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This article is based on scientific evidence, written by experts and fact checked by experts.

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How to Heal Your Gut in 8 Steps: A Clinician-Approved Guide

Written by Michael Ruscio on April 25, 2024

Written by Michael Ruscio on April 25, 2024 — Reviewed by Aimee Gallo

8 Simple Steps for Healing Your Gut & Boosting Your Overall Health

Your gut is at the center of your overall health and well-being. It’s the seat of your immune system, it’s where most of your body’s serotonin is made, and it’s where nutrients are broken down and assimilated to feed all the systems of your body. In other words, gut health is not just digestive health, it’s whole-body health.

So when things are a little off—whether you’re experiencing digestive symptoms (like bloating or diarrhea) or other seemingly unrelated symptoms like exhaustion, aches and pains, skin eruptions, or mood changes—improving your gut health is the critical first line of defense.

But how and whether your gut needs attention might not be immediately obvious. In fact, you might be unwittingly doing things you don’t realize are harmful to the human gut. For example, taking over-the-counter pain meds like ibuprofen (or other NSAIDs) can compromise your gut lining 1 2. And prolonged, strenuous exercise may temporarily harm the gut lining and contribute to leaky gut syndrome, which I describe in detail in the Cause and Effect section 3.

Reducing gut irritants and accidental damage are the first steps to healing your gut. From there, a diet particular to your condition could come into play, but you may simply find that removing inflammatory foods and adding in probiotics, other supplements, and a few lifestyle tweaks will be enough to get you going in the right direction and feeling better. Let’s discuss science-backed ways of healing your gut and the full-body health benefits of healthy gut maintenance.

Action Plan: How to Heal Your Gut Naturally

A healthy gut is one with an intact, sealed barrier between it and the rest of the systems in your body. Nothing should be leaking through the tight junctions of your intestinal lining, and everything should be moving through the system smoothly. The food you’re digesting should stay inside the digestive tract until it’s time for your body to release it as waste (poop).

At the beginning of the gastrointestinal (GI) tract, a healthy gut contains adequate amounts of digestive enzymes (in the salivary glands and stomach) and stomach acid to break down the food you’ve eaten before it enters your small intestine. A healthy gut contains a wide array of microbes, mainly in the large intestine, that aid in digestion, reduce inflammation, and play an active role in keeping the gut wall sealed.

To begin outlining how to heal your gut, I recommend that my patients use an evidence-backed, step-by-step process that starts by resetting the gut (typically with a short-term liquid fast) and supporting it while we remove potentially problematic foods from the diet. After the gut has had a chance to recover, we move to slowly reintroducing some of the foods that we eliminated and eventually get to a happy place of gut maintenance. I call this protocol the Great-in-8 Action Plan, but not everyone needs all eight steps. 

I’ll briefly outline the steps as I use them in the clinic, but you can also find them in great detail with specific instructions and dosing in my book, Healthy Gut, Healthy You. Ideally, you’ll go through the steps with support from your trusted healthcare provider. 

Step 1: Reset

This first step is a two-to-four-day modified fast, in which I suggest my patients drink bone broth or a cleansing lemonade to reduce inflammation and let the gut rest. A popular alternative to this is an elemental diet, which can have the added benefit of reducing inflammation 4 5 and starving any potential bacterial overgrowths in your small intestine 6. 

Whichever they choose, the next step is a modified fast with an anti-inflammatory elimination diet that reduces allergens and irritants. For some, that means a Paleo diet. For others, a low-FODMAP diet is more helpful.

Step 1 also involves some lifestyle resets, such as removing alcohol (for now), introducing easy exercise like walking, drinking plenty of water, reducing stress, and creating a consistent sleep schedule.

A Note on Stress

Sometimes simply telling someone to reduce stress actually causes them stress. I understand that this advice given out of context can sometimes feel like pressure when so many stressors in life feel outside of our control. The way you choose to reduce stress is personal to you—it’s about finding something that provides a release valve for you and allows you to take time for yourself. Here are some science-backed suggestions for managing stress.

