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Dr. Danielle Desroche


It’s no secret that your gut microbiome has a profound impact on your overall health. In fact, the relationship between your gut health and overall health is so strong that some experts call the gut a “second brain.” 

When your gut microbiome is out of balance, you’re likely to experience a variety of side effects. Symptoms ranging from brain fog to gastrointestinal upset and impaired digestion may signal a need to heal your gut.

Although the concept of gut-healing may sound intimidating, there are simple interventions you can implement to begin your healing journey. Nutrition is the most cost-effective and low-risk intervention tool we have to begin healing the gut. 

Many people are turning to gut healing foods to help them get their digestive systems back on track. As new research continues to uncover the critical role of the microbiome in overall health and immunity, it’s becoming more important than ever to eat the right foods to support digestive health.

Thanks to their healing properties, many foods and spices have become increasingly popular treatments for supporting gut health. In this edition, we’ll be looking at 13 gut-healing foods that can help balance gut flora and promote optimal digestive health.

What Foods Can Provide Optimal Gut Health?


Introducing good bacteria via probiotic-rich foods can help reverse intestinal permeability and promote tight junction proteins within the gut. (Source) One of the mechanisms for causing disease is by promoting inflammation and increased permeability of the intestinal lining (AKA “leaky gut”), which can cause harmful metabolites to cross the blood–brain barrier and reach the central nervous system, even affecting the brain. (Source)

Evidence suggests that pickles and other fermented foods (e.g., sauerkraut, kimchi) modify the gut microbiome in a positive way through their antioxidant, antifungal, and antimicrobial properties. Additionally, fermented foods may help prevent inflammation and atherosclerosis (clogging of blood vessels). (Source)

Coconut Oil

Coconut oil is rich in high-density lipoprotein (HDL), which is more commonly referred to as “good cholesterol.” HDL is positively associated with a more diverse gut microbiota, which is one sign of a healthy gut. (Source)

As a saturated fat, coconut oil is unique in that it contains medium-chain triglycerides (MCTs). Compared to long-chain fats, MCTs are more easily digested, and are metabolized and then converted into energy, rather than being stored as fat.

In addition to its potential role in improving digestion, coconut oil has also shown potential as a gut healing food, thanks to its antimicrobial and antifungal properties. 

For example, a study in mice that evaluated the potential of dietary coconut oil and beef tallow in combating yeast overgrowth in the gut, researchers found that coconut oil reduced the amount of C. albicans by more than 90% compared to a beef tallow-rich diet. (Source)


Sardines have been deemed a superfood thanks to their anti-inflammatory properties. These fish contain some of the highest levels of omega-3 fatty acids, which have been shown to contribute to microbial diversity and even reverse dysbiosis. (Source) Omega-3’s encourage bacteria that produce increased short-chain fatty acids, such as butyrate, which provide intestinal cells fuel to maintain the integrity of the gut lining. (Source

Replacing inflammatory foods and oils with sardines is not only beneficial for metabolic disorders, such as obesity, but also supports a healthy gut. One study evaluated the effects of enriching a standard diet with 100 g of sardines 5 days a week for 6 months and found a positive impact on participants’ gut microbiota composition, which was demonstrated by increasing populations of beneficial bacteria. (Source)  


Perhaps the most commonly consumed probiotic food in the Western world, yogurt is an excellent source of beneficial bacteria that are crucial to the body’s digestive system, and a prime gut healing food.The fermented dairy product also contains live and active cultures of Lactobacillus, which is believed to improve the integrity of the intestinal wall and prevent the growth of harmful bacteria. 

Studies have shown that regular consumption of yogurt or yogurt-like products (e.g., kefir) may help repopulate good bacteria in the gut, such as L. acidophilus and Bifidobacteria (Source), as well as reduce inflammation. (Source) More study is needed, however, to confirm these findings.

Lactic acid-producing bacteria (LAB) are used to make yogurt, and these hard-working organisms do more than just whip up a tasty treat. These specific strains are also thought to improve numerous gastrointestinal conditions, including lactose intolerance, constipation, diarrhea, colon cancer, inflammatory bowel disease (IBD), Helicobacter pylori infection, and allergies. (Source)


Beans are true nutritional staples, and are one of the best sources of protein, fiber, and complex carbohydrates (hello resistant starch!). In fact, legumes are so nutrient-dense that the United Nations declared 2016 the “International Year of Pulses” — a class that includes peas, beans, lentils, and chickpeas. (Source)

Scientists have found that the myriad nutrients found in beans can help improve digestion and boost immunity. One study, published in the Journal of Nutritional Biochemistry, found that navy and black beans enhanced gut health by improving intestinal barrier function, and may improve gut microbe diversity and help curb inflammation. (Source)


Tempeh is a fermented food made from cooked soybeans. With a nutty, mushroom-like flavor, tempeh is a protein-rich gut healing food that is often used as a meat substitute in vegetarian and vegan cooking. In addition to its protein content, tempeh is also rich in fiber, vitamins, minerals, and micronutrients, including calcium and iron. (Source)

One small study found that participants who ate 100g of tempeh daily for 28 days had significant increases in gut populations of beneficial Bifidobacterium and A. muciniphila bacteria. (Source)


Papaya is a nutrient-dense tropical fruit that is anti-inflammatory and rich in antioxidants, namely carotenoids, which are more bioavailable in papayas than in most other food sources. (Source) Papaya’s main gut-friendly action derives from a unique enzyme called papain that can break down protein and aid digestion. 

