Gut Dysbiosis: Integrative Care for Gut Health and Autoimmune Conditions

Can gut dysbiosis cause autoimmune disease? What the research shows

They are linked, but cause in humans is not yet proven: a 2022 review in Frontiers in Immunology describes dysbiosis and leaky gut as frequent in people with lupus, type 1 diabetes and multiple sclerosis, with possible cause and effect shown mainly in animal models [2]. Treatment trials point the same way, but not for every condition.

• Treatment trials: a 2024 meta-analysis of 80 randomised trials in 14 autoimmune and rheumatic diseases found that probiotics and other microbiota-based therapies may improve symptoms or inflammation in coeliac disease, lupus, psoriasis, Sjögren’s syndrome, multiple sclerosis, systemic sclerosis, Crohn’s disease and ulcerative colitis, and did not increase side effects [3].
• Studies that disagree: the same meta-analysis found no clear benefit in rheumatoid arthritis or spondyloarthritis [3], and a 2025 review of 4 trials in systemic sclerosis (scleroderma) found low-certainty evidence and no clear effect on gut symptoms [4].
• Leaky gut and inflammation: a 2024 review links a weakened gut barrier, often caused by infections, alcohol, a high-fat diet and dysbiosis, with inflammation in metabolic and autoimmune diseases [5].
• What this means for you: gut care is one part of managing an autoimmune condition, alongside the treatment you already receive, not a replacement for it.

What is gut dysbiosis?

Gut dysbiosis is an imbalance in the mix of bacteria, yeasts and other microbes in the gut. A 2025 scoping review in Probiotics and Antimicrobial Proteins found its symptoms broad and non-specific, with no agreed clinical measures to diagnose it [1]. In practice, doctors look for the problems that can be measured, such as an infection, small intestinal bacterial overgrowth (SIBO), H. pylori, coeliac disease or bowel inflammation.

• How common gut symptoms are: in the Rome Foundation study of 73,076 adults in 33 countries, 40% of people surveyed online met the criteria for at least one functional gut disorder, more often women [6].
• What this page covers: gut balance, leaky gut, SIBO, probiotics and the gut and immune link; irritable bowel syndrome (IBS) has its own page, and so does acidity and acid reflux.

What are the symptoms of gut dysbiosis?

The symptoms most often linked with dysbiosis are bloating, stomach pain and diarrhoea, according to a 2025 scoping review [1]; the NHS describes bloating as a full, uncomfortable stomach, often with rumbling and more wind than usual [7]. In our clinic we also see:

• Bowel changes: constipation, loose stools, or both in turn
• Tiredness and low energy
• Skin problems
• Food intolerances, such as feeling unwell after milk or wheat

These symptoms are not specific: the same symptoms occur in IBS, coeliac disease, lactose intolerance and other conditions, which is why we test before treating. This is a clinic observation; individual results vary, and further studies are needed.

What causes gut dysbiosis?

The main causes of gut dysbiosis are antibiotics, acid-reducing medicines, anti-inflammatory painkillers, gut infections such as H. pylori, and a low-fibre diet high in processed foods.

• Antibiotics: in a 2018 study in Nature Microbiology, 12 healthy men took a 4-day course of three strong antibiotics; their gut microbes recovered to near their earlier state within about 6 weeks, although 9 common species were still missing in most of them after 6 months [8].
• Acid-reducing medicines: proton pump inhibitors (PPIs, such as omeprazole) are linked with changes in gut bacteria and with SIBO in observational studies [9]; a 2025 meta-analysis of randomised trials found no higher risk of C. difficile infection, while SIBO may be more common in PPI users [10]. Studies disagree.
• Painkillers: anti-inflammatory painkillers (NSAIDs, such as ibuprofen) can damage the small intestine, and gut bacteria play a key role in this damage, a 2017 review found, mainly from animal studies [11].
• Diet: a 2022 controlled-feeding study found that a common food additive (the emulsifier carboxymethylcellulose) reduced the diversity of gut bacteria in 16 healthy adults within 11 days [12], while adding fibre increased beneficial bifidobacteria and lactobacilli in a meta-analysis of 64 trials [13].
• Infections: H. pylori infection can cause indigestion, stomach ulcers and stomach cancer, according to the American College of Gastroenterology [14].