  • Breathwork or meditation can reduce stress and may improve digestion 7.
  • Time in nature may improve mood, calm the nervous system, reduce reactivity to stress, lower blood pressure, boost immunity, and increase the diversity of beneficial gut microbes 8 9 10 11 12.
  • Moderate exercise can reduce stress and may help reduce gut-related symptoms 3 13 14 15 16 17 18 19. 
  • Psychological support: Working with a therapist who offers cognitive-behavioral therapy (CBT) or mindfulness-based stress reduction (MBSR) may improve gut-related symptoms 20 21 22 23 24 25 26.
  • Gut-focused hypnotherapy, in person or online, may help reduce digestive symptoms 27 28.

Maybe one of these will work for you, or perhaps you have something else in mind, like a relaxing art project, working on a puzzle, or calling a supportive family member or a friend who makes you laugh. Whatever works to provide relief is something to engage in regularly to lower your stress levels.

Back to Step 1 of how to heal your gut. For many of my patients, following Step 1 for a month or more brings complete relief. In that case, they can skip to step 5 (see below) and begin reintroducing some of the foods they removed. It’s important to do this slowly and deliberately to figure out which foods are irritating and which are fine to eat without causing symptoms. 

However, if Step 1 doesn’t bring a patient significant relief, they have the option of continuing onto steps 2, 3, and 4. Steps 5–8 are all about easing up on restrictions and enjoying life.

Step 2: Support

The second step of healing your gut is about getting additional gut support with probiotic supplements and sometimes digestive enzymes and hydrochloric acid (HCl) acid supplements. Additionally, amino acids and other helpful nutrients, like vitamin D, may support the intestinal lining and reduce inflammation. 

Step 2 helps to further heal and seal the gut lining and support the gut as it breaks down foods that could be creating stress for the system. 

Probiotic Supplements

Probiotics are easily the best way I’ve found to tackle the first part of Step 2. Both my clinical experience and high-quality research point to probiotics as the cornerstone of effective gut treatment 29 30 31 32 33 34 35 36 37 38. A blend of different types of bacteria can work to encourage healthy populations of intestinal bacteria and inhibit the growth of inflammation-causing microbes in the GI tract.

Many clinicians have overlooked a trend in the research suggesting that three well-studied categories of probiotic supplements are particularly effective at balancing gut microbiota and improving gut health 39 40 41 42 43 44 45 41 44 46 47. These most effective probiotic categories are as follows:

  1. A blend of gut bacteria called Lactobacillus and Bifidobacterium 
  2. A single strain of Saccharomyces boulardii, a healthy fungus 
  3. Soil-based microorganisms, typically species of Bacillus

In my clinical experience, combining these three categories leads to substantially better improvements than standard single- or double-strain probiotic treatments. I call this approach to probiotics triple therapy. To correct microbial imbalances and reduce inflammation, I recommend the following approach to my patients:

  1. Try a quality formula probiotic from category 1, category 2, and category 3—take all three together.  
  2. Track symptoms for 2–3 months. If symptoms improve, stick with this regimen until you reach a plateau.
  3. Continue the same protocol for about another month to allow your system to adjust. Then reduce the dose incrementally to find the minimal effective dose. Once you’ve found it, stay on that dose.
How to Heal Your Gut Naturally

Probiotics are also present in fermented foods, but you’d have to eat a lot of them consistently every day. Although fermented foods can be part of a healthy diet*, they likely aren’t potent enough to reach the therapeutic levels—good bacteria and fungi in the billions or trillions per dose—that probiotics have. For more detail, see this table comparing the doses of probiotics in foods versus supplements.

*Some people may benefit from eating fermented foods, such as kefir, sauerkraut, and kimchi. However, some people may find these foods irritating and should eat them with caution or avoid them. 

Digestive Enzymes or Acid

If combining diet and lifestyle changes with probiotics for a few weeks hasn’t led to a significant improvement, we then consider digestive enzymes or focusing on stomach acid. 

