TL;DR:

  • Your intestines host 3–6 lbs of bacteria called the microbiome.
  • Good bacteria support digestion, immunity, and detox; bad bacteria create toxins and inflammation.
  • Leaky gut allows toxins and undigested food into the bloodstream, triggering chronic health problems.
  • Microbiome imbalance is linked to obesity, diabetes, depression, autoimmune disease, allergies, IBS, IBD, and cardiovascular disease.
  • Probiotics, diet, and digestion support can rebalance the microbiome and heal gut lining integrity.

What Is the Microbiome?

Chemical byproducts from intestinal bacteria have a powerful effect on health. Over 70% of the immune system is connected to the GI tract. Conventional medicine usually ignores this.

The intestines are an ecosystem. You have between 3–6 pounds of bacteria (called bowel flora) in your colon. There are more bacterial cells in your colon than there are cells in your entire body (though bacterial cells are smaller). When describing this system, the word “microbiome” is frequently used.

Bacteria are like little chemical factories:

  • Good flora produce vitamins, heal the intestinal lining, break down toxins, and suppress harmful bacteria.
  • Bad flora produce toxins, irritate the intestinal lining, and suppress good flora.

Leaky Gut and the Intestinal Barrier

The cells of the intestines are designed to be tightly packed together, forming a barrier that keeps bacteria and undigested food out of the bloodstream.

Poor diet, drug therapies, inadequate digestion (low stomach acid or pancreatic enzymes), or the wrong kind of flora can break down this barrier. This condition is known as increased intestinal permeability or “leaky gut.”

When leaky gut develops, bacteria, partially digested proteins, and toxins can enter the bloodstream. These substances interact with the immune system and contribute to chronic health problems. Treating imbalances in bowel flora has been shown to improve leaky gut.9

Disease and the Microbiome

Balancing the microbiome and improving intestinal lining integrity may be key to addressing many chronic health issues.

  • GI symptoms are strongly linked to flora imbalance. Studies confirm this.13,14,15
  • Liver disease has also been shown to improve with microbiome support.16,17

But the impact doesn’t stop at digestion. Bacterial byproducts affect toxicity, nutrient absorption, immune activity, and overall biochemistry.

Metabolic Disorders: Diabetes, Obesity, and Syndrome X

Several studies link insulin resistance and type 2 diabetes to the microbiome.1,2,3,4 The flora makeup is also linked to obesity.5,6 Overweight individuals often have a different microbiome profile than lean individuals.

Berberine, a plant compound, has been widely studied for diabetes and insulin sensitivity. Interestingly, part of its benefit may come from its effect on the microbiome.7,8

Cardiovascular Health and the Microbiome

  • Cardiovascular improvements have been noted when the microbiome is addressed.18,19
  • High cholesterol has been linked to bowel flora imbalances.47,48

The Gut-Brain Connection

Research shows gut bacteria can influence the brain and nervous system.20 Imbalance in flora may even contribute to neurodegenerative conditions like Parkinson’s disease.21

Microbiome and Depression

There is growing evidence connecting microbiome health, inflammation, and depression.22,23,24,25 Addressing gut ecology may offer new hope for supporting mental health.

Immunity, Allergies, and Autoimmune Disease

General Immunity

Because so much of the immune system is tied to the GI tract, microbiome problems can affect resistance to infections. Probiotic studies show improvements in immune resilience.10,11,12

Allergies

Both leaky gut and dysbiosis are linked to allergies.32–36

  • Fecal transplant studies suggest improving the microbiome can reduce atopic dermatitis.37,38
  • Probiotic supplementation has helped allergy patients.39
  • Supplementation during pregnancy may lower allergy risk in newborns.45,46,49

Autoimmune Diseases

The microbiome is linked with autoimmune severity and intestinal lining integrity.

  • Psoriasis and psoriatic arthritis patients have distinct flora profiles.41,42
  • In rheumatoid arthritis, microbiome changes improved symptoms through diet.43,44
  • IBD has immune and autoimmune overlaps.50,51

IBS, SIBO, and IBD

IBS and SIBO

  • SIBO is thought to drive many cases of IBS.51,52
  • IBS is linked to bacterial imbalance.53–62
  • Fecal transplants and infection history highlight the microbiome’s role in IBS.59,60

IBD (Crohn’s & Ulcerative Colitis)

  • Microbiota are heavily involved in both Crohn’s disease and ulcerative colitis.
  • Fecal transplants have induced remission in UC.63–65
  • Saccharomyces boulardii has shown promise in IBD.66,67
  • Enteral feeding alters microbial metabolites and may drive Crohn’s improvement.69
  • The Specific Carbohydrate Diet, developed in the 1940s, has been studied as an effective dietary strategy.70–72

What Disrupts the Microbiome?

