How to Heal Your Gut Naturally - Dr. Michael Ruscio, DC

Does your gut need a reset?

Yes, I'm Ready

Do you want to start feeling better?

Yes, Where Do I Start?

Do you want to start feeling better?

Yes, Where Do I Start?

How to Heal Your Gut Naturally

Heal your gut with these simple and surprising diet and lifestyle tips that will benefit your overall health and wellness

Key Takeaways:

  • Your gut is the seat of your overall health and well-being.
  • You can support a healthy gut by identifying your own ideal anti-inflammatory diet, through a simple elimination diet process.
  • Supplements like probiotics, collagen, omega-3 fatty acids, and l-glutamine can all help you heal and seal your gut (but you may not need them all at once).
  • Getting enough sleep and reducing stress can improve your gut health.
  • Working through the potential treatments in a systematic way and addressing things in strategic order is the most effective way to resolve gut problems.

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 of 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 harming your gut. Taking over-the-counter pain meds like ibuprofen (or other NSAIDs) can compromise your gut lining, for example [1, 2]. And prolonged, strenuous exercise has been linked to leaky gut syndrome, likely because of the spike in body temperature that results [3].

Reducing gut irritants and accidental damage is the first step to healing your gut naturally. From there, a diet particular to your condition could come into play, but you may simply find that adding in anti-inflammatory foods, probiotics, and a few lifestyle tweaks will be enough to get you going in the right direction and feeling better. Let’s discuss how to heal your gut naturally.

Action Plan: How to Heal Your Gut Naturally

How to Heal Your Gut Naturally - A%20Winning%20Combination Landscape L

A healthy gut is one with an intact, impermeable barrier to 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 let it out.

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

To get to this state of gut health naturally, we recommend a step-by-step process that starts by removing the potentially problematic inputs from your diet and ends with slowly reintroducing some of the things you cut after the gut has had a chance to fully recover. This process is called the Great-in-8 Action Plan, but not everyone needs all eight steps. Here are the steps put simply, which you can find outlined in great detail with specific instructions and dosing in my book, Healthy Gut, Healthy You. 

Step 1: Reset

This first step is a two-to-four-day modified fast, in which you drink bone broth or a cleansing lemonade to reduce inflammation and stimulation to the gut. The modified fast is immediately followed by an anti-inflammatory diet that reduces allergens and irritants. For some, that means a paleo diet. For others, a low-FODMAP diet is more helpful.

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

For some, undertaking this step for a month or more brings complete relief, in which case you can skip down to the last step and begin reintroducing some of the foods you removed, ideally slowly and deliberately, to help you determine which foods are irritating and which foods are fine to eat without causing symptoms. Each step between step one and step five is optional if the previous step didn’t bring you a lot of relief. Steps five through eight are all about easing up on restrictions and enjoying your life.

Step 2: Support

The second step provides additional gut support with probiotic supplements, digestive enzymes, and sometimes Hydrochloric acid (HCl) acid. It also provides adrenal support with herbs and optional vitamin D (or a daily dose of sunshine). This step helps to further heal and seal the gut lining and support your gut in breaking down the foods that could be creating stress on the system. 

Our triple therapy approach to probiotics is the best way to tackle the first half of this step. It takes microbes from the three different categories of probiotics to introduce a wide array of diversity into the system. Taking digestive enzymes that address each type of food (carbohydrates, fats, proteins, and various types of sugar, especially lactose) and/or an HCl supplement at each meal is the best way to tackle the second.

Step 3: Remove 

This step is only necessary if you aren’t feeling better after Steps 1 and 2. It involves eliminating any bad bacteria that persist after the first two steps. The natural option here is to take antimicrobial herbs. The blend of herbs that have been tested to remove unwanted gut bacteria has shown in clinical research to be just as effective as Rifaxamin, the targeted prescription antibiotic that gastroenterologists prescribe for the same purpose [4, 5, 6].

How to Heal Your Gut Naturally - 3 Steps for Gut Health Landscape L

Next Steps

Once you’ve cleared up the harmful bacteria, it’s time for Step 4: Rebalance. If you need help moving things through with a little bit more speed to help continue to support the healthy bacteria in the gut, a prokinetic supplement is the bulk of this step. A prokinetic supplement improves motility so that partially-digested food doesn’t sit too long in any part of the digestive system. 

