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Nutrition to Improve the Gut Microbiome

gut microbiome nutrition

Over 2,000 years ago, Hippocrates, the father of Western medicine, understood that:

"All disease begins in the gut."

Many of society's problems often have an unhealthy, leaky gut at their root. This includes weight gain, autoimmunity, food allergies, diabetes, heart disease, skin problems, depression, inflammatory bowel disease, and a laundry list of other conditions (1,2,3,4,5).

What is Dysbiosis?

The gut microbiome is home to TRILLIONS of bacteria that play a crucial role in digestion, immune function, and overall health. Dysbiosis is the official term for an unhealthy gut. It refers to an imbalance in the bacteria of the gut, where there's an overgrowth of harmful bacteria and a decrease in beneficial bacteria. This imbalance can disrupt the normal functioning of the gut, leading to various physical, and sometimes even mental health problems.

Signs of an unhealthy gut include bloating, gas, diarrhea or constipation, food intolerances, fatigue, mood swings, skin problems, and weakened immune function.

Factors that Contribute to Dysbiosis

POOR DIET: a diet high in processed foods, gluten, refined flours, sugar, alcohol, unhealthy fats, and low in fiber can disrupt the balance of gut bacteria and promote the growth of harmful bacteria.

CHRONIC STRESS: stress can disrupt the gut-brain axis, affecting the balance of gut bacteria and impairing digestive processes. The gut is extremely sensitive to stress, and this can contribute to gut-related issues.

MEDICATIONS: certain meds, such as antibiotics, nonsteroidal anti-inflammatory drugs (NSAIDs), and proton pump inhibitors (PPIs), can disrupt the gut microbiota and increase the risk of gut-related issues.

FOOD INTOLERANCES AND SENSITIVITIES: intolerance or sensitivity to certain foods, such as lactose or gluten, can cause GI symptoms like bloating, diarrhea, constipation, mood swings, fatigue, skin problems, weakened immune system, and abdominal pain, indicating an unhealthy gut.

INFLAMMATION: chronic inflammation in the gut can lead to gut dysfunction and compromise overall health.

LACK OF PHYSICAL ACTIVITY: sedentary behavior and a lack of exercise have been linked to imbalances in gut bacteria and impaired gut motility, which contribute to an unhealthy gut. Research shows exercising increases gut microbial diversity in the gut.

Best Foods for the Gut Microbiome

Based on a ton of research, these are the foods to prioritize when you're trying to improve the health of your gut microbiome. If you want to feel better, prioritizing nutrition for your gut microbiome is your #1 priority.

FERMENTED FOODS (add probiotics)

Fermented foods are basically edible probiotics. Probiotics are the ‘good’ or helpful bacteria that reside in the gut and help maintain our health. Along with promoting digestive health, probiotics enhance the functioning of the immune system.

Adding fermented foods into your daily diet helps boost good gut bugs.

Fermented food options:

• Fermented Vegetables (ie: Pickles, Sauerkraut, Kimchi, Ginger)

• Tempeh

• Miso

• Natto

• Kombucha (no added sugar)

• Kefir and Kefir water (no added sugar)

• Yogurt and other cultured dairy products (no added sugar). Non-dairy options are usually made from coconut or almond milk, and if you're really ambitious, consider making your own yogurt with a culture starter.


Vegetables are an excellent source of prebiotics, which are fibers that pass through the upper part of the digestive tract undigested. Prebiotics create a favorable environment for the growth of beneficial bacteria in the large bowel.

The beneficial bacteria use these prebiotic fibers to create postbiotics, such as butyrate (a short chain fatty acid), vitamins, neurotransmitters like serotonin, enzymes, and more. Butyrate is a good fuel source for gut bacteria, gut cells, and helps in lowering inflammation.

When probiotics and prebiotics are combined, you have the perfect combination for a healthy gut.

Prebiotics are naturally found in these foods:

• Chicory Root

• Jerusalem Artichoke

• Dandelion Greens

• Garlic

• Leeks

• Onion

• Garlic

• Banana (The greener the better)

• Asparagus

• Jicama

If you are already eating organic foods, keep it up. If you are not 100% organic, don’t stress about it and just slowly make the transition. Organic foods typically have more nutrients and less chemicals. Pesticides are very disruptive to the gut and one of the reasons so many people struggle with gut issues in the first place.