  • Drugs: Antibiotics, acid suppressors, and others.26–30
  • Diet: Refined foods, chemical additives, gluten, and dairy.
  • Poor digestion: Undigested food promotes harmful flora growth.

Strategies to Improve the Microbiome and Heal Leaky Gut

  1. Probiotics: Strain-specific supplementation (e.g., Bifidobacterium, Saccharomyces boulardii) can help restore balance.
  2. Create the right environment: A healthy gut lining, good diet, and proper digestion allow probiotics to thrive.
  3. Diet: Avoid refined foods, GMOs, and chemical additives. Eat more vegetables rich in polyphenols and fiber.74–77
  4. Specific Carbohydrate Diet (SCD): Limiting starches and disaccharides may rebalance flora and reduce symptoms.
  5. Healing the Gut Lining: Nutrients like glutamine, bone broth, and polyphenols support repair.
  6. Improve Digestion:
    • Chew food thoroughly.
    • Support stomach acid (low HCl allows pathogens).
    • Ensure pancreatic enzyme and bile production for proper digestion.

FAQ: The Gut Microbiome

Q: What exactly is the microbiome?
A: The microbiome is the collection of bacteria and microbes living in your intestines. They help digest food, produce vitamins, support immunity, and keep harmful organisms in check.

Q: What causes the microbiome to get out of balance?
A: Antibiotics, acid-blocking drugs, poor diet, stress, and infections can all disrupt healthy gut bacteria. When this happens, harmful bacteria or yeast can overgrow.

Q: What is leaky gut?
A: Leaky gut happens when the lining of the intestines becomes too porous. This allows toxins, food particles, and bacteria to leak into the bloodstream, triggering inflammation and immune problems.

Q: Can probiotics fix the microbiome?
A: Probiotics can help restore balance, but strain selection matters. Supplements work best when combined with a healthy diet and good digestion to create an environment where good bacteria can thrive. Probiotics can help the immune system. Click to learn more.

Q: How long does it take to heal the gut?
A: It varies. Some people feel better in weeks, while others may need months. Healing usually requires more than just probiotics—it also involves diet changes, digestive support, and reducing inflammation.