What is leaky gut, and is it real?

“Leaky gut” means increased permeability of the gut lining; it can be measured in research with sugar-absorption tests, and a 2019 review in Gut by Michael Camilleri of the Mayo Clinic found that endurance exercise, anti-inflammatory painkillers, pregnancy, bile acids and food emulsifiers can increase it [15]. The same review cautions that many claims about leaky gut in the public domain need confirmation before dietary exclusions or supplements are recommended for it [15].

• What is established: gut permeability is often increased in inflammatory bowel disease, type 1 diabetes and some other autoimmune diseases [2][5].
• What is not yet established: whether “leaky gut syndrome” is a disease of its own, and whether treating it changes the course of other diseases; further studies are needed.

What is SIBO, and how is it tested and treated?

Small intestinal bacterial overgrowth (SIBO) is the presence of excessive numbers of bacteria in the small bowel, causing gut symptoms; the American College of Gastroenterology guideline uses a breath test (glucose or lactulose) to diagnose it and antibiotics, most often rifaximin, to treat it [16].

• Symptoms: nausea, bloating, wind, stomach cramps or pain, diarrhoea or constipation, according to the ACG guideline [16].
• Methane type: a breath test high in methane points to intestinal methanogen overgrowth, a related condition often linked with constipation [16].
• Before the test: the guideline advises avoiding antibiotics for 4 weeks before breath testing [16].
• Who gets it: SIBO is more common after long-term use of acid-reducing medicines, after some gut surgery, and in conditions that slow the gut, such as systemic sclerosis [9][16].
• Probiotics: in a 2017 meta-analysis of 18 studies, people taking probiotics cleared SIBO more often than those not taking them (pooled clearance 62.8%), although most studies were small, and probiotics did not clearly prevent SIBO [17].
• Herbal therapy: in a Johns Hopkins study of 104 patients that was not randomised, herbal therapy cleared the breath test in 46% and rifaximin in 34%, a difference that was not statistically significant [18]; further studies are needed. Our approach is described below.

How is gut dysbiosis treated at Cure4Pain?

Cure4Pain looks for the causes of each person’s gut symptoms and treats them together: tests first, then diet, probiotics and gut support, supervised gut protocols, vitamin D therapy where it applies, chewing and sleep habits, and a careful review of medicines. Any change to medicines is made under clinical guidance from Team Cure4Pain. We see people with autoimmune conditions, and people with bloating, gas, constipation or loose stools, tiredness, skin problems or food intolerances. The plan includes:

1. Tests first: our standard panel of more than 100 measures, including vitamin D, B12, iron, thyroid and ANA by the IFA method, with stool, breath, H. pylori and coeliac tests (see below).
2. Diet: milk and most dairy, wheat or gluten, sugar, processed foods, nightshades and raw foods removed, with home-set curd where it suits the person, cruciferous (Brassica) vegetables such as cabbage and cauliflower generally limited as an observational clinic practice, prebiotic and probiotic support, and meal timing or fasting where it is safe for you (see below).
3. Probiotics and gut support: Saccharomyces boulardii and broad-spectrum probiotics, prebiotics, digestive enzymes, bile support, glutamine and zinc for the gut lining, thiamine (vitamin B1) and magnesium.
4. Supervised gut protocols: for SIBO and bacterial overgrowth, structured protocols managed directly by Dr Krushal Pabari, with prescription medicines where needed and probiotics (see below).
5. Supervised-dose vitamin D therapy (Coimbra Protocol-based methods): mainly for people with an autoimmune condition or low vitamin D (see below).
6. Chewing, salivation and sleep: chewing each mouthful slowly, seeing and smelling food before eating, no water with meals, and restorative sleep.
7. Medicines: acid-reducing medicines, antibiotics and painkillers reviewed case by case and, where suitable, reduced slowly.
8. Further tests and referral when needed: Dr Krushal Pabari recommends endoscopy or colonoscopy where the diagnosis calls for it, and we refer you to a gastroenterologist when an ulcer, cancer or other serious cause is suspected.