All veggies are wonderful, and especially prioritize leafy greens and the cruciferous family such as cauliflower and broccoli. You can’t over eat the veggies, so load up.

Try a new veggie every week and experiment with new recipes using the new veggie, this way you can expand your recipe arsenal and veggie intake.


Organic apples are wonderful for gut - they provide polyphenols, which support gut health and overall health. Apples can lower inflammation in the gut lining and apple pectin and apple peels act as prebiotic fiber to feel beneficial bacteria in the gut.

Fruit can spike blood sugar, so choose lower glycemic fruits, such as: apples, grapefruit, lemon, lime, plums, apricot, nectarine, peach, cherry, and avocado. All fruits that ends in berry are excellent choices - strawberry, blueberry, raspberry, blackberry, huckleberry, etc. Frozen fruit of any of these is fine too.

Avoid fruit juices since they are just sugary drinks without the fiber, which will cause insulin spikes. Limit fruit intake to 2-3 servings per day.


Include these high-quality proteins: fish, chicken, turkey, beef, lamb, pork, and wild game meat. Here is where I would choose organic, or in the case of fish, choose wild-caught. You can at least wash the pesticides off vegetables, but it’s kind of hard to wash off the hormones and antibiotics that are injected into nonorganic meat or farm-raised fish.

If you eat bacon, choose nitrite-free, pastured bacon for better quality.


Include more of these healthy fats: coconut oil (used in high temperature cooking), coconut butter, coconut cream, coconut flakes, ghee, grass-fed butter, olives, olive oil (low heat or on salad), avocado, avocado oil, nuts, nut butter, seeds, and omega-3 fatty acids.

Coconut oil is made up of medium-chain fatty acids, which have antimicrobial and antifungal properties which help to balance the gut bacteria, support the gut lining, and provide an energy source for the body.

Omega-3 fats are used in the lining of every cell in the body and are powerhouses in reducing inflammation. Omega-3's have demonstrated positive effects on beneficial gut microbes. Eating wild-caught fatty fish several times a week or supplementing with a quality, third-party-tested fish oil is beneficial for healing leaky gut, lowering systemic inflammation, and is a great way to get your omega-3s.

When looking for the best type of fish, think SMASH: salmon, mackerel, anchovies, sardines and herring.


Bone Broth is rich in collagen, minerals, and gelatin—components that are key for rebuilding the gut and gut lining. Broth can be sipped throughout the day or added to soups and stews.

If you don't have time to always eat bone broth, consider adding a scoop or two of a quality collagen powder is an easy way to compound the therapeutic benefits of collagen's amino acids.

The key to a flourishing microbiome is to eat diverse, fresh whole foods and fermented foods while avoiding processed foods, sugar, and seed oils, and also finding ways to reduce stress.

It becomes clear that tending to the health of your gut lining should be made a #1 priority.

The takeaway is Gut health = overall health. Include gut nourishing foods at least everyday, and at every meal is even more ideal!

Please let me know if you have any questions, or feel free to leave me a comment. What are your favorite gut nourishers?

Much love,

Kelly xo


31 Jan. 2020.

2. de Kort S, Keszthelyi D, Masclee AA. Leaky gut and diabetes mellitus: what is the link? Obes Rev. 2011 Jun;12(6):449-58.

3. Sandek A, Bauditz J, et al. Altered intestinal function in patients with chronic heart failure. J Am Coll Cardiol. 2007 Oct 16;50(16):1561-9.

4. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. Gut microbiota's effect on mental health: The gut-brain axis. Clin Pract. 2017 Sep 15;7(4):987.

6. Gillois, Kévin, et al. Mucus: an underestimated gut target for environmental pollutants and food additives. Microorganisms, MDPI. 15 June 2018.

7. Case Western Reserve University. High fat diet reduces gut bacteria, Crohn’s disease symptoms. ScienceDaily. 22 June 2017.

8. Rezac, Shannon, et al. Fermented foods as a dietary source of live organisms. Frontiers in Microbiology [Internet], Frontiers Media S.A. 24 Aug. 2018.

9. Cândido, FG, et al. Impact of dietary fat on gut microbiota and low-grade systemic inflammation: mechanisms and clinical implications on obesity. International Journal of Food Sciences and Nutrition, U.S. National Library of Medicine. 4 July 2017.

10. Costantini, Lara, et al. Impact of omega-3 fatty acids on the gut microbiota. International Journal of Molecular Sciences, MDPI. 7 Dec. 2017.


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