Papaya has been widely used throughout Central and South America as a digestive aid, and is believed to be a gut healing food that helps a variety of gastrointestinal disorders, including diarrhea, constipation, bloating, and irritable bowel syndrome (IBS). In a clinical trial of a commercial papaya-based preparation, participants reported positive effects on these symptoms. (Source) (It also doesn’t hurt that papaya is a delicious, low-sugar fruit you can enjoy in a salad or by itself!)

Bone Broth

Whether you drink it straight or incorporate it into dishes, bone broth is a kitchen pantry must-have (if your diet allows it). Not only is it relatively easy to prepare at home, but it’s also readily available in many grocery stores and is one of the most healing foods for gut repair.

In addition to being rich in vitamins and minerals, bone broth also contains collagen. The collagen in bone broth is metabolized into its component amino acids, which provide the raw materials for the body to produce its own collagen where needed. Research suggests that collagen may help repair the gut lining in response to damage to the intestinal wall. (Source, Source)

The gelatinous texture of bone broth contains other important amino acids, such as glutamine, that support digestion and healthy gut mucosa. Thanks to its rich source of collagen and gelatin, bone broth can be a nutrient-dense way to support treating symptoms of leaky gut syndrome. (Source, Source)


Korean traditional fermented foods, like kimchi, are recognized for their health benefits, especially as they pertain to the gut. As a fermented food, kimchi is a rich source of live and active probiotic cultures, which support the growth of healthy gut flora by increasing the number of beneficial bacteria in the gut.

Kimchi is the product of a fermentation technique called lacto-fermentation that uses Lactobacillus bacteria to break down sugar into lactic acid, giving kimchi its signature sour taste. (Source) This bacteria, on its own, has multiple gut-related benefits, including antifungal effects.

One study using Lactobacillus bacteria isolated from kimchi demonstrated positive effects in the treatment of candida infection. (Source) The researchers concluded that kimchi exerted an antimicrobial effect on pathogens, which helps to maintain a healthy and diverse gut microbiome, while supporting mucosal health as well.


Although ginger is well known for its culinary uses, the rhizome is a favorite traditional remedy for treating indigestion, nausea, and even migraines. In fact, the World Health Organization recognizes ginger as an effective antinausea agent, and it has been studied for its potential to combat inflammation that is responsible for many disease processes, including diabetes, osteoarthritis, and other chronic pathological conditions. (Source)

In addition to its role as a key player in immune health, ginger’s antimicrobial and anti-inflammatory properties make it a powerful gut healing food and ally in the fight against gut imbalances, including ulcers, colitis, Crohn’s disease, and a wide range of other conditions. (Source) In the gut ginger, like some other spices, promotes the production of “good” bacteria, specifically Lactobacillus and Bifidobacterium species. Moreover, there is evidence that these spices promote “prebiotic-like activity,” helping to support the growth of beneficial bacteria while decreasing the growth of harmful bacteria. (Source


Liver is a nutrient-dense organ meat that contains a variety of vitamins, minerals, essential fatty acids, and amino acids. This vitamin-rich superfood is also one of the most abundant sources of bioavailable vitamin A (in the form of retinol), which is needed for the proper functioning of the immune system.

Recent research has shown that vitamin A plays a role in the regulation of the immune response in the intestine, specifically helping your immune system detect the difference between beneficial and harmful gut bacteria. (Source)

Growing evidence suggests that vitamin A has anti-inflammatory benefits and that its supplementation can help those with inflammatory conditions. (Source) In addition, aside from providing vitamin A, liver is a great source of vitamins B12, riboflavin, and nutrients such as copper, folate, iron, and choline. (Source

Tip: Always opt for liver from pasture-raised animals as opposed to those from factory farms, due to its higher concentration of vitamins and omega-3 fatty acids.


Like liver, ghee is rich in bioavailable forms of essential vitamins like A and D. Despite its reputation as a health-promoting food, ghee (or clarified butter) has been vilified in recent years due to its high saturated fat content. However, ghee has also been used in traditional Indian medicine for thousands of years, and is traditionally consumed for its anti-inflammatory and antimicrobial properties.

Ghee is made by simmering butter, removing milk solids, and allowing the water to evaporate, leaving behind a pure form of fat. This process also removes the milk proteins, lactose, and other sugars, rendering ghee lactose-free and suitable for people with dairy sensitivities.

And remember butyrate? Ghee is also rich in this short-chain fatty acid, which protects the gut lining and reduces inflammation. (Source)

The clarified butter also has a high smoke point, meaning that it is a safer oil to cook at high heat, like frying or sauteing. Paired with some of the above-mentioned gut healing foods, and you have a delicious gut-friendly meal!

Apple Cider Vinegar

Apple cider vinegar (ACV) is made from the fermentation of crushed apples and is often consumed as a dietary supplement and folk remedy. While ACV is largely prized as a tonic for its therapeutic and healing properties, its antibiotic properties have recently been highlighted in both laboratory and clinical studies. 

A study in Scientific Reports found that the acetic acid found in ACV has a potent antifungal effect, citing its efficacy against C. albicans, a common fungus that can cause thrush and yeast infections. It was also found to have antibacterial effects against E. coli and Staphylococcus aureus. (Source)

Apple cider vinegar also shows promise as a way to balance gut microbiota, which may have the additional benefit of helping lower body weight in those struggling with obesity. (Source) ACV can be a quick and easy addition to your diet as a way to help balance beneficial bacteria.

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13 Science-Backed Gut Healing Foods

The gut microbiome is key to overall health and many people are turning to gut healing foods to help them get their digestive systems back on track.
Medically Reviwed
Medically Reviewed by
Dr. Danielle Desroche
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