Does your gut need a reset?

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Do you want to start feeling better?

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Do you want to start feeling better?

Yes, Where Do I Start?

Gut-Healing Foods: Support Your Gut Microbiota Through Diet

A Gut-Based Approach to Improving Your Overall Health and Wellness

Key Takeaways
  • Gut-healing foods include prebiotics, fermented foods, bone broth, and anti-inflammatory foods.
  • Balancing your gut microbiome with gut healing foods is the most important aspect of gut health.
  • The microbes in your gut help promote digestion, reduce inflammation, and protect your gut lining.
  • Foods that don’t support gut health include potential food allergens and sensitivities, as well as pro-inflammatory foods.
  • Supplements that support gut health include probiotics, digestive enzymes, HCl, and omega-3 supplements.

A healthy gut is the foundation of your overall health and wellness. So it’s very likely the starting point when addressing a huge number of health conditions, especially chronic issues like IBS (irritable bowel syndrome), autoimmune diseases, and mood disorders [1].

It follows that taking care of your gut through the foods you eat, the supplements you take, and your lifestyle choices (like sleep, stress management, and exercise) will impact your overall health.

If you’re experiencing digestive symptoms (like acid reflux, bloating, diarrhea, or constipation), mood changes, allergies, skin conditions, or other indicators of chronic inflammation, supporting your gut health (especially the health of your gut lining) with gut-healing foods is the first step in getting your health back on track.

Gut-healing foods include those that support the gut microbiome (such as fermented foods and prebiotic foods). A balanced gut microbiome reduces inflammation, assists in digestion, and heals the lining of the gut to prevent not only digestive issues but a host of other health challenges. 

Foods that are good for your gut health include prebiotics like onions and garlic, cruciferous veggies like cabbage, potatoes, and bone broth, which contains collagen, an integral ingredient in the health of your gut lining.

That being said, there are also foods that we all consider healthy (like certain fruits and veggies) that could create some challenges to an already compromised digestive system, namely if you’re dealing with SIBO (small intestinal bacterial overgrowth).

We’ll outline the foods that best support healthy gut flora, which foods to avoid while you’re in the gut-healing process, which supplements will support the process of healing, and how to maintain digestive health for the long-term.

Gut-Healing Foods to Know

Gut-healing foods include prebiotics, fermented foods, and anti-inflammatory foods. We will cover these categories more in-depth, but here’s a quick list of some of the best foods for healing for your gut:

  • Bone broth 
  • Apple cider vinegar
  • Cauliflower
  • Broccoli
  • Apples
  • Mangos
  • Kombucha
  • Sauerkraut
  • Flaxseeds and chia seeds

These are just a few examples of the many foods that can all work in concert to help heal and seal the gut over time. 

Diet and the Microbiome

A healthy gut starts with biodiversity in your gut microbiome. The microbes (bacteria and fungi) that live in your large intestine play a huge role in the digestive process, especially when it comes to carbohydrate and fiber digestion. And for these beneficial bacteria and fungi to do their jobs, they need to be present in high numbers and with lots of variety as far as species and strain.

They also need to outnumber potentially bad bacteria that increase inflammation, cause bloating and other digestive issues, and irritate the gut lining. So eating foods that feed the good bacteria and avoiding foods that feed the bad bacteria is the way to go. 

Fruits, vegetables, nuts, beans, and grains help feed the good bacteria in your large intestine, while processed sugar and refined carbohydrates feed the bad ones [2, 3, 4].


Prebiotics are specific types of fiber and carbohydrates that the good bacteria in your gut want to eat [1]. Prebiotic foods reduce inflammation, bolster the production of short-chain fatty acids (which function as the fuel to create healthy cells that make up the gut lining), and therefore help reduce the risk of leaky gut [5]. This can help prevent (or heal) the cascade of health issues that can result from intestinal permeability.

A 2020 meta analysis of nine randomized controlled trials showed that dietary fiber can significantly increase the amount of Bifidobacterium living in your gut, which can improve energy levels, boost the immune system, and help with fat metabolism [5]. Another study showed that consuming more fiber was associated with lower risk of Crohn’s disease [6].

There are seven types of prebiotics: fructose, lactose, fructans, mannitol, sorbitol, galactans, and resistant starch. The best approach to adding these (in moderation) into your diet is to select a few foods in each category (though a number of foods contain more than one type of prebiotic fiber). Here are a few examples, although this isn’t an exhaustive list [7, 8, 9]:

  • Fructose: apples, mango, watermelon, asparagus, artichoke, peas
  • Lactose: yogurt, hard cheeses
  • Fructans: nectarines, alliums (garlic, onions, leeks), grains, nuts, legumes
  • Mannitol/sorbitol: cauliflower, mushrooms, legumes
  • Galactans: broccoli, legumes, Brussels sprouts
  • Resistant starch: rice, bananas, potatoes that have been cooked and cooled

By eating a few of these foods each day, you will be giving your microbiota the fuel it needs to heal your gut. Just don’t overdo it — you don’t want too much of a good thing. Every person is different in what types of fiber they can tolerate, so if you find that eating some of these foods causes adverse digestive symptoms, then cut back. 