What tests does Cure4Pain do for gut problems?

Before the first consultation, Cure4Pain tests for the measurable causes of gut symptoms and for deficiencies, hormones, metabolic health and autoimmune activity; the blood panel of more than 100 measures is our clinic protocol, not a guideline requirement:

• Stool tests: faecal calprotectin, a marker of bowel inflammation, which NICE recommends to help tell inflammatory bowel disease from IBS in adults with recent bowel symptoms when cancer is not suspected [19], and tests for parasites
• Breath test for SIBO [16] and an H. pylori test (breath or stool) [14][20]
• Coeliac antibody tests: keep eating foods that contain gluten until testing is done, because avoiding gluten can make the result inaccurate, according to the NHS [21]; we test before removing wheat or gluten
• Blood panel: vitamin D with PTH and calcium, vitamin B12, iron studies, thyroid tests, blood sugar and HbA1c, complete blood count, kidney and liver function, lipid profile, hsCRP
• ANA (antinuclear antibodies) by the IFA method, part of our standard panel for every patient; a positive ANA alone does not mean you have an autoimmune disease

In India, the panel is available at a lower cost through our patient portal, with home collection across India. Outside India, the tests are done at a laboratory near you and reviewed with you in the consultation.

Are commercial gut microbiome tests worth it?

Not yet for treatment decisions: in a 2024 European study, one stool sample sent to 6 microbiome testing companies was reviewed by 21 experts, who found the reports’ interpretations premature and of limited clinical use, with little transparency about methods [22]. Cure4Pain rarely uses commercial stool microbiome tests, and relies on your symptoms and validated tests: stool inflammation and parasite tests, the breath test, H. pylori and coeliac tests, and blood tests.

How does Cure4Pain use vitamin D therapy for gut and autoimmune conditions?

Cure4Pain uses supervised-dose vitamin D therapy, mainly for people with an autoimmune condition or low vitamin D, alongside gut care; it is set and monitored by a clinician with blood tests including PTH and calcium. Doses are above standard supplement amounts but below high-dose protocols, based on methods of the Coimbra Protocol [23]; vitamin D is used as an immune modulator rather than only as a bone supplement, and doses differ by condition. See our Coimbra Protocol page.

• Vitamin D and gut bacteria: a 2019 systematic review of 14 human and 10 mouse studies in the European Journal of Nutrition found evidence that vitamin D influences the make-up of gut bacteria, but most human studies were small and observational [24].
• Safety limit: the upper limit for adults is 4,000 IU a day, and too much vitamin D can raise blood calcium, according to the US National Institutes of Health [25]; doses above this are used only under medical supervision with regular blood tests.
• Safety data: in a 2022 study of 319 people with autoimmune diseases on supervised high-dose vitamin D, average calcium and kidney results stayed normal; it came from a single centre without a comparison group [23].
• The cautious view: a 2020 review in multiple sclerosis notes that the long-term safety of high-dose vitamin D is not well studied and requires physician supervision [26].
• Never on your own: please do not copy doses from the internet or from videos.

What is the best diet for gut dysbiosis? What we remove and what we add

No single diet is proven to treat gut dysbiosis, but diet clearly shapes gut bacteria: in a 17-week Stanford randomised study in 36 healthy adults, a diet high in fermented foods such as yogurt, kefir and fermented vegetables increased the diversity of gut bacteria and lowered inflammatory markers [27], and a meta-analysis of 64 trials found that fibre increased beneficial bifidobacteria and lactobacilli [13]. As clinic practice, Cure4Pain removes several foods, and we state the research on each plainly.