Some people don’t make enough of the enzymes required to break down certain carbohydrates, proteins, or fats and may notice bloating, gas, abdominal discomfort, or bowel movement changes. In such cases, taking digestive enzymes that include amylase, protease, or lipase at the start of a meal could help reduce or eliminate such symptoms 48. I tend to recommend trying each of these separately for 2–3 weeks each, looking for improvements, worsened symptoms, or no effect at all. 

Others may have low stomach acid and could benefit from taking betaine HCl to improve digestive function and nutrient absorption 49 50. Check out my video explaining how to do this safely and effectively:

If they feel worse or no different after trialing these digestive aids, we stop using them and look to some other supplements that may benefit a potentially damaged gut lining.

Supplements to Heal the Gut Lining

If diet, stress reduction, probiotics, and digestive enzymes or HCl haven’t helped someone after a few weeks, leaky gut could be at play. Now we might consider trying supplements that can strengthen the intestinal wall and repair a leaky gut, which I’ll detail in the Cause and Effect section. In short, a strong gut wall keeps microorganisms and undigested food particles from escaping into your bloodstream, where they should not be. Research shows that these supplements may directly help heal a leaky gut:

Although bone broth has less clinical research behind it, it’s a whole-food source of L-glutamine, other amino acids, and minerals that may help heal the gut lining. However, given its lower concentrations of healing elements, bone broth may also be less effective than supplements. 

As with the digestive aids, I typically recommend that my patients try each gut-lining supplement separately for 2–3 weeks to gauge whether they help, harm, or make no difference. If neither digestive aids nor gut-lining supplements clearly help, they might consider trialing any of the next types of supplements.

Supplements to Reduce Inflammation

Sometimes, when none of the previous steps or supplements seem to have helped considerably, chronic inflammation is at play. The good news is that certain supplements can help reduce inflammation and support the gut microbiome. Those with signs of leaky gut may want to give any of the following science-backed supplements a try:

With all supplements, it’s good to give each one a try, ideally with a clinician’s support, for 2–3 weeks and make note of whether they help, harm, or do nothing. Keep track of those that help and stop taking those that don’t.

I’ll acknowledge that high-quality supplements can add up quickly, and it’s not necessary for most people to take everything I’ve mentioned above. That amount of supplementation would quickly get expensive, unwieldy, and stressful, which is not what anyone wants when working to heal the gut. If you ever find yourself lost in a heap of supplements, it’s a good idea to get some guidance.

One option is to read through the full Great-in-8 Action Plan in my book, Healthy Gut Healthy You. Another option is to work with someone who specializes in gut health and functional medicine, such as the clinicians at our clinic.

Step 3: Remove

This step is only necessary for those who aren’t feeling better after Steps 1 and 2. It involves eliminating any harmful bacteria that persist after the first two steps. The natural option here is to try antimicrobial herbs that can remove unwanted gut bacteria. Clinical research has shown some herbal antimicrobials to be just as effective as rifaximin, the prescription antibiotic that gastroenterologists often prescribe to target harmful gut microbes 77 78 79.

Next Steps

Once we’ve cleared out any harmful microbes, I move my patients on to Step 4: Rebalance. If their digestion is still sluggish (causing constipation), it’s likely that their gut microbes are having a hard time staying balanced. Step 4 introduces prokinetic supplements, which can improve motility (the rate at which contents move through the digestive tract) to support healthy gut bacteria. A natural prokinetic supplement, such as peppermint oil 80 81 82 83 or ginger 84 85 86, can improve motility so that partially-digested food doesn’t sit too long in any part of the digestive system and encourage bacterial overgrowth. 

In Step 5: Reintroduce, we start bringing back eliminated foods slowly and strategically. Reintroducing one (typically lower-allergen) food at a time can help my patients develop a clear sense for which foods are best for their unique system. This trial-and-error approach also helps people build the confidence to know that if a flare-up occurs, they can return to the diet that worked best in Step 1 until things calm down and try again.

In Step 6: Feed, we work to incorporate foods that feed the beneficial bacteria the healthier gut now supports. Prebiotic foods, like legumes, onions, and whole grains, contain fiber that beneficial gut bacteria and fungi eat. But it’s important to start slowly when reintroducing prebiotic foods because too much at one time can be stressful on the digestive system 87 88.