Footnotes

  1. Cell Metab. 2020 Jan 7;31(1):77-91.e5 Determines the Efficacy of Exercise for Diabetes Prevention
  2. 2018 Apr;61(4):810-820 Aberrant intestinal microbiota in individuals with prediabetes
  3. Orv Hetil. 2016 Jan 3;157(1):13-22 [Physiological patterns of intestinal microbiota. The role of dysbacteriosis in obesity, insulin resistance, diabetes and metabolic syndrome]
  4. Physiol Genomics. 2018 Apr 1;50(4):244-254 Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis
  5. 2016 Aug 23;7(4):e01018-16. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome
  6. 2016 Mar;65(3):426-36 Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology
  7. Nat Commun. 2020 Oct 6;11(1):5015 Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study)
  8. Biomed Pharmacother. 2020 Nov;131:110669 Berberine alleviates type 2 diabetic symptoms by altering gut microbiota and reducing aromatic amino acids
  9. Clin Infect Dis. 2014 Apr;58(8):1107-15 Immune response and intestinal permeability in children with acute gastroenteritis treated with Lactobacillus rhamnosus GG: a randomized, double-blind, placebo-controlled trial
  10. JPEN J Parenter Enteral Nutr. 2013 Mar;37(2):243-53. A meta-analysis of probiotic and synbiotic use in elective surgery: does nutrition modulation of the gut microbiome improve clinical outcome?
  11. World J Pediatr. 2019 Jun;15(3):255-261 Alterations of intestinal flora and the effects of probiotics in children with recurrent respiratory tract infection
  12. Nutr Res. 2019 Apr;64:1-8 Short-term probiotic supplementation enhances cellular immune function in healthy elderly: systematic review and meta-analysis of controlled studies
  13. Aliment Pharmacol Ther. 2021 Feb;53(4):499-509. Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures
  14. Inflamm Bowel Dis. 2014 Jun;20(6):978-86. Alterations in the intestinal microbiome (dysbiosis) as a predictor of relapse after infliximab withdrawal in Crohn’s disease
  15. 2015 Oct;149(4):883-5.e9. Proton Pump Inhibitors Alter Specific Taxa in the Human G astrointestinal Microbiome: A Crossover Trial
  16. Inflamm Bowel Dis. 2010 Aug;16(8):1286-98. Immunosuppressive effects via human intestinal dendritic cells of probiotic bacteria and steroids in the treatment of acute ulcerative colitis
  17. Nurs Res. 2010 Nov-Dec;59(6):426-32 Probiotic yogurt effects on intestinal flora of patients with chronic liver disease
  18. Aliment Pharmacol Ther. 2011 Mar;33(6):662-71 Meta-analysis: the effects of gut flora modulation using prebiotics, probiotics and synbiotics on minimal hepatic encephalopathy
  19. Biomed Res Int. 2017;2017:3796359. Association Study of Gut Flora in Coronary Heart Disease through High-Throughput Sequencing
  20. Br J Nutr. 2014 Oct 28;112(8):1341-52 Patterns of dietary intake and serum c Gut Microbes. 2018 Nov 2;9(6):486-496. Probiotics drive gut microbiome triggering emotional brain signatures
  21. 2020 Feb 6;9(2):376 Interventional Influence of the Intestinal Microbiome Through Dietary Intervention and Bowel Cleansing Might Improve Motor Symptoms in Parkinson’s Disease
  22. 2020 Jun 18;12(6):1815. Flavonoid-Rich Orange Juice Intake and Altered Gut Microbiome in Young Adults with Depressive Symptom: A Randomized Controlled Study
  23. 2018 Dec;98:52-60 Marital distress, depression, and a leaky gut: Translocation of bacterial endotoxin as a pathway to inflammation
  24. Sci Rep. 2020 Feb 28;10(1):3680 Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression
  25. Neuro Endocrinol Lett. 2008 Feb;29(1):117-24. The gut-brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of LPS from gram negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression
  26. 2019 Sep 5;178(6):1313-1328.e13 Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
  27. BMC Biol. 2019 Sep 18;17(1):76. Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study
  28. Nat Med. 2020 Apr;26(4):589-598 Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans
  29. Sci Rep. 2020 Mar 25;10(1):5397 Rosuvastatin alters the genetic composition of the human gut microbiome
  30. Medicine (Baltimore). 2020 Aug 28;99(35):e21488 Celiac disease serology and gut microbiome following proton pump inhibitor treatment
  31. Clin Exp Allergy. 2015 Sep;45(9):1419-29 Gut microbiome and innate immune response patterns in IgE-associated eczema
  32. West Indian Med J. 1994 Sep;43(3):87-8. The intestinal permeability test applied to the diagnosis of food allergy in paediatrics
  33. Orv Hetil. 1996 Jan 14;137(2):65-9 [Relationship between intestinal permeability and antibodies against food antigens in IgA nephropathy]
  34. Scand J Rheumatol. 1982;11(1):33-8. Intestinal permeability in dermatitis herpetiformis
  35. Pediatr Med Chir. 1991 Mar-Apr;13(2):169-72. Intestinal permeability, atopic eczema and oral disodium cromoglycate
  36. Scand J Rheumatol. 1982;11(1):33-8. Intestinal permeability in dermatitis herpetiformis
  37. JCI Insight. 2018 May 3;3(9):e120608 First-in-human topical microbiome transplantation with Roseomonas mucosa for atopic dermatitis
  38. J Clin Gastroenterol. 2012 Oct;46 Suppl:S56-63 Changing of fecal flora and clinical effect of L. salivarius LS01 in adults with atopic dermatitis
  39. Benef Microbes. 2019 Feb 8;10(1):5-17 Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT
  40. Sci Rep. 2020 Jul 29;10(1):12754. Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index
  41. Exp Dermatol. 2018 Dec;27(12):1336-1343. Intestinal microbiota profiling and predicted metabolic dysregulation in psoriasis patients
  42. Sci China Life Sci. 2019 Jun;62(6):807-815. Dysbiosis of gut microbiota was closely associated with psoriasis