• Milk and most dairy: removed, with home-set fermented yogurt (curd) included when it suits the person. Removing milk is clinic practice; we found no trial of dairy removal in dysbiosis. Fermented foods raised gut bacteria diversity in the Stanford study [27].
• Wheat or gluten: removed as clinic practice, after coeliac testing [21]. A gluten-free diet is essential in coeliac disease; in people without it, a small 2009 study in 10 healthy adults found that a month without gluten reduced some beneficial gut bacteria [28], so the research does not support gluten-free eating for everyone.
• Sugar and processed foods: removed. The NHS advises not eating lots of processed, sugary or fatty foods to ease bloating [7], and a common emulsifier in processed foods reduced gut bacteria diversity in a controlled study [12].
• Nightshades (tomato, potato, brinjal, peppers): removed as clinic practice; we found no study of avoiding nightshades in gut dysbiosis.
• Cruciferous vegetables (cabbage, cauliflower, broccoli): as an observational clinic practice, we generally suggest limiting them. The NHS lists cabbage among foods that cause gas and advises not eating lots of them when bloated [7]; research has not shown that these vegetables harm gut bacteria, and they are a source of fibre.
• Raw foods: as clinic practice, we advise cooked rather than raw foods during gut care; research has not tested raw against cooked foods in dysbiosis.
• Fibre and prebiotics: because these exclusions lower fibre variety, we add prebiotic fibre and cooked vegetables and other permitted foods to keep fibre in the diet [13].
• Meal timing and fasting: where it is safe for you, we use a daily eating window. A 2024 systematic review of 8 human studies found that intermittent fasting can change gut bacteria and may increase their diversity, with mixed results [29].

Which probiotic is best for gut dysbiosis?

No single probiotic is best for everyone: according to the NHS, different probiotics have different effects and little is known about which types are best [30], and the best evidence is for specific strains in specific situations. Probiotics are live bacteria and yeasts [30]; prebiotics are fibres that feed gut bacteria [13]. Cure4Pain uses Saccharomyces boulardii (a probiotic yeast) and broad-spectrum probiotics, chosen for each person.

• Saccharomyces boulardii with antibiotics: a meta-analysis of 21 randomised trials (4,780 people) found that it lowered the risk of diarrhoea during antibiotics from 18.7% to 8.5% [31].
• With H. pylori treatment: in a meta-analysis of 18 trials (3,592 patients), adding Saccharomyces boulardii raised eradication rates slightly and reduced side effects such as diarrhoea [32].
• In autoimmune conditions: see the 80-trial meta-analysis above, with no clear benefit in rheumatoid arthritis or spondyloarthritis [3].
• Safety: probiotics are unlikely to cause harm in healthy people, but rare serious infections, including fungal infections with probiotic yeasts, have occurred, mostly in people who were severely ill or had weak immunity, according to the US National Institutes of Health [33][34]. Ask us first if you have a weak immune system, a central line or a serious illness.
• Labels: probiotics are generally sold as food or supplements, so a product may not contain the bacteria or amount stated on the label [30].
• Probiotics and magnesium: the US National Institutes of Health magnesium fact sheet does not list probiotics among magnesium’s interactions; magnesium can interact with some antibiotics (tetracyclines and quinolones) and bisphosphonates [35]. See our article on magnesium and autoimmune disease.

Do glutamine, zinc, digestive enzymes and bile support help the gut?

The evidence for these supplements is limited and specific: glutamine improved symptoms and gut permeability in one well-designed trial in people with diarrhoea-type IBS after a gut infection [36], zinc improved gut permeability in a small study in Crohn’s disease [37], and enzyme replacement is an established treatment only for proven deficiencies such as pancreatic insufficiency or lactose intolerance [38]. We use them as part of the plan, within official limits where these exist.