In Step 5: Reintroduce, you begin reintroducing foods slowly and strategically with the knowledge that if a flare-up occurs, you are equipped to return temporarily to the diet that worked best for you in step one.

In Step 6: Feed, you want to ensure that you’re eating foods that feed the good bugs you’ve now populated in your gut. Prebiotic foods contain fiber that  beneficial gut bacteria and fungi eat. Start slowly on this, as eating too much fiber at one time can be stressful on the system.

In Step 7: Wean, you will begin to cut down the supplements you’ve added during the previous steps. The goal of this step is to get you to the bare minimum number of supplements your body needs to remain in a good state of gut health, so remove one at a time to see how you feel without each one. You’ll likely find that you need to stay on one or a few supplements to feel your best and maintain, which brings me to the last step.

Step 8: Maintenance and Fun is the final step in this process. Everyone’s step eight looks different, but now that you have all the tools you need to assess how you feel and what you should tweak to get to a better state, maintenance is about feeling good and having fun with your newfound gut health. A sample maintenance plan could look like this:

  1. A diet that remains 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
  2. A great, broad-spectrum probiotic supplement (taken daily) [7, 8, 9]
  3. Probiotic and prebiotic foods in moderation [10]
  4. Plenty of water
  5. Moderate daily exercise [11]
  6. Consistent, restful sleep (seven to nine hours a night) [12]
  7. A stress management/reduction activity like yoga or meditation [13, 14, 15]

Cause and Effect: Digestive Health and Overall Health

How to Heal Your Gut Naturally - what%20is%20leaky%20gut Landscape%20copy L

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 damage.

While there’s a wide array of potential causes for gut disturbance, one common culprit at the root of many health challenges is leaky gut syndrome. Leaky gut allows partially digested food particles and potentially harmful microorganisms into the bloodstream via a compromised gut lining. This is also called increased gut permeability. Increased gut permeability can lead to a host of health issues, including [16]:

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

It’s also very highly correlated with chronic illnesses such as celiac disease, Crohn’s disease, Type 1 diabetes, and cardiovascular disease [17, 18, 19, 20, 21, 22]. Interestingly, leaky gut both exacerbates and is caused by inflammation, which is why reducing inflammatory foods and activities is such a vital part of the dietary and lifestyle changes that come with healing your gut naturally.

Gut Dysbiosis

Gut dysbiosis, while not necessarily considered the “cause” of gastrointestinal problems, is also correlated with a number of chronic illnesses and needs to be rebalanced in order to heal your gut naturally [23]. Whether due to metabolic dysfunction, the use of certain medications, or excessive inflammation, gut dysbiosis can further tax the digestive system if left unaddressed.

Gut dysbiosis is an imbalance in the gut microbiome, meaning the balance of beneficial bacteria and bad bacteria within your digestive tract is off-kilter and is creating negative health outcomes. Candida overgrowth is one example of an imbalance in which a harmful fungus grows too prominent in the gut (often after taking an antibiotic that kills off important gut bacteria) [24].

Dysbiosis may also mean that you have excess bacteria growing in the small intestine, where it doesn’t belong, a condition called SIBO (small intestinal bacterial overgrowth).

While leaky gut syndrome and gut dysbiosis aren’t the only gut problems or diseases of the gut a person could have, solving them can help resolve quite a lot of symptoms and lead to a much better quality of life. These two conditions are interrelated (in that leaky gut can easily lead to dysbiosis), and the solutions to ameliorate them will help you heal and seal your gut over time.

Why Does Gut Health Matter?

It might not seem obvious that health issues like eczema or a skin rash, depression, food allergies or food intolerances, constipation, and low energy could all stem from the same underlying condition, but it’s true. It bears repeating that gut health is at the center of it all, and starting with the gut could clear up a long list of seemingly unrelated issues.