If these symptoms are persistent and problematic, it may also be a sign of a larger issue, like SIBO.

SIBO: The Caveat to Eating Prebiotics

I hinted in the introduction that sometimes healthy foods aren’t always ideal if you’re struggling with digestive issues like SIBO (small intestinal bacterial overgrowth). In the case of SIBO, many of the beneficial, gut-healing foods I listed could actually make your symptoms worse. 

That’s because they feed bacteria, and if bacteria (even the ”good” bacteria) is living in the wrong place (like your small intestine instead of your large intestine), they can cause gas, bloating, and other digestive upset when consuming these otherwise beneficial foods.

If you suspect you have SIBO or find that prebiotic foods are causing you digestive issues, the opposite approach — a low-FODMAP diet — should be the next course of action.


FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols — difficult to digest carbohydrates that land on many food sensitivity lists. Many FODMAP foods are also prebiotic foods, and in the case of SIBO (and IBS), avoiding these foods temporarily while using probiotic supplements and eating an anti-inflammatory diet to allow your gut to heal is the best course of action. 

Certain fruits and veggies, nuts, seeds, dairy, whole grains, and proteins are perfectly fine to eat on this type of diet. Find a more thorough list of foods to enjoy on this diet and a deeper explanation of its benefits, a low FODMAP snack list, and foods SIBO patients should avoid to learn more.

Fermented Foods and Probiotic Supplements

Fermented foods and probiotic supplements are full of the same organisms that make up the good gut bacteria you’re looking to bolster with gut-healing foods. Eating them in small quantities alongside a larger meal is part of a number of Eastern cultural traditions, due to their digestive benefits. They include things like:

  • Yogurt: If you can tolerate lactose [10, 11]
  • Kombucha: Sweetened black tea fermented by a SCOBY (symbiotic colony of bacteria and yeast) and transformed into a living, carbonated beverage
  • Kimchi: A spicy, wild-fermented Korean preparation of vegetables like cabbage, carrots, and cucumbers [12]
  • Sauerkraut: A fermented preparation of shredded cabbage (look for the word “raw” when shopping and avoid “pasteurized”)
  • Kvass: A lacto-fermented eastern European beverage with a very low alcohol content
  • Kefir: A lacto-fermented beverage made from dairy (if you can tolerate lactose) or coconut water [13]
  • Lacto-fermented pickles: Pickles made with wild yeast
  • Miso and natto: Each of these is made with fermented soybeans, but natto can be an acquired taste
  • Apple cider vinegar: Both a probiotic food and a digestive aid that helps stimulate the production of stomach acid

While it’s a great idea to include these foods in your healthy diet, eating these foods (even daily) likely won‘t provide you with a therapeutic dose of probiotics. Rather, multi-strain probiotic supplements that contain CFUs (colony-forming units) in the tens of billions are the way to go [14].

Probiotics have shown to decrease transit time (the time it takes for your body to process and eliminate food), increase stool frequency in those that need it, improve several GERD symptoms — regurgitation, reflux, heartburn, and indigestion — and reduce inflammation in IBD (inflammatory bowel disease) patients [14, 15, 16, 17].

Long-term use of probiotics appears to reduce the risk of developing disorders associated with the gastric inflammation caused by H. pylori infection, such as ulcers, gastritis, and cancer [18].

Furthermore, a 2017 systematic review of nine good-quality randomized controlled studies representing 361 patients found that probiotics lowered the pro-inflammatory cytokine IL-6, which plays a role in joint destruction and disease progression in rheumatoid arthritis (an autoimmune disease) [19].

While probiotics had no effect on disease activity scores when compared with placebo, this study highlights the important role of good bacteria in healing the gut,  promoting a healthy immune response, and lowering inflammation levels.

Due to the many gut-healing benefits of probiotics, daily use is also associated with improvements in skin health, mental health, and cognitive function, making them a great option for improving overall health.

Bone Broth: Nature’s Golden Elixir

To make bone broth, you simmer collagen-rich bones (especially joints) in water, veggies, and herbs on low heat for six to 24 hours (low and slow). The resulting broth is a delicious food ingredient filled with amino acids (especially glutamine), minerals (like calcium and magnesium), and the nutrients from the veggies and herbs you’ve cooked with the bones. You know you’ve prepared it correctly if it turns to gelatin when refrigerated.