• Glutamine: in a randomised placebo-controlled trial of 106 adults with diarrhoea-type IBS and increased gut permeability after a gut infection, 79.6% improved (a fall of at least 50 points in the IBS symptom score) with glutamine compared with 5.8% with placebo, and gut permeability returned to normal [36]. One trial in a specific group; larger trials are needed.
• Zinc: in 12 people with inactive Crohn’s disease, zinc supplements for 8 weeks improved gut permeability [37]. The upper limit for adults is 40 mg of zinc a day, and too much zinc over weeks can lower copper absorption and immune function, according to the US National Institutes of Health [39].
• Digestive enzymes and bile support: we found no trial of these for gut dysbiosis; our use of them is clinic practice, and further studies are needed.
• Thiamine (vitamin B1): see our article on thiamine, gut health and autoimmune disease for what the research shows.
• Magnesium: the upper limit from supplements is 350 mg of elemental magnesium a day for adults, acid-reducing medicines (PPIs) can affect magnesium status, and a blood magnesium test does not show how much the body holds, according to the US National Institutes of Health [35].

Why does Cure4Pain prefer supervised gut protocols to herbal antimicrobials?

Cure4Pain prefers non-herbal, structured gut protocols supervised by Dr Krushal Pabari, with prescription medicines where needed and probiotics, because many of our patients tolerate herbal antimicrobials poorly and because herbal products carry a documented risk of liver injury. In the US Drug-Induced Liver Injury Network, herbal and dietary supplements (including bodybuilding products) caused 15.5% of 839 liver injury cases between 2004 and 2013, rising from 7% to 20% over that time [40], and in an Indian case series of liver injury from a single herbal supplement, 3 of the 5 people with existing liver disease died [41].

• What these studies cover: herbal and dietary supplements in general, not the herbal antimicrobials used for SIBO; we found no trial comparing their safety with supervised protocols.
• For SIBO: antibiotics are the guideline treatment [16], and Dr Krushal Pabari prescribes them within the protocol when they are needed; probiotics increased SIBO clearance in a 2017 meta-analysis of mostly small studies [17].
• Liver and kidney disease: we take particular care with herbal products in people with liver or kidney disease, and ask you to tell us about every herbal or Ayurvedic product you take.
• Our observation: in our clinic, these protocols with probiotics are better tolerated than herbal antimicrobials. This is a clinic observation; individual results vary, and further studies are needed.

Does how you eat affect digestion and bloating?

Yes, partly: the sight, smell and taste of food start digestion before food reaches the stomach: these “cephalic phase” responses set off stomach acid, pancreatic enzymes and gut movement, and account for more than half of the digestive response to a meal, according to a 2000 review in Appetite [42]. The NHS advises chewing with your mouth closed to avoid swallowing air and eating smaller, more frequent meals to ease bloating [7].

• At Cure4Pain: we teach chewing each mouthful slowly, seeing and smelling food before eating, and not drinking water with meals. This is clinic practice; we found no trial of these habits in gut dysbiosis, and further studies are needed.
• Restorative sleep: we work on deep, restful sleep as part of gut care; see our Insomnia & Sleep Problems page.

Do acid-reducing medicines, antibiotics and painkillers affect gut bacteria?

Yes, they can: antibiotics change gut bacteria for weeks to months [8], acid-reducing medicines are linked with gut bacteria changes and SIBO in observational studies, although trials disagree on some risks [9][10], and anti-inflammatory painkillers can damage the small intestine [11].

• At Cure4Pain: Dr Krushal Pabari reviews acid-reducing medicines, antibiotics and painkillers case by case and, where suitable, reduces them slowly under clinical guidance from Team Cure4Pain.
• Do not stop acid-reducing medicines suddenly: in a randomised trial in 120 healthy volunteers, 44% had acid symptoms in the weeks after stopping 8 weeks of a PPI, compared with 15% on placebo [43]. A Canadian deprescribing guideline supports reducing the dose, stopping or taking it only when needed in adults who have finished at least 4 weeks of treatment for heartburn or mild to moderate reflux [44]. Never stop or change prescribed medicines on your own; changes are made under clinical guidance from Team Cure4Pain, with your prescribing doctor. See also our Acidity & Hyperacidity page.
• Painkillers: regular use of anti-inflammatory painkillers such as ibuprofen is a common cause of stomach ulcers, and the NHS advises people with a stomach ulcer not to take them without speaking to a doctor first [20].

