Below, we discuss several dietary components and their impact on the gut microbiome.


Dietary protein, which is primarily digested in the small intestine, is an important component of the human diet. However, when consumed in excess, higher amounts of protein can be found in the colon, which can be detrimental to the health of the microbiota. Protein in the colon is fermented by the microbes, a process that may encourage the growth of pathogenic bacteria. (6) Further, research suggests that excessive protein intake may result in reduced production of short-chain fatty acids (SCFAs) such as butyrate. SCFAs, produced by bacteria in the colon, help to maintain the intestinal mucosal barrier and are believed to reduce inflammation in the gut. (13)

A bowl of Asian noodles with mushrooms, tofu, and greens on a grey backdrop.

Moderating protein intake may result in less fermentation of excessive protein in the colon. (6)


In addition to protein, dietary fat intake may also impact microbial composition. High-fat diets have been associated with reduced abundance of Akkermansia in the gut, a genus of bacteria that may improve markers of metabolic syndrome. Conversely, intake of polyunsaturated fatty acids (PUFAs) found in fish oils may positively influence gut microbiota by promoting specific beneficial strains such as Bifidobacterium, Akkermansia, and Lactobacillus, indicating that the type of fat consumed may be a determinant of microbial changes. (16)


Probiotics are defined as live microorganisms that confer a health benefit to the host when consumed. The health impacts and benefits of probiotics have been well-established. Probiotics have been shown to improve the composition of intestinal microbiota, as well as support digestive health and immune function. Probiotics may be used in the treatment of several health conditions, such as insulin resistance, type 2 diabetes, obesity, non-alcoholic fatty liver disease, (7) ulcerative colitis, and depressive symptoms, as well as preventing upper respiratory tract infections, diarrhea, and eczema in children. (15)

Probiotics from dietary sources, such as fermented milk or yogurt, have been shown to exert benefits by increasing counts of Bifidobacteria, Lactobacilli, and total bacterial load, as well as possibly increasing the production of interleukin-10 (IL-10), an anti-inflammatory cytokine. (13)

Probiotics have been shown to interact with the human gut microbiome.

Prebiotic fiber

Prebiotics are a type of indigestible dietary fiber that undergo fermentation by intestinal bacteria, producing metabolites that are used as fuel for other bacteria, such as pyruvate, lactate, and ethanol. (1) Other metabolites of prebiotic fermentation, including SCFAs such as propionate, butyrate, and acetate, (1) act as communication mediators between the microbiome and the host’s immune system. (11) Consuming prebiotics, such as inulin and galactooligosaccharides (GOS), has also been shown to selectively stimulate the growth of beneficial Bifidobacterium and Lactobacillus bacteria. (1)

Artificial sweeteners

Non-caloric artificial sweeteners (NAS) include sucralose (e.g., Splenda), saccharin (e.g., Sugar Twin, Sweet’N Low), and aspartame (e.g., Equal, NutraSweet). A publication in the journal Nature suggests that NAS consumption is associated with gut dysbiosis, an imbalance in microbiota. In turn, gut dysbiosis may result in metabolic changes such as glucose intolerance. (14)


Polyphenols, a broad class of plant-based compounds, may inhibit the growth of potentially pathogenic bacteria. For example, polyphenols found in citrus, including poncirin, naringenin, hesperetin, and diosmetin, were found to inhibit the growth of H. pylori, (16) a strain of bacteria whose overgrowth increases the risk of gastritis and peptic ulcers. (12) Additionally, polyphenols found in green and black tea, including epigallocatechin gallate, catechin, and gallocatechin, may inhibit strains such as E. coli, H. pylori, as well as Staphylococcus aureus, (1) which is commonly known for resulting in hospital- and community-acquired infections. (5)

Salad of tomatoes, cheese, black olives, and olive oil.

The Mediterranean diet, high in olive oil, vegetables, legumes, and whole grains, has been associated with increases in beneficial bacteria and metabolites. (13)

Special diets and the microbiome

Certain special diets have also been studied for their effects on the microbiome. A systematic literature review found that a typical Western diet, high in fat and animal protein and low in fiber, is associated with a decreased total bacterial count and decreased numbers of beneficial Eubacterium and Bifidobacterium species. (13) Similarly, individuals following a gluten-free diet, which restricts any gluten-containing grains (e.g., wheat, barley, rye), for 30 days were found to have decreased beneficial Lactobacillus and Bifidobacterium strains, as well as increased numbers of potentially pathogenic bacteria such as E. coli. (13)

While certain diets may impair the health of the microbiota, others may be beneficial. The well-established health benefits of the Mediterranean diet, such as improvements in lipid profile, obesity, and inflammation, may be a result of favorable changes to the composition of gut bacteria. A review study found that high adherence to the Mediterranean diet was associated with increased levels of short-chain fatty acids (SCFAs) and Firmicutes bacteria, including Prevotella. This diet incorporates plenty of olive oil, vegetables, fruit, legumes, grains, and nuts with smaller amounts of poultry, seafood, fermented dairy products, and red wine, while limiting red meat and sweets. (13)

Putting it all together: A healthy microbiome diet

Below are 5 dietary tips to help support a healthy gut microbiome.

1. Focus on fiber

Eat a high-fiber diet rich in vegetables, fruit, legumes, nuts, seeds, and whole grains. Include prebiotic-rich foods, such as unrefined barley, oats, soybeans, and sources of inulin (e.g., onion, garlic, leeks, bananas). (1)(13)

Anthropologists estimate that our modern human ancestors ate a total of approximately 100 grams of fiber per day. (2) Today, an estimated 95 percent of American adults and children don’t meet the minimum recommended amounts of fiber. (10)

The Institute of Medicine’s recommended daily fiber intake by population is outlined in the table below. (10)

The dietary reference intake (DRI) for fiber varies by population. (10)

2. Limit sugar and artificial sweeteners

Both natural sugars (e.g., beet sugar, cane sugar, date sugar) and artificial sweeteners may result in modified gut microbiota, such as decreased counts of Bacteroides. (13) To help with the transition, you can start by replacing sweets and desserts high in sugar with fresh fruits, which contain natural sugars but also provide polyphenols, fiber, vitamins, minerals, and water. If you currently consume regular or diet soda, try to substitute your soda with sparkling water or soda water with lemon or lime juice.

3. Choose the right protein

Overall, moderate consumption of protein may benefit microbial diversity. (13) Favor vegetarian protein sources, such as pea protein and whey protein, and consume animal-based proteins in moderation. The Institute of Medicine’s recommended dietary allowance (RDA) for adult women and men is 0.8 grams of protein per kilogram of body weight per day. (3) For example, for a 150lb (68kg) individual, this translates to approximately 54 grams of protein daily. Consuming two eggs, one chicken breast, a handful of almonds, and a scoop of whey protein powder yields approximately 54 grams of protein in a day.

4. Include polyphenols

Foods high in polyphenols that may benefit gut microbiota include black and green tea, citrus fruit, red wine, berries, (1) cocoa, and seeds. (13)

5. Fermented foods are your friends

Probiotics can be obtained through your diet by incorporating cultured dairy products (e.g., kefir, yogurt), fermented vegetables (e.g., sauerkraut, kimchi, unpasteurized pickles), and fermented soy products (e.g., miso, tempeh, natto).

The bottom line

Eating a diet designed to support your microbiome may result in improved overall health. Dietary components such as fiber, polyphenols, probiotics, and polyunsaturated fatty acids from fish oil have all been found to benefit the microbiome, while sugar, artificial sweeteners, and excessive protein and fat may negatively impact the microbiome. Give the tips in this article a try to improve the health of your microbiome, or speak with your integrative healthcare provider for more information.

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  1. Duda-Chodak, A., Tarko, T., Satora, P., & Sroka, P. (2015). Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: A review. European Journal of Nutrition, 54(3), 325–341.
  2. Eaton, S. B. (2006). The ancestral human diet: What was it and should it be a paradigm for contemporary nutrition? Proceedings of the Nutrition Society, 65(1), 1–6.
  3. Institute of Medicine. (2005). Protein and amino acids. In Dietary Reference Intakes (pp. 589–768). Washington, D.C.: The National Academies Press.
  4. Integrative HMP (iHMP) Research Network Consortium (2019). The Integrative Human Microbiome Project. Nature, 569(7758), 641–648.
  5. Lowy, F. D. (1998). Staphylococcus aureus Infections. The New England Journal of Medicine, 339, 520-532.
  6. Ma, N., Tian, Y., Wu, Y., & Ma, X. (2017). Contributions of the interaction between dietary protein and gut microbiota to intestinal health. Current Protein & Peptide Science, 18(8).
  7. Markowiak, P., & Śliżewska, K. (2017). Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients, 9(9), 1021.
  8. Meyer, K. A., & Bennett, B. J. (2016). Diet and gut microbial function in metabolic and cardiovascular disease risk. Current Diabetes Reports, 16(10), 93.
  9. Paoli, A., Mancin, L., Bianco, A., Thomas, E., Mota, J. F., & Piccini, F. (2019). Ketogenic diet and microbiota: Friends or enemies? Genes, 10(7), 534.
  10. Quagliani, D., & Felt-Gunderson, P. (2016). Closing America’s fiber intake gap: Communication strategies from a food and fiber summit. American Journal of Lifestyle Medicine, 11(1), 80–85.
  11. Ratajczak, W., Rył, A., Mizerski, A., Walczakiewicz, K., Sipak, O., & Laszczyńska, M. (2019). Immunomodulatory potential of gut microbiome-derived short-chain fatty acids (SCFAs). Acta Biochimica Polonica, 66(1), 1–12.
  12. Reshetnyak, V. I., & Reshetnyak, T. M. (2017). Significance of dormant forms of Helicobacter pylori in ulcerogenesis. World Journal of Gastroenterology, 23(27), 4867–4878.
  13. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., … Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15(1), 73.
  14. Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., … Elinav, E. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 514(7521), 181–186.
  15. Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ, 361, k2179
  16. Yang, B. G., Hur, K. Y., & Lee, M. S. (2017). Alterations in gut microbiota and immunity by dietary fat. Yonsei Medical Journal, 58(6), 1083–1091.


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