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How to Heal Your Gut Naturally: A Clinician’s Guide

Written by Dr. Michael Ruscio, DC on January 27, 2025

Written by Dr. Michael Ruscio, DC on January 27, 2025 — Reviewed by Aimee Gallo

• Gut Health Basics|
• How to Heal Your Gut Naturally|
• Reset|
• Support|
• Remove|
• Rebalance|
• Reintroduce|
• Feed|
• Wean|
• Maintain|

I learned the importance of gut health firsthand when I was in my twenties. I had always been a happy, high-energy guy, but some life events changed my entire life.

I noticed I was always tired—some days, I needed two or three naps. I also had a hard time thinking, I was often cold, and my hair was thinning. On top of that, I couldn’t sleep—it was maddening! 

I knew this wasn’t normal but it took me quite some time (and the right practitioner) to figure out the root causes of my symptoms—a gut infection. It was frustrating at the time, but looking back, the infection shaped my career path. 

My experience was personal but not rare—many people struggle with poor gut health. In my clinic, I’ve seen that healing the gut can improve all kinds of symptoms, even those that don’t seem directly related. 

Now, let’s dive into the step-by-step plan for how to heal your gut naturally—the same approach  that has worked so well for my clients and me.  

Gut Health Basics 

I’m a total gut geek, so I find digestive health and the digestive process fascinating. Our digestive tract takes something foreign to our body (food) and filters out what we need to keep and what we should eliminate.

To do this amazing work, the gut needs enough digestive enzymes and stomach acid to break down food before it enters the small intestine. It then needs a healthy small intestinal lining to help us absorb the nutrients we need and keep out potential threats. 

A healthy gut contains trillions of microbes, known as the gut microbiome. These microbes help with digestion, reduce inflammation, and protect the gastrointestinal (GI) lining 1.

There’s a lot going on there! When gut health is out of balance, the body can’t absorb nutrients properly, inflammation can develop, and the immune system may become overactive 2. This can lead to digestive symptoms like heartburn, diarrhea, or food sensitivities, and other health issues that might not seem directly related—just like what I experienced. 

Here are some of the downstream side effects of poor gut health:

• Fatigue 3 
• Mental health symptoms such as depression or anxiety 4 
• Brain fog 5
• Insomnia 6
• Acne 7, rosacea 8, or other skin conditions, such as eczema 9, or psoriasis 10 
• Female hormone imbalances, showing up as premenstrual syndrome (PMS), polycystic ovary syndrome (PCOS), abnormal cycle length or flow, low libido, or hot flashes 11
• Male hormone imbalances, showing up as fatigue, low libido, erectile dysfunction, muscle loss, and poor memory 12
• Weight loss 13
• Dry or thinning hair 14
• Joint pain 15
• Autoimmune thyroid disease 16
• Celiac disease or gluten intolerance 17
• Histamine intolerance 18
• Food intolerances 19

The excellent news is that the gut is resilient! With just a few foundational steps—such as changing what we eat and taking probiotics—it’s possible to right the ship and regain vibrant health. 

How To Heal Your Gut Naturally: 8 Powerful Steps

I’ve shared my Great-in-8 gut-healing action plan in my book, Healthy Gut, Healthy You. I’ll also describe each step here so you’ll better understand the steps for how to heal your gut naturally.

Ideally, you’ll go through this process with the support of a trusted healthcare provider.

Step 1: Reset

Step 1 creates the foundation for great gut health and is the most important step most of us can take toward improving our total health. For many of my clients, Step 1 brings complete relief.

Liquid Fast

This first step starts with a brief liquid fast to quickly calm symptoms and reduce inflammation. 

In practice, this modified fast involves avoiding solid food and instead drinking homemade bone broth or an elemental diet formula for 2–4 days. An elemental diet especially helps to reduce inflammation 20 and starve bacterial overgrowths 21. 

Elimination Diet

Once the modified fast is complete, the next step in the reset phase is to transition to an anti-inflammatory elimination diet that reduces allergens and irritants. For some of my clients, that means a Paleo diet. For others, a low-FODMAP diet is more helpful.

In the clinic, we work through a process to help our clients understand which type of dietary plan works best for them, and we’d be honored to do the same for you.

Diet is a powerful tool for gut healing, but if your lifestyle doesn’t support a healthy gut, it’s difficult to make lasting progress. So, in this first step, we also work on lifestyle resets to address stress, a lack of movement, and poor sleep. 