How long does it take to improve gut health?

In our clinic, most people notice meaningful improvement within 18 to 30 weeks (about 4 to 7 months). This is a clinic observation; individual results vary, and further studies are needed. Gut balance is maintained over the long term with diet, sleep and habits, and symptoms can return after antibiotics, infections or stress.

• What the research shows: fermented foods changed gut bacteria steadily over a 17-week trial [27], and gut bacteria took about 6 weeks to recover after a short course of antibiotics, with some species still missing at 6 months [8].

When are gut symptoms a warning sign?

See a doctor if you have changes in your bowel habit that are not usual for you, blood in your stool, weight loss without trying, or tiredness and shortness of breath that may be signs of anaemia, according to the NHS [45]; also see a doctor if bloating comes with weight loss or blood in your stool, or does not go away [7].

• Get urgent help: if your stool is black or dark red, or you are bleeding heavily from your bottom, contact a doctor or emergency services straight away (112 in India, 911 in the US, 999 in the UK) [45].
• Further tests and referral: Dr Krushal Pabari recommends endoscopy or colonoscopy where the diagnosis calls for it. As clinic practice, we refer you to a gastroenterologist when an ulcer, cancer or other serious cause is suspected, and for symptoms at night, a family history of bowel cancer, or new bowel symptoms after the age of 50 to 60.

Does Cure4Pain work with my doctor or gastroenterologist?

Yes. We work alongside your existing consulting physician or gastroenterologist, share our findings with them, and any change to medicines is made under clinical guidance from Team Cure4Pain, in coordination with them.

What happens at a gut health consultation?

After your tests, your first consultation (in Mumbai or online) covers your gut symptoms, diet and meal timing, medicines, sleep, stress and any autoimmune condition, and a written plan for diet, probiotics and gut support, any supervised gut protocol, vitamin D where it applies, and chewing and sleep habits. We see adults and young people aged 16 and over. Follow-up reviews are planned at regular intervals. Individual results vary.

Evidence: key studies

Who treats you

• Dr Krushal PabariMD, PGCP - Rheumatic & Musculoskeletal Diseases. Assistant Professor, Cooper Hospital; Guest Professor, CMP Homoeopathic Medical College.
• AT. Chintan Dalal, N.D.BNYS, R.AP. Functional nutrition and Coimbra Protocol practitioner.

Consultations look at the whole person: alongside the medical and nutritional plan, we bring a strong interest in behavioural science to counselling on stress, sleep and lasting lifestyle change.

How consultations work: Mumbai or online worldwide

Book through our patient portal. You can see us in person at our clinic in Malad West, Mumbai, or online from anywhere. Your first consultation reviews your history and tests; we then agree a plan together and set the monitoring schedule.

Related conditions and articles

• Hashimoto's ThyroiditisAutoimmune thyroid; antibodies, vitamin D, selenium and thyroid care.
• PsoriasisScaly, inflamed skin patches; vitamin D, nutrition and patient cases.
• Lupus (SLE)A whole-body autoimmune condition; vitamin D, magnesium and monitoring.
• Insomnia & Sleep ProblemsTrouble falling or staying asleep; vitamin D, nutrition, breathing and sleep habits.

• Autoimmune and inflammatory conditions
• Coimbra Protocol

This page is for education and does not replace medical advice. Do not start, stop or change any medicine or supplement without medical guidance.