A skin issue is a gut issue [25, 26, 27]. This includes acne, rosacea, eczema, psoriasis, and other autoimmune conditions that manifest on the skin [28, 29, 30, 31]. Mental health challenges also correlate to gut problems, especially IBS (irritable bowel syndrome), IBD (inflammatory bowel syndrome), and low diversity in the gut microbiome [32, 33]. Obesity and unintentional or sudden weight loss could both be caused by a gut imbalance or digestive issue. Joint and muscle pain and fatigue have also been linked to digestive challenges [34, 35].

While each type of health challenge comes with its own list of confounding factors, functional medicine starts with the gut to see what improves by just rebalancing and healing the gut wall naturally. From there, if further specialized interventions are necessary, then those things can be addressed individually (e.g. psychotherapy for psychological issues or topicals for the skin).

Where to Start to Heal Your Gut Naturally

When it comes to healing your gut naturally, each step requires time, energy, and focus. Ask for help if you need it, and expect things not to go perfectly all the time. The process isn’t always linear. It’s ok to have occasional setbacks along the way. A setback doesn’t mean you should give up. It just means that you’re working on it. 

You might find that having a mindset of adding in rather than subtracting out is helpful in getting more beneficial foods into your diet, especially after step one in the process. Consider starting every meal with a few bites of kimchi or sauerkraut, or make it a goal to drink half a bottle of kombucha or 8 oz of kefir every day. You could even challenge yourself to make any of these yourself at home to make the task of eating them regularly more fun.

Or you might find that starting your day with a quick walk and a 5-minute meditation is a great place to start. Just start somewhere. You’ll find that, as each new change becomes a habit, the next task on the list is easier to incorporate. Get support to help you on your gut-healing journey. We’d love to help you get started at our clinic.

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.