Holistic Lifestyle Boosts

Managing stress, spending time in nature, exercising, seeking psychological support, and prioritizing sleep can all support gut healing. Here are some of the most impactful lifestyle strategies for gut healing:

• Breathwork or meditation can reduce stress and may improve digestion 22.
• 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 23 24 25 26.
• Moderate exercise can support mental health and may help reduce gut-related symptoms 27 28. 
• Psychological support from a therapist who offers cognitive-behavioral therapy (CBT) or from learning mindfulness-based stress reduction (MBSR) may improve gut-related symptoms 29 30.
• Optimizing sleep can help promote a healthy gut and is critical for overall well-being 31.

If your issues aren’t resolved after giving these lifestyle boosts at least a month to take hold, move to Step 2.

Step 2: Support

Step 2 involves using probiotics and other digestive supports. For many of my clients who don’t feel measurably better after Step 1, Step 2 can get them there. 

Probiotic Supplements

Probiotics are easily the best way to tackle Step 2. Both my clinical experience and high-quality research point to probiotics as a cornerstone (along with diet) of effective gut treatment 32. 

A blend of different types of probiotic bacteria and yeast can encourage healthy intestinal bacteria and limit the growth of GI microbes that cause inflammation.

Some clinicians have overlooked a trend in the research showing that blends of probiotic supplements are often better than single strains at balancing gut microbiota and improving gut health 33 34.

In our clinic, we find the best results when blending these highly effective probiotic categories:

1. A Lactobacillus and Bifidobacterium blend 35 36
2. A single strain of Saccharomyces boulardii, a healthy fungus 37
3. Soil-based microorganisms, typically species of Bacillus 38

We call this science-based approach probiotic triple therapy and generally have our clients follow our protocol (see table below) for 2–3 months. Time and time again, this approach leads to much better improvements than standard single- or double-strain probiotic treatments.

You may be thinking, can’t I just eat probiotic foods? 

Fermented foods contain probiotics, so they’re great to have as part of a healthy diet. But you’d have to eat a huge amount of them every day to get the same clinical benefit as probiotic supplements. Some people with poor gut health and dysbiosis (an imbalance of gut microbes) don’t tolerate fermented foods well until they’ve healed their gut. 

If fermented foods such as kombucha, kefir, sauerkraut, and kimchi cause digestive distress, it’s best to avoid them until symptoms improve.

Digestive Enzymes or Acid

If combining diet and lifestyle strategies with probiotics for a few weeks hasn’t led to a meaningful improvement, it may be time to consider digestive enzymes or supporting your stomach acid. 

Some people don’t make enough of the enzymes required to break down carbohydrates, proteins, or fats. This can lead to bloating, gas, abdominal discomfort, or unpleasant bowel movements. 

In these cases, taking digestive enzymes that include amylase, protease, and lipase at the start of a meal can often reduce or eliminate these symptoms 39. 

Other people may have low stomach acid and could try taking betaine hydrochloride (HCl) to improve digestive function and nutrient absorption 40. Check out my video explaining how to try HCl safely and effectively.

If our clients feel worse or no different after trying these digestive aids, we stop using them and look to other supplements that may benefit the gut lining.

Supplements to Heal the Gut Lining

If diet, lifestyle, probiotics, and digestive enzymes or HCl haven’t helped after a few weeks, leaky gut syndrome (increased intestinal permeability) could be at play.

Eventually, a leaky gut gives rise to chronic inflammation that may contribute to a host of health issues, including 41:

• Food sensitivities or allergies
• Unregulated blood sugar
• Overactive immune system (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 42
• Crohn’s disease (an inflammatory bowel disease) 43
• Type 1 diabetes 44
• Food sensitivities 45
• Cardiovascular disease 46

Supplements that can strengthen the intestinal wall and repair a leaky gut may be a great addition. Here are a few science-backed options:

• L-glutamine, an amino acid 47
• Colostrum 48
• Zinc 49 or zinc carnosine 50 51

Bone broth, although it has less research supporting its effectiveness, is a whole food that contains L-glutamine, other amino acids, and minerals that may help heal the gut lining. However, because it has lower amounts of these healing elements, bone broth may not be as effective as supplements. 

If digestive aids or gut-lining supplements don’t clearly help, supplements to reduce inflammation might be useful. 

Supplements to Reduce Inflammation

Sometimes, when none of the previous steps or supplements have helped much, chronic inflammation may be the reason why. Here are some anti-inflammatory supplements to consider: 

• Vitamin D 52, ideally as a daily dose of sunshine 53
• Quercetin 54
• Collagen 55
• Curcumin 56

With all supplements, it’s best to give each one a try separately, ideally with a clinician’s support. I usually suggest trying each for 2–3 weeks and taking note of whether they help, harm, or do nothing. If they don’t help, stop taking them.