References

1. Carías Domínguez AM, et al. Intestinal Dysbiosis: Exploring Definition, Associated Symptoms, and Perspectives for a Comprehensive Understanding – a Scoping Review. Probiotics Antimicrob Proteins 2025;17(1):440-449. doi:10.1007/s12602-024-10353-w

2. Christovich A, Luo XM. Gut Microbiota, Leaky Gut, and Autoimmune Diseases. Front Immunol 2022;13:946248. doi:10.3389/fimmu.2022.946248

3. Zeng L, et al. Efficacy and safety of gut microbiota-based therapies in autoimmune and rheumatic diseases: a systematic review and meta-analysis of 80 randomized controlled trials. BMC Med 2024;22(1):110. doi:10.1186/s12916-024-03303-4

4. Wach AA, et al. The efficacy of probiotics, prebiotics or synbiotics in scleroderma: A systematic review. Clin Nutr ESPEN 2025;68:206-215. doi:10.1016/j.clnesp.2025.04.004

5. Di Vincenzo F, et al. Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review. Intern Emerg Med 2024;19(2):275-293. doi:10.1007/s11739-023-03374-w

6. Sperber AD, et al. Worldwide Prevalence and Burden of Functional Gastrointestinal Disorders, Results of Rome Foundation Global Study. Gastroenterology 2021;160(1):99-114.e3. doi:10.1053/j.gastro.2020.04.014

7. NHS. Bloating. nhs.uk/symptoms/bloating

8. Palleja A, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 2018;3(11):1255-1265. doi:10.1038/s41564-018-0257-9

9. Naito Y, et al. Intestinal Dysbiosis Secondary to Proton-Pump Inhibitor Use. Digestion 2018;97(2):195-204. doi:10.1159/000481813

10. Floria DE, et al. Proton pump inhibitors are not associated with an increased risk of Clostridioides difficile infection: a systematic review and meta-analysis of randomized controlled trials. Gut Microbes 2025;17(1):2562341. doi:10.1080/19490976.2025.2562341

11. Otani K, et al. Microbiota Plays a Key Role in Non-Steroidal Anti-Inflammatory Drug-Induced Small Intestinal Damage. Digestion 2017;95(1):22-28. doi:10.1159/000452356

12. Chassaing B, et al. Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome. Gastroenterology 2022;162(3):743-756. doi:10.1053/j.gastro.2021.11.006

13. So D, et al. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr 2018;107(6):965-983. doi:10.1093/ajcn/nqy041

14. Chey WD, et al. ACG Clinical Guideline: Treatment of Helicobacter pylori Infection. Am J Gastroenterol 2024;119(9):1730-1753. doi:10.14309/ajg.0000000000002968

15. Camilleri M. Leaky gut: mechanisms, measurement and clinical implications in humans. Gut 2019;68(8):1516-1526. doi:10.1136/gutjnl-2019-318427

16. Pimentel M, et al. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol 2020;115(2):165-178. doi:10.14309/ajg.0000000000000501

17. Zhong C, et al. Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence. J Clin Gastroenterol 2017;51(4):300-311. doi:10.1097/MCG.0000000000000814

18. Chedid V, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med 2014;3(3):16-24. doi:10.7453/gahmj.2014.019

19. National Institute for Health and Care Excellence (NICE). Faecal calprotectin diagnostic tests for inflammatory diseases of the bowel (HTG320, formerly DG11). nice.org.uk/guidance/htg320/chapter/1-Recommendations

20. NHS. Stomach ulcer. nhs.uk/conditions/stomach-ulcer

21. NHS. Coeliac disease: diagnosis. nhs.uk/conditions/coeliac-disease/diagnosis

22. Rodriguez J, et al. Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges. Microbiome 2024;12(1):258. doi:10.1186/s40168-024-01991-x

23. Amon U, et al. Safety Data in Patients with Autoimmune Diseases during Treatment with High Doses of Vitamin D3 According to the “Coimbra Protocol”. Nutrients 2022;14(8). doi:10.3390/nu14081575