➕ References
  1. Bjarnason I, Hayllar J, MacPherson AJ, Russell AS. Side effects of nonsteroidal anti-inflammatory drugs on the small and large intestine in humans. Gastroenterology. 1993 Jun;104(6):1832–47. DOI: 10.1016/0016-5085(93)90667-2. PMID: 8500743.
  2. Mujagic Z, de Vos P, Boekschoten MV, Govers C, Pieters H-JHM, de Wit NJW, et al. The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial. Sci Rep. 2017 Jan 3;7:40128. DOI: 10.1038/srep40128. PMID: 28045137. PMCID: PMC5206730.
  3. Pires W, Veneroso CE, Wanner SP, Pacheco DAS, Vaz GC, Amorim FT, et al. Association Between Exercise-Induced Hyperthermia and Intestinal Permeability: A Systematic Review. Sports Med. 2017 Jul;47(7):1389–403. DOI: 10.1007/s40279-016-0654-2. PMID: 27943148.
  4. Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014 May;3(3):16–24. DOI: 10.7453/gahmj.2014.019. PMID: 24891990. PMCID: PMC4030608.
  5. Gatta L, Scarpignato C. Systematic review with meta-analysis: rifaximin is effective and safe for the treatment of small intestine bacterial overgrowth. Aliment Pharmacol Ther. 2017 Mar;45(5):604–16. DOI: 10.1111/apt.13928. PMID: 28078798. PMCID: PMC5299503.
  6. Chen C, Tao C, Liu Z, Lu M, Pan Q, Zheng L, et al. A Randomized Clinical Trial of Berberine Hydrochloride in Patients with Diarrhea-Predominant Irritable Bowel Syndrome. Phytother Res. 2015 Nov;29(11):1822–7. DOI: 10.1002/ptr.5475. PMID: 26400188.
  7. Hoveyda N, Heneghan C, Mahtani KR, Perera R, Roberts N, Glasziou P. A systematic review and meta-analysis: probiotics in the treatment of irritable bowel syndrome. BMC Gastroenterol. 2009 Feb 16;9:15. DOI: 10.1186/1471-230X-9-15. PMID: 19220890. PMCID: PMC2656520.
  8. Demirel G, Celik IH, Erdeve O, Saygan S, Dilmen U, Canpolat FE. Prophylactic Saccharomyces boulardii versus nystatin for the prevention of fungal colonization and invasive fungal infection in premature infants. Eur J Pediatr. 2013 Oct;172(10):1321–6. DOI: 10.1007/s00431-013-2041-4. PMID: 23703468.
  9. Toribio-Mateas M. Harnessing the power of microbiome assessment tools as part of neuroprotective nutrition and lifestyle medicine interventions. Microorganisms. 2018 Apr 25;6(2). DOI: 10.3390/microorganisms6020035. PMID: 29693607. PMCID: PMC6027349.
  10. Shokryazdan P, Faseleh Jahromi M, Navidshad B, Liang JB. Effects of prebiotics on immune system and cytokine expression. Med Microbiol Immunol. 2017 Feb;206(1):1–9. DOI: 10.1007/s00430-016-0481-y. PMID: 27704207.
  11. Petersen AMW. The anti-inflammatory effect of exercise. J Appl Physiol. 2005 Apr 1;98(4):1154–62. DOI: 10.1152/japplphysiol.00164.2004. PMID: 15772055.
  12. Swanson GR, Burgess HJ. Sleep and circadian hygiene and inflammatory bowel disease. Gastroenterol Clin North Am. 2017 Dec;46(4):881–93. DOI: 10.1016/j.gtc.2017.08.014. PMID: 29173529.
  13. Schumann D, Anheyer D, Lauche R, Dobos G, Langhorst J, Cramer H. Effect of yoga in the therapy of irritable bowel syndrome: a systematic review. Clin Gastroenterol Hepatol. 2016 Dec;14(12):1720–31. DOI: 10.1016/j.cgh.2016.04.026. PMID: 27112106.
  14. Yoshikawa K, Kurihara C, Furuhashi H, Takajo T, Maruta K, Yasutake Y, et al. Psychological stress exacerbates NSAID-induced small bowel injury by inducing changes in intestinal microbiota and permeability via glucocorticoid receptor signaling. J Gastroenterol. 2017 Jan;52(1):61–71. DOI: 10.1007/s00535-016-1205-1. PMID: 27075753.
  15. Vanuytsel T, van Wanrooy S, Vanheel H, Vanormelingen C, Verschueren S, Houben E, et al. Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans by a mast cell-dependent mechanism. Gut. 2014 Aug;63(8):1293–9. DOI: 10.1136/gutjnl-2013-305690. PMID: 24153250.
  16. Leech B, McIntyre E, Steel A, Sibbritt D. Risk factors associated with intestinal permeability in an adult population: A systematic review. Int J Clin Pract. 2019 Oct;73(10):e13385. DOI: 10.1111/ijcp.13385. PMID: 31243854.
  17. Sander GR, Cummins AG, Henshall T, Powell BC. Rapid disruption of intestinal barrier function by gliadin involves altered expression of apical junctional proteins. FEBS Lett. 2005 Aug 29;579(21):4851–5. DOI: 10.1016/j.febslet.2005.07.066. PMID: 16099460.
  18. Michielan A, D’Incà R. Intestinal permeability in inflammatory bowel disease: pathogenesis, clinical evaluation, and therapy of leaky gut. Mediators Inflamm. 2015 Oct 25;2015:628157. DOI: 10.1155/2015/628157. PMID: 26582965. PMCID: PMC4637104.