While there isn’t a lot of scientific research to support the benefits of bone broth, it’s a rich source of collagen, the most abundant protein in the human body.

Collagen is a whole-food source of beneficial amino acids and minerals that support the tight junctions of the gut lining, and collagen-containing bone broth likely provides those same benefits. Collagen supports healthy skin and joint tissues, which leads health professionals to believe that it can provide the same benefits to the gut lining [20, 21, 22, 23].

Anti-Inflammatory Foods

Foods rich in omega-3 fatty acids support the reduction of inflammation in the gut so that it can heal and seal over time. Foods such as flaxseeds, chia seeds, certain fatty fish like wild salmon, sardines, and anchovies, as well as DHA-rich algae supplements are associated with a healthy gut microbiota and can help reduce inflammation [1, 24].

Omega-3-rich foods like the ones I just named, as well as fish oil supplements have also shown, in conjunction with other dietary interventions, to help reduce the symptoms and biomarkers of inflammation in autoimmune patients [25, 26].

Foods to Avoid When in the Gut-Healing Process

Adding gut-healing foods and supplements into your diet is a great place to start, since it’s a lot easier than subtracting when it comes to dietary change. But removing inflammatory foods is also important to expedite the gut-healing process and to help you put the best foods front and center.

The question of which foods cause problems for you, specifically, is something you’ll hone over time by paying attention to your body (and ideally keeping a food journal for a few weeks to help you identify patterns). But there are common allergens and food sensitivities to refer to as a starting point. 

Here are the foods that cause people problems most frequently:

  • Gluten-containing grains (wheat, rye, spelt, and the foods that contain them) [27]
  • Dairy [28]
  • Soy
  • Eggs
  • Nuts
  • Higher carb intake overall

Many pro-inflammatory foods also play a role in feeding bad bacteria, which leads to gut dysbiosis and symptoms of poor gut health (gas, bloating, diarrhea, constipation, indigestion, acid reflux, etc.). These foods include:

  • Artificial sweeteners [29, 30]
  • Food additives like food coloring, emulsifiers, stabilizers, and fat replacements [31, 32, 33]
  • Processed foods, especially processed sugars, carbs, and meats [34, 35, 36]
  • Added sugar [34]
  • Alcohol [34]
  • Fried foods
  • Red meat

Completely eliminating all of these foods at once is a big ask for anyone, so start with the foods on this list that are easiest for you to cut back on. With the help of a food journal, you’ll be more likely to discern which ones cause you problems, and you might find that certain foods, especially on the first list of potential allergens, are tolerable for you within a certain threshold. 

Many of our patients have trouble with too much dairy, for example, but find that dairy in moderation, or certain lower-lactose dairy products like hard cheeses, ghee, and butter, don’t create any problems for them. For some, however, dairy of any kind causes problems. So it’s really important for you to get to know your body and how it reacts to certain foods.

Gut-Healing Supplements

Supplements can help support the addition of gut-healing foods into your diet. As I’ve already mentioned, probiotic supplements are the first place to start when it comes to bringing your gut microbiota back into balance and healing your gut. Many probiotics on the market also contain prebiotics, so you might find that you’re getting two-in-one as you shop.

Digestive enzymes and hydrochloric acid (HCl) are also great supplements to help with the early part of digestion that takes place in the stomach. Both types of supplements help break down food in your stomach to help move things along more smoothly through the remainder of your gastrointestinal tract. By aiding in the breakdown of your food bolus before it gets to your small intestine, you can help prevent putrefaction that can lead to SIBO.

Omega-3 supplements like fish oil, flax oil, and algae-derived DHA supplements can help reduce inflammation and provide overall benefit to your gut lining.

Maintain Your Gut Health Over Time

Understanding the root cause of your gut health challenges is step one in figuring out the solution. Imbalanced gut bacteria can lead to poor gut health, and prebiotic foods can help restore it. 

However, if you find prebiotic foods to be irritating, it may be a sign you have SIBO and should try a low FODMAP diet.

Stick to gluten-free carbohydrates, a colorful array of fruits and vegetables, fermented foods, and unprocessed protein sources. Add in a daily dose of bone broth to support the health of your gut lining, and consider using a daily probiotic supplement. 

Listen to your body and keep a food journal to better understand which foods could be triggering undesirable digestive symptoms and restrict accordingly to allow your gut to heal. You might find that you can reintroduce some of these foods in moderation as your symptoms improve, but you might also discover that you’re better off without them. 

We’d love to help you on your gut-healing food journey. Reach out to our clinic for more information on how to get started.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

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