24. Waterhouse M, et al. Vitamin D and the gut microbiome: a systematic review of in vivo studies. Eur J Nutr 2019;58(7):2895-2910. doi:10.1007/s00394-018-1842-7

25. Office of Dietary Supplements, US National Institutes of Health. Vitamin D: Fact Sheet for Health Professionals. ods.od.nih.gov/factsheets/VitaminD-HealthProfessional

26. Feige J, et al. Vitamin D Supplementation in Multiple Sclerosis: A Critical Analysis of Potentials and Threats. Nutrients 2020;12(3). doi:10.3390/nu12030783

27. Wastyk HC, et al. Gut-microbiota-targeted diets modulate human immune status. Cell 2021;184(16):4137-4153.e14. doi:10.1016/j.cell.2021.06.019

28. De Palma G, et al. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br J Nutr 2009;102(8):1154-60. doi:10.1017/S0007114509371767

29. Paukkonen I, et al. The impact of intermittent fasting on gut microbiota: a systematic review of human studies. Front Nutr 2024;11:1342787. doi:10.3389/fnut.2024.1342787

30. NHS. Probiotics. nhs.uk/tests-and-treatments/probiotics

31. Szajewska H, Kołodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Aliment Pharmacol Ther 2015;42(7):793-801. doi:10.1111/apt.13344

32. Zhou BG, et al. Saccharomyces boulardii as an adjuvant therapy for Helicobacter pylori eradication: A systematic review and meta-analysis with trial sequential analysis. Helicobacter 2019;24(5):e12651. doi:10.1111/hel.12651

33. Office of Dietary Supplements, US National Institutes of Health. Probiotics: Fact Sheet for Health Professionals. ods.od.nih.gov/factsheets/Probiotics-HealthProfessional

34. National Center for Complementary and Integrative Health, US National Institutes of Health. Probiotics: Usefulness and Safety. nccih.nih.gov/health/probiotics-usefulness-and-safety

35. Office of Dietary Supplements, US National Institutes of Health. Magnesium: Fact Sheet for Health Professionals. ods.od.nih.gov/factsheets/Magnesium-HealthProfessional

36. Zhou Q, et al. Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut 2019;68(6):996-1002. doi:10.1136/gutjnl-2017-315136

37. Sturniolo GC, et al. Zinc supplementation tightens “leaky gut” in Crohn’s disease. Inflamm Bowel Dis 2001;7(2):94-8. doi:10.1097/00054725-200105000-00003

38. Ianiro G, et al. Digestive Enzyme Supplementation in Gastrointestinal Diseases. Curr Drug Metab 2016;17(2):187-93. doi:10.2174/138920021702160114150137

39. Office of Dietary Supplements, US National Institutes of Health. Zinc: Fact Sheet for Health Professionals. ods.od.nih.gov/factsheets/Zinc-HealthProfessional

40. Navarro VJ, et al. Liver injury from herbals and dietary supplements in the U.S. Drug-Induced Liver Injury Network. Hepatology 2014;60(4):1399-408. doi:10.1002/hep.27317

41. Philips CA, et al. Ashwagandha-induced liver injury-A case series from India and literature review. Hepatol Commun 2023;7(10). doi:10.1097/HC9.0000000000000270

42. Katschinski M. Nutritional implications of cephalic phase gastrointestinal responses. Appetite 2000;34(2):189-96. doi:10.1006/appe.1999.0280

43. Reimer C, et al. Proton-pump inhibitor therapy induces acid-related symptoms in healthy volunteers after withdrawal of therapy. Gastroenterology 2009;137(1):80-7, 87.e1. doi:10.1053/j.gastro.2009.03.058

44. Farrell B, et al. Deprescribing proton pump inhibitors: Evidence-based clinical practice guideline. Can Fam Physician 2017;63(5):354-364. pubmed.ncbi.nlm.nih.gov/28500192

45. NHS. Symptoms of bowel cancer. nhs.uk/conditions/bowel-cancer/symptoms