In Step 7: Wean, it’s time to cut back on the supplements we added during the previous steps. The goal of this step is to get each patient to the bare minimum of supplements they need to remain in a good state of gut health. I typically recommend a methodical approach of removing one supplement at a time while noting how it feels to go for a few days or a week without each one. People often find they need to stay on one or a few supplements to feel their best and maintain feeling well, which brings me to the last step.

Step 8: Maintenance and Fun is the final step in this process. Everyone’s Step 8 looks different, but reaching it means they have the tools they need to assess how they feel and what they should tweak to recover from dips in gut health. Maintenance is about feeling good and having fun with your newfound gut health. A sample maintenance plan could look like this:

  • Adopt a regular diet that is lower in inflammatory foods (like sugar and processed foods) and higher in anti-inflammatory, gut-healing foods like fruits and veggies, wild fish and meat, and gluten-free grains and legumes.
  • Take a broad-spectrum probiotic supplement 89 90 91.
  • Eat probiotic and prebiotic foods in moderation and to tolerance 92.
  • Drink plenty of water.
  • Get moderate daily exercise 93.
  • Get consistent, restful sleep (7–9 hours a night) 94.
  • Incorporate a regular stress management/reduction activity like yoga or meditation 95 96 97.
  • As a gut healing meal replacement, use an elemental diet for one or more meals daily.
  • To reset the gut after an occasional splurge, use an elemental diet for one or more meals per day for 1–4 days.

How Do You Know It’s Time for Healing Your Gut?

The most obvious signs that your gastrointestinal health may be compromised are recurring digestive symptoms, such as gas, bloating, constipation, diarrhea or loose stools, reflux, indigestion, or heartburn. However, there are many other seemingly unrelated symptoms that could emerge as a result of an unhealthy gut.

A poorly functioning digestive system may limit nutrient absorption 98 99 100 and promote inflammation, which can deregulate your entire immune system. Over time, insufficient nutrients, chronic inflammation, and immune dysregulation may manifest as one or more of the following symptoms or diagnoses:

Each of these is an indication that it may be time to start healing your gut. With support from your healthcare provider, you can start with Step 1 and take it slowly, day by day.

Cause and Effect: Digestive Health and Overall Health

Addressing the symptoms of poor gut health is important so you can get relief, but getting to the root cause is the best way to prevent further and future poor gut health.While there’s a wide array of potential causes of gut disturbance, one common culprit at the root of many health challenges is leaky gut syndrome. A leaky gut is a compromised gut lining that allows partially digested food particles and potentially harmful microorganisms into the bloodstream. Also called increased gut permeability, a leaky gut can arise from gut insults like chronic stress, toxins, unhealthy microbes, inflammatory food particles, certain drugs and medications, and infections.

How to Heal Your Gut Naturally

Eventually, intestinal permeability gives rise to chronic gut inflammation, which has the potential to contribute to a host of health issues, including 154:

  • Food sensitivities or allergies
  • Unregulated blood sugar
  • Overactive immunity (autoimmune disease)
  • Excessive inflammation
  • Skin problems
  • Mood issues
  • Weight loss or weight gain
  • Liver disease

Leaky gut is also highly correlated with chronic conditions such as celiac disease, Crohn’s disease (an inflammatory bowel disease), type-1 diabetes, food allergies, and cardiovascular disease 155 156 157 158 159 160. Since a leaky gut can both arise from and worsen inflammation, dietary and lifestyle approaches that reduce inflammation are vital for healing the gut.

Gut Dysbiosis

A leaky gut can contribute to gut dysbiosis, and vice-versa. Gut dysbiosis is an imbalance in the gut microbiome, meaning you have too few healthy microbes and too many harmful ones within the digestive tract. A healthy gut microbiome is important for digestion, gut health, immune system health, detoxification, and metabolism 161. So, when gut dysbiosis is present, it can negatively impact the gut, brain, and every other major organ in the body 161.

