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  • Larissa Spafford, NTP

What to eat (and not eat) to improve your gut microbiome health

Hippocrates, father of modern medicine

I’m with Hippocrates, the father of modern medicine, who said “All disease begins in the gut.” Modern scientific research is confirming that there is a connection between the health of our gut microbiomes, health and disease.

We know now that the gut of a healthy person has trillions of microbes (1). When your gut microbiome is healthy, the microbes contribute to your health in SO many ways. They make vitamins, essential amino acids, short chain fatty acids, improve immune function, reduce inflammation, protect you from pathogens and more. They create byproducts that help absorb minerals, regulate metabolism and provide energy.

My personal favorite is, their byproducts nourish and strengthen the cells that line the intestines. Why is this important? Because when the lining is damaged it can cause increased intestinal permeability, aka leaky gut, which can trigger the development of autoimmune diseases!(2).

The good news is that you can improve the health of your gut microbiome with what you eat and don’t eat.

What to eat for a healthy gut microbiome:

Fiber* Only plant foods contain fiber. Microbes ferment fiber which creates byproducts that benefit our health. There are many kinds of fiber, so eat a wide variety and lots of plant foods to make sure you’re getting all the kinds your microbes need.

Here is a recipe for a delicious fiber rich lentil salad.

Probiotic foods contain microbes that benefit health. Here’s a guide to probiotic foods and how to shop for them.

Tea, grapes, cacao, coffee and berries contain polyphenols that aren't completely digested by us. They're metabolized by microbes and may reduce pathogenic bacteria (3).

What to not eat for a healthy gut microbiome:

Refined sugars can feed pathogenic microbes. When the pathogenic ones flourish, the beneficial ones are outnumbered. Fruit sugars can also feed the pathogens so some people need to avoid sugars from fruit too, at least until they restore more of the beneficial microbes.

Genetically Modified Organisms (GMOs) are often modified to tolerate herbicides so a crop can be sprayed with an herbicide to kill the weeds but not the crop.

Glyphosate is the active ingredient in Round Up, the world’s most widely used herbicide. Glyphosate disrupts the beneficial bacteria in our gut (4).

According to the National Institutes of Health Toxicology Data Network, glyphosate may be an endocrine disruptor, damages human DNA and there is evidence of being a carcinogen in experimental animals (5).

Corn, soybeans, canola, alfalfa, sugar beets, papaya, squash, Arctic Apples, Innate Potatoes and Aquabounty Salmon are GMO foods. Corn, soy, canola and sugar beets make up a large percentage of the Standard American Diet. Many ingredients in processed foods are derived from them. If it’s organic, it’s non GMO. On non-organic food labels, look for a logo that says non-GMO.

Tap water that contains chlorine and/or fluoride. You can find out if they are in your water here.

*Some people who have impaired digestion, don’t digest plant foods properly. If this is true for you, there’s probably things you can do to help you digest them better. If you’re not digesting properly, the maldigested food can become foods for the pathogenic microorganisms. There are also specific health conditions where it’s actually beneficial and necessary to avoid fermentable fibers for a period of time. If you’d like help discovering what’s best for you, I’d love to work with you! You can see my in person and virtual services here.

I hope that this post is informative and helps you on your way to better digestive health!

Take care,

Larissa :)


1. Cresci, G. A., & Bawden, E. (2015). The Gut Microbiome: What we do and don’t know. Nutrition in Clinical Practice : Official Publication of the American Society for Parenteral and Enteral Nutrition, 30(6), 734–746.

2.Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2017). Leaky Gut As a Danger Signal for Autoimmune Diseases. Frontiers in Immunology, 8, 598.

3.Fernando Cardona, Cristina Andrés-Lacueva, Sara Tulipani, Francisco J. Tinahones, María Isabel Queipo-Ortuño,Benefits of polyphenols on gut microbiota and implications in human health,The Journal of Nutritional Biochemistry,Volume 24, Issue 8,2013,Pages 1415-1422,ISSN 0955-2863,

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