  19. Vaarala O. Leaking gut in type 1 diabetes. Curr Opin Gastroenterol. 2008 Nov;24(6):701–6. DOI: 10.1097/MOG.0b013e32830e6d98. PMID: 19122519.
  20. Ventura MT, Polimeno L, Amoruso AC, Gatti F, Annoscia E, Marinaro M, et al. Intestinal permeability in patients with adverse reactions to food. Dig Liver Dis. 2006 Oct;38(10):732–6. DOI: 10.1016/j.dld.2006.06.012. PMID: 16880015.
  21. Mujagic Z, Ludidi S, Keszthelyi D, Hesselink MAM, Kruimel JW, Lenaerts K, et al. Small intestinal permeability is increased in diarrhoea predominant IBS, while alterations in gastroduodenal permeability in all IBS subtypes are largely attributable to confounders. Aliment Pharmacol Ther. 2014 Aug;40(3):288–97. DOI: 10.1111/apt.12829. PMID: 24943095.
  22. Moludi J, Maleki V, Jafari-Vayghyan H, Vaghef-Mehrabany E, Alizadeh M. Metabolic endotoxemia and cardiovascular disease: A systematic review about potential roles of prebiotics and probiotics. Clin Exp Pharmacol Physiol. 2020 Jun;47(6):927–39. DOI: 10.1111/1440-1681.13250. PMID: 31894861.
  23. Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents. Cell. 2020 Jan 23;180(2):221–32. DOI: 10.1016/j.cell.2019.12.025. PMID: 31978342.
  24. McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, et al. Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions. J Nutr. 2019 Nov 1;149(11):1882–95. DOI: 10.1093/jn/nxz154. PMID: 31373365. PMCID: PMC6825832.
  25. O’Neill CA, Monteleone G, McLaughlin JT, Paus R. The gut-skin axis in health and disease: A paradigm with therapeutic implications. Bioessays. 2016 Nov;38(11):1167–76. DOI: 10.1002/bies.201600008. PMID: 27554239.
  26. Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, et al. Probiotic bacteria induce a “glow of health”. PLoS ONE. 2013 Jan 16;8(1):e53867. DOI: 10.1371/journal.pone.0053867. PMID: 23342023. PMCID: PMC3547054.
  27. Polkowska-Pruszyńska B, Gerkowicz A, Krasowska D. The gut microbiome alterations in allergic and inflammatory skin diseases – an update. J Eur Acad Dermatol Venereol. 2020 Mar;34(3):455–64. DOI: 10.1111/jdv.15951. PMID: 31520544.
  28. Lee YB, Byun EJ, Kim HS. Potential role of the microbiome in acne: A comprehensive review. J Clin Med. 2019 Jul 7;8(7). DOI: 10.3390/jcm8070987. PMID: 31284694. PMCID: PMC6678709.
  29. Parodi A, Paolino S, Greco A, Drago F, Mansi C, Rebora A, et al. Small intestinal bacterial overgrowth in rosacea: clinical effectiveness of its eradication. Clin Gastroenterol Hepatol. 2008 Jul;6(7):759–64. DOI: 10.1016/j.cgh.2008.02.054. PMID: 18456568.
  30. Lee SY, Lee E, Park YM, Hong SJ. Microbiome in the Gut-Skin Axis in Atopic Dermatitis. Allergy Asthma Immunol Res. 2018 Jul;10(4):354–62. DOI: 10.4168/aair.2018.10.4.354. PMID: 29949831. PMCID: PMC6021588.
  31. Bhatia BK, Millsop JW, Debbaneh M, Koo J, Linos E, Liao W. Diet and psoriasis, part II: celiac disease and role of a gluten-free diet. J Am Acad Dermatol. 2014 Aug;71(2):350–8. DOI: 10.1016/j.jaad.2014.03.017. PMID: 24780176. PMCID: PMC4104239.
  32. Geng Q, Zhang Q-E, Wang F, Zheng W, Ng CH, Ungvari GS, et al. Comparison of comorbid depression between irritable bowel syndrome and inflammatory bowel disease: A meta-analysis of comparative studies. J Affect Disord. 2018 Sep;237:37–46. DOI: 10.1016/j.jad.2018.04.111. PMID: 29758449.
  33. Simpson CA, Mu A, Haslam N, Schwartz OS, Simmons JG. Feeling down? A systematic review of the gut microbiota in anxiety/depression and irritable bowel syndrome. J Affect Disord. 2020 Apr 1;266:429–46. DOI: 10.1016/j.jad.2020.01.124. PMID: 32056910.
  34. Skodje GI, Minelle IH, Rolfsen KL, Iacovou M, Lundin KEA, Veierød MB, et al. Dietary and symptom assessment in adults with self-reported non-coeliac gluten sensitivity. Clin Nutr ESPEN. 2019 Jun;31:88–94. DOI: 10.1016/j.clnesp.2019.02.012. PMID: 31060839.
  35. Maeda Y, Kurakawa T, Umemoto E, Motooka D, Ito Y, Gotoh K, et al. Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine. Arthritis Rheumatol. 2016 Nov;68(11):2646–61. DOI: 10.1002/art.39783. PMID: 27333153.

Need help or would like to learn more?
View Dr. Ruscio’s, DC additional resources

Get Help


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!