The cost of high-quality supplements can add up quickly, and it’s not necessary for most people to take everything I’ve mentioned. That could quickly get overwhelming, which is not what anyone wants when working to heal their gut.

We want to create a healthy foundation with diet, lifestyle, and probiotics first, and then use only the supplements we need. 

If you ever find yourself lost in a heap of supplements, it’s a good idea to get some guidance from a dietitian or other healthcare professional.

Step 3: Remove

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Step 3 of how to heal your gut naturally is only necessary for those who aren’t feeling a lot better after steps 1 and 2. For this step, we use herbal antimicrobials to eliminate harmful microbes that persist in the gut after the first two steps. 

Research has shown that herbal antimicrobials can be just as effective as rifaximin, the prescription antibiotic that doctors often use to treat small intestinal bacterial overgrowth (SIBO) 57. Herbal antimicrobials are also effective for treating fungi and parasites.

When our clients start taking herbal antimicrobials, they continue following the diet they found helpful in Step 1 and keep taking the probiotics (with or without other supplements) they started in Step 2. 

Our antimicrobial protocol lasts for two months. In the first month, we use two types of antimicrobial formulas, and in the second month, we switch to two different ones, as follows:

We have sensitive clients start each formula separately to make sure they can tolerate it before adding in the next one a couple days later. 

It’s possible to experience a die-off reaction for a few days to a week when starting herbal antimicrobials. This may look like fatigue, irritability, headaches, flu-like symptoms, digestive symptoms, or changes in bowel movements. 

This is normal, but if it goes on longer than a week, a supplement intolerance could be involved.

Step 4: Rebalance

Once harmful gut microbes are gone, if digestion is still sluggish (causing constipation), I recommend Step 4.

A natural prokinetic supplement, such as peppermint oil 58 or ginger 59, can improve motility (help food move through the digestive tract at a healthy pace). This prevents food from sitting too long in the gut, which can lead to bacterial overgrowth. 

When digestion is running smoothly again, it’s time to start expanding the diet.

Step 5: Reintroduce

Once our clients are feeling much better, whether that’s after Step 1, Step 2, Step 3, or Step 4, we start bringing back eliminated foods slowly and strategically. Reintroducing one low-allergen food at a time helps make it clear which foods are best for their body. 

This trial-and-error method helps build confidence by demonstrating that if a flare-up occurs, returning to Step 1 can help restore balance. Then, it’s safe to try reintroducing foods again.

Step 6: Feed

In Step 6, we add foods that help nourish the beneficial bacteria in the gut, which is now healthier. 

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 stress the digestive system 60. 

Step 6 is also a great time to try fermented foods if they caused symptoms earlier.

Step 7: Wean

In Step 7, it’s time to cut back on supplements. The goal of this step is to get each client to the bare minimum of supplements they need to remain in a good state of wellness and gut health. 

In the clinic, I 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. My clients often find they need to stay on one or a few supplements to feel their best and maintain that feeling.

Step 8: Maintain and Have Fun

This is the final step in how to heal your gut naturally! Everyone’s Step 8 looks different, but reaching it means you have the tools to figure out how you feel and what to tweak if you have later dips in gut health. 

Maintenance is about feeling good and having fun with newfound gut health. A sample maintenance plan could look like this:

• Eat a regular diet that’s lower in inflammatory foods (like sugar and ultraprocessed foods) and higher in anti-inflammatory, gut-healing foods like fruits and veggies, wild fish and meat, legumes, and whole grains.
• Take a broad-spectrum probiotic supplement. 
• Eat probiotic and prebiotic foods to tolerance.
• Drink plenty of filtered water.
• Get moderate daily exercise. 
• Get consistent, restful sleep (7–9 hours a night). 
• Do a regular stress management/reduction activity like yoga or meditation. 
• Regularly spend time in nature and in the sunshine.

Start With the Foundations to Heal Your Gut Naturally

Poor gut health can cause digestive and non-digestive symptoms, not to mention rob us of energy and vitality. Learning how to heal your gut naturally can help you regain a great quality of life and better overall health.

When embarking on any gut-healing journey, it’s always best to start with diet and lifestyle changes for a few weeks, and then add in probiotics if symptoms persist. 

If those initial steps aren’t 100% helpful, taking additional steps, such as adding digestive supports, inflammation-fighting supplements, and herbal antimicrobials, may be necessary.

It’s important to ask for help and not aim for perfection—gut healing doesn’t always follow a straight path, and setbacks are normal. And please don’t forget to reintroduce foods! I encourage my clients to include as many different healthy foods as possible in their diet.

We’d love to assist you on your gut-healing journey, so please reach out to our clinic if you’d like support.

The Ruscio Institute has developed a range of high-quality formulations to help our clients 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. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.