top of page

Diet and your gut microbiome

A healthy gut microbiome protects our bodies and GI tract from infection, inflammation, and diseases.  Researchers have found that which bacteria thrive depends on what you eat.  These bacteria can change very quickly, within 24 hours for some.  This would be great news if we could identify exactly which bacteria were the most important. However, no precise way of eating that fits all.  We are all unique individuals with unique microbiomes!


So, what do we know?  The microbiome is very sensitive to changes in diet.  Research does suggest that there are some general guidelines that could help provide the best environment to protect the gut.  These guidelines may sound familiar as they represent an overall healthful way of eating.  Research studies have been conducted in the following areas and have found disturbance in the microbiota when not following these recommendations.  Therefore, you can create the best environment possible for your gut microbiome through the food you eat.  These general guidelines include

  • Eat mostly plants such as colorful fruits and vegetables, and whole grains. These provide much needed fiber and non-digestible carbohydrates.

  • Choose low fat animal proteins and plant proteins

  • Choose whole foods; limit processed foods

  • Limit artificial sweeteners, polysorbate 80 and carboxymethylcellulose (CMC)

  • Choose unsaturated fats over saturated fats

  • Choose food over supplemental prebiotics and probiotics

Studies have shown that eating higher amounts of fiber (plants) leads to a greater microbial diversity and activity, producing short chain fatty acids (SCFAs).  These SCFAs include butyrate, propionate, and acetate.  Butyrate, in particular, helps keep the cells in our colon healthy.

When you eat lots of plants (fruits, vegetables, whole grains), you are eating different types of fiber.  This fiber is not broken down in the stomach and small intestine.  When it gets to the colon, it feeds the bacteria that produce SCFAs and protect the cells in your GI tract.


Being vegetarian is not a requirement for a healthy gut.  However, focusing on plant-based eating is recommended.  The balance of carbohydrates to protein is important as well as the type of food - whole vs processed.

Select a Category to Learn More!

Prebiotics and Fiber

One of the fastest growing segments of the microbiome market is the creation of supplemental prebiotics and the enrichment of highly refined food products with added fiber.  We would argue that eating foods that naturally contain fiber - fresh fruits, vegetables, whole grains, nuts, and legumes - should be the first choice.  These carbohydrates are GOOD!  They provide important vitamins, minerals, energy, and the many forms of fiber needed by your body. 


Carbohydrates contain multiple types of fiber. Fiber helps move food through the digestive system, can make you feel full, and control cholesterol and blood glucose levels. The carbohydrates left undigested by the body’s enzymes become important food for the gut microbiome in the colon. When in the colon, fermentable fibers called microbiota accessible carbohydrates (MACs) feed and stimulate bacterial growth. Through fermentation, the bacteria create short-chain fatty acids (SCFAs) such as butyrate, propionate, and acetate. Butyrate is especially important as it helps protect the cells in the colon.

How can I get fiber in my diet?


Eating a variety of plant-based foods helps support a diverse microbiome.  A diverse microbiome helps prevent dysbiosis and gut permeability as it maintains a healthy balance in the bacteria.  Making sure you eat a variety of fruits, vegetable, whole grains, nuts, and legumes every day is the best way to make sure you get the different fibers you need.  

Current dietary recommendations suggest that adult women ages 19-50 should aim for about 25 grams of fiber per day and men, 38 grams.  Once over 51 years old, recommended intake for women is 21 grams and for men 31 grams per day.  The average American gets about 18 grams of fiber per day.


Making sure that your plate has colorful fruits and vegetables at each meal and whole grains can help increase your fiber intake.  Eating plant-based proteins like lentils and beans instead of meat can also increase your fiber.  Those foods that have fermentable dietary fibers include

  • Citrus fruits

  • Strawberries

  • Apples

  • Raspberries

  • Legumes

  • Nuts

  • Asparagus

  • Onion

  • Garlic

  • Artichokes

  • Tomatoes

  • Bananas

  • Rye

  • Barley

  • Oat products

  • Potatoes

  • Rice

  • Pasta

  • Whole wheat

Grapefruit Slices

Grapefruit Slices





Banana bunches

Banana bunches

Fresh Organic Vegetables

Fresh Organic Vegetables

Colorful Pasta

Colorful Pasta



Fresh Lemons

Fresh Lemons

Organic Tomatoes

Organic Tomatoes

Stalks of Wheat

Stalks of Wheat







How much fiber is in a serving?

It depends on the item, but some fruits have about 3-4 grams per serving. These include an orange, tangerine, an apple or pear with skin, 1 cup of blueberries, 1 cup of strawberries.  Raspberries have about twice that fiber amount with 8 grams per cup.  For vegetables, 10 spears of asparagus have about 3 grams, ½ cup of lentils have 8 grams, ½ cup of black beans have 14 grams.  For breads and grains, you will need to read the nutrition label to see how much fiber is in each serving. The fiber content can vary widely between brands and products, but ingredients should include whole grains.


Eating a raw piece of fruit like an apple with the peel will have more fiber than eating applesauce.  Although juicing whole fruits can give you great nutrients, juices do not contain the fiber that your gut needs. 


Because different foods provide different types of fiber, focusing on just one form of fiber is not recommended.  It is really important to include as many grains, vegetables, legumes and fruits as possible, even if they aren’t listed above.  Although prebiotic products or fiber-enriched products are on the market, whole foods should be your first choice.

learn more about

Processed Foods vs Whole Foods

In industrialized countries like the United States, our diet has changed over the years.  All you have to do is go to the grocery store and see that the fresh foods are on the outside aisles and the center of the store is filled with food products – products you did not even know you wanted! Frozen foods, ready-to-eat foods, drinks of all colors of the rainbow, desserts that could stay on the shelf for a very long time, which seem convenient and cheap.  But watch out!  Some of these food products can have artificial sweeteners and emulsifiers added to them.