Dysbiosis often conjures an image of off-kilter bacteria in the large intestine, but it may also mean you have too many bacteria growing in the small intestine, where their numbers should be low. This condition is called small intestinal bacterial overgrowth, or SIBO for short.

Fungal dysbiosis is common, too. For example, Candida overgrowth is when a normal fungus in most people’s digestive tracts becomes too numerous (often after taking antibiotics) and causes harm 162. 

Gut dysbiosis can arise from gut stressors like poor diet, certain medications (like antibiotics or proton-pump inhibitors), chronic stress, an infection, or excessive inflammation 161. So, it’s important to take steps to minimize these insults whenever possible.

While leaky gut syndrome and gut dysbiosis aren’t the only gut-related problems you could have, they are common and resolvable. Correcting them can help eliminate a lot of symptoms and lead to a better quality of life. Indeed, these two conditions are interrelated, and the solutions to ameliorate both will help with healing your gut over time.

Why Does Gut Health Matter?

It might not seem like health issues like depression, food allergies, food intolerances, constipation, low energy, bladder problems, or a skin rash from eczema could all stem from the same underlying condition, but it’s true. It bears repeating that gut health is often at the center of a wide variety of overall health issues, and healing your gut could clear up a long list of seemingly unrelated symptoms. For example (and this is by no means exhaustive), 

  • Skin issues are often gut issues 125 126 163. This includes acne 123, rosacea 124, eczema 127, psoriasis 130, hives 164, and other conditions that manifest on the skin 161. 
  • Mental health challenges also correlate to gut problems 161, especially IBS (irritable bowel syndrome), IBD (inflammatory bowel syndrome), and low diversity in the gut microbiome 110 114. 
  • Hormonal imbalances could arise in part from gut dysbiosis 161.
  • Overweight and obesity could arise in part from a leaky gut 154 or gut dysbiosis 161. 
  • Joint and muscle pain and fatigue have also been linked to digestive challenges 112 143 161.
  • Bladder problems, like urinary tract infections or bladder pain, could arise in part from gut dysbiosis 161.

While each type of health challenge is multifaceted, my approach to functional medicine starts with the gut. In my practice, I’ve been amazed over and over again to see a wide array of symptoms improve with simple, science-based, natural steps to rebalance and heal the gut. From there, if my patients need further specialized interventions to clear up remaining symptoms, we’ll address those individually. For example, we might bring in psychotherapy for persistent mental health issues or topical treatments for the skin.

Where to Start When Healing Your Gut

When it comes to learning how to your gut, each step requires time, energy, and focus. It’s important in the process to ask for help if you need it, and expect things not to go perfectly all the time. The process isn’t always linear, and it’s normal and ok to have occasional setbacks along the way. A setback doesn’t mean you should give up—it just means you’re learning what works and what doesn’t for your unique body. 

You might find that having a mindset of adding in rather than taking out is helpful for getting more beneficial foods into your diet, especially after Step 1 of the Great-in-8 gut-healing process. For example, if you’re in Step 6 and learning how to feed your beneficial gut microbes, you might try adding a few bites of prebiotic-rich whole grains or legumes to one meal per day, if you tolerate them, and increase your servings over time. 

Or, if you’ve discovered in Step 5 that you can tolerate some fermented foods, you could start each meal with a few bites of kimchi or sauerkraut, or make it a goal to drink half a bottle of kombucha or 4–8 oz of kefir every day. You could even challenge yourself to make any of these foods at home so eating them regularly is more satisfying.

Similarly, throughout every step, you might find that starting your day with a 10-minute walk and a 5-minute meditation is a great place to start building those foundations of regularly moving and offsetting stress. By starting where you are and adding a little at a time, you’ll likely find that, as each new change becomes a habit, the next task on the list is easier to incorporate. 

Last but not least, make sure you have the support of a trusted healthcare provider. If you’re looking for one, we welcome you to reach out to our clinic for support as you dive in to understanding how to heal your gut.

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.

Dr. Michael Ruscio is a DC, natural health provider, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.

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