  43. Br J Rheumatol. 1997 Jan;36(1):64-8. Faecal microbial flora and disease activity in rheumatoid arthritis during a vegan diet
  44. Cell Metab. 2018 Jun 5;27(6):1222-1235.e6 Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota
  45. Allergol Int. 2014 Dec;63(4):575-85. Effects of bifidobacterial supplementation to pregnant women and infants in the prevention of allergy development in infants and on fecal microbiota
  46. J Pediatr Gastroenterol Nutr. 2015 Aug;61(2):200-7 Does Maternal Perinatal Probiotic Supplementation Alter the Intestinal Microbiota of Mother and Child?
  47. Eur J Nutr. 2019 Oct;58(7):2713-2729. Effects of products designed to modulate the gut microbiota on hyperlipidaemia
  48. Biomed Res Int. 2017;2017:8127814. Bacterial Community Profile of the Gut Microbiota Differs between Hypercholesterolemic Subjects and Controls
  49. Nat Commun. 2018 Feb 16;9(1):707. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementationClinical Experimental Rheumatology (2006 Jan-Feb;24(1):25-30)
  50. Inflamm Bowel Dis. 2012 Oct;18(10):1809-17 Pediatric ulcerative colitis associated with autoimmune diseases: a distinct form of inflammatory bowel disease?
  51. Scand J Gastroenterol. 2015;50(9):1076-87 Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel
  52. J Gastroenterol Hepatol. 2011 Apr;26 Suppl 3:135-8 Small intestinal bacterial overgrowth (SIBO) in irritable bowel syndrome: frequency and predictors
  53. Dig Dis Sci. 2009 Jan;54(1):132-5 Incidence of predominant methanogenic flora in irritable bowel syndrome patients and apparently healthy controls from North India
  54. J Ethnopharmacol. 2019 Jun 12;237:182-191 Effect of water extract from Berberis heteropoda Schrenk roots on diarrhea-predominant irritable bowel syndrome by adjusting intestinal flora
  55. Dig Liver Dis. 2017 Apr;49(4):331-337 Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis
  56. Zhong Xi Yi Jie He Xue Bao. 2004 Sep;2(5):340-2 [Observation on intestinal flora in patients of irritable bowel syndrome after treatment of Chinese integrative medicine]
  57. Zhongguo Zhong Xi Yi Jie He Za Zhi. 2006 Mar;26(3):218-20 [Preliminary study on intestinal flora in diarrhea type irritable bowel syndrome with pi-wei dampness-heat syndrome]
  58. World J Gastroenterol. 2014 Mar 14;20(10):2449-55 Overgrowth of the indigenous gut microbiome and irritable bowel syndrome
  59. Expert Rev Gastroenterol Hepatol. 2018 May;12(5):439-445. Fecal microbiota transplantation for managing irritable bowel syndrome
  60. J Clin Gastroenterol. 2017 Nov/Dec;51(10):869-877 Postinfection Irritable Bowel Syndrome: The Links Between Gastroenteritis, Inflammation, the Microbiome, and Functional Disease
  61. Curr Opin Endocrinol Diabetes Obes. 2014 Feb;21(1):15-21 Irritable bowel syndrome, inflammatory bowel disease and the microbiome
  62. Chin Med J (Engl). 2019 Apr 20;132(8):889-904 Characteristic dysbiosis of gut microbiota of Chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome
  63. 2019 Jan 15;321(2):156-164 Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis: A Randomized Clinical Trial
  64. 2017 Mar 25;389(10075):1218-1228 Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial
  65. Inflamm Bowel Dis. 2017 Oct;23(10):1702-1709 Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis
  66. Immunopharmacol Immunotoxicol. 2018 Dec;40(6):465-475 Review of Saccharomyces boulardii as a treatment option in IBD
  67. World J Gastroenterol. 2019 May 14;25(18):2188-2203 Diversity of Saccharomyces boulardii CNCM I-745 mechanisms of action against intestinal infections
  68. Sci Rep. 2019 Sep 13;9(1):13263 Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production
  69. Eur J Clin Nutr. 2016 Sep;70(9):1052-6 Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study
  70. World J Gastroenter 2016 feb 14;22(6):2111-7 Response to strict and liberalized specific carbohydrate diet in pediatric Crohn’s disease
  71. Cureus 2018 feb 9;10(2)e2177 Effect of the Specific Carbohydrate Diet on the Microbiome of a Primary Sclerosing Cholangitis and Ulcerative Colitis Patient
  72. J Pediatr Gastroenterol Nutr 2014 Jan;58(1):87-91. Nutritional therapy in pediatric Crohn disease: the specific carbohydrate diet
  73. Nat Commun. 2018 Nov 13;9(1):4630. A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults
  74. Curr Pharm Des. 2017;23(16):2344-2351. Gut Microbiota Modulation and Anti-Inflammatory Properties of Dietary Polyphenols in IBD: New and Consolidated Perspectives
  75. J Nutr Biochem. 2019 Feb;64:228-236. Impact of dietary fiber supplementation on modulating microbiota-host-metabolic axes in obesity
  76. BMC Microbiol. 2016 Nov 3;16(1):255. Pectin enhances the effect of fecal microbiota transplantation in ulcerative colitis by delaying the loss of diversity of gut flora
  77. 2020 Jul;69(7):1218-1228. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries
  78. Antioxidants (Basel). 2017 May 17;6(2):34 A Study of the Protective Properties of Iraqi Olive Leaves against Oxidation and Pathogenic Bacteria in Food Applications
  79. Endocr Metab Immune Disord Drug Targets 2018;18(1):85-93 Olive Leaf Extracts Act as Modulators of the Human Immune Response
  80. Biomed Pharmacother. 2019 Oct;118:109131 Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice
  81. Appl Microbiol Biotechnol. 2020 Feb;104(4):1737-1749 Berberine ameliorates colonic damage accompanied with the modulation of dysfunctional bacteria and functions in ulcerative colitis rats
  82. Acta Pharmacol Toxicol (Copenh) 1952;8(1):71-8 Toxicity of alkaloids to certain bacteria. II. Berberine, physostigmine, and