Research has suggested that emulsifiers and non-caloric sweeteners affect the microbiota in the large intestine.  Emulsifiers like polysorbate-80 and carboxymethylcellulose (CMC) can be used to increase shelf-life, improve mouth feel, or thicken foods.  However, initial animal studies show that eating these in a similar amount to a human diet could cause a decrease in butyrate, a fatty acid that protects the colon.  A decrease in butyrate can increase the risk of colon inflammation.  Artificial, non-caloric sweeteners such as saccharin and sucralose have also shown a negative impact to gut microbiota in animal studies.  However, more research needs to be done to know exactly how these translate to humans.

Avoiding Processed Foods

What should you do?  Read the list of ingredients looking for polysorbate-80, carboxymethylcellulose, saccharin, and/or sucralose.  Find another product that does not have these ingredients or limit the number of servings you have of these per day.  Some items where you might find these ingredients include

  • Cottage cheese

  • Pickles

  • Fat-soluble vitamins

  • Shortenings and oils

  • Gelatin desserts and dessert mixes

  • Frozen desserts: ice cream, frozen custard, ice milk, fruit sherbet

  • Barbecue sauces

  • Soft drinks - regular and diet

  • White and sparkling wines

  • Tortillas

  • Ready-to-eat cereals

Processed Foods
Prebiotics and Fiber

You are what you eat

Additives for foods are considered safe according to food industry studies but we still are learning what the impact these foods could be for the long-term. Choosing whole foods – buying and cooking foods close to their original state is what is recommended to maximize your health.

learn more about


When you eat high amounts of animal protein and low carbohydrates, you are starving the bacteria that keep your gut healthy.  The high amounts of animal protein travel to the colon and are fermented there. When this happens, the environment for the bacteria changes. The pH of the colon increases which causes a reduction in the healthful bacteria that produce butyrate.

Can I still eat protein?  Yes, you should always eat some type of protein! Your body needs it for muscles and to function. But you should balance it with complex carbohydrates too.  Your plate should be ¼ protein such as a lean meat, ¼ whole grain like brown rice or a potato, and ½ vegetables like broccoli, tomatoes, peppers, cauliflower, carrots


Think of a colorful plate – like a rainbow.

What are non-animal sources of protein?

Plant-proteins are always a good option as well such as from soy (tofu), beans (black beans and pinto beans), legumes (lentils and chickpeas), nuts, and grains like quinoa. Avocado even can be a good source of protein. Eating plant-based meals a few times per week is always a good idea for your gut and overall health.  An added bonus, these plant proteins feed the bacteria that are best for our gut.

learn more about

Repopulating the Gut - Probiotics

As with most areas of health, companies are always trying to find a quick fix to sell; the gut microbiome is no different. One supplement that seems to be everywhere is probiotics.  We do not know yet exactly which bacteria we need.  Lactobacillus and bifidobacteria have generally been recognized as beneficial; however, we do not know yet which strain(s) we need for which condition.


Marketed as “nutraceuticals”, probiotics cannot make health claims nor does the FDA regulate them.  That makes it hard to regulate quality and quantity of bacterial strains.  Everyone’s gut microbiome is unique; therefore, we do not know yet which probiotic would be best for your gut health. 


The best thing you can do is to continue to eat lots of complex carbohydrates, especially when given antibiotics. Choose whole food sources of naturally occurring probiotics like yogurt, kefir, sauerkraut, and kimchi.

learn more about


  1. David, L.A., et al., Diet rapidly and reproducibly alters the human gut microbiome. Nature, 2014. 505(7484): p. 559-63.

  2. De Filippo, C., et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A, 2010. 107(33): p. 14691-6.

  3. Mills, S., et al., Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients, 2019. 11(4).

  4. Singh, R.K., et al., Influence of diet on the gut microbiome and implications for human health. J Transl Med, 2017. 15(1): p. 73.

  5. Sonnenburg, E.D. and J.L. Sonnenburg, Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab, 2014. 20(5): p. 779-786.

  6. Gropper, S.S. and J.L. Smith, Advanced nutrition and human metabolism. 2012: Cengage Learning.

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

  8. Chassaing, B., et al., Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature, 2015. 519(7541): p. 92-6.

  9. Duncan, S.H., et al., Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol, 2007. 73(4): p. 1073-8.

  10. Hemarajata, P. and J. Versalovic, Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol, 2013. 6(1): p. 39-51.

  11. Ma, N., et al., Contributions of the Interaction Between Dietary Protein and Gut Microbiota to Intestinal Health. Curr Protein Pept Sci, 2017. 18(8): p. 795-808.

  12. Miclotte, L. and T. Van de Wiele, Food processing, gut microbiota and the globesity problem. Crit Rev Food Sci Nutr, 2019: p. 1-14.

  13. Riviere, A., et al., Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol, 2016. 7: p. 979.

  14. Ruiz-Ojeda, F.J., et al., Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials. Adv Nutr, 2019. 10(suppl_1): p. S31-S48.

  15. Russell, W.R., et al., High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr, 2011. 93(5): p. 1062-72.

  16. Suez, J., et al., Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 2014. 514(7521): p. 181-6.

  17. Wolfram, T. Prebiotics and Probiotics: Creating a Healthier You. 2018  [cited 2019 May 27]; Available from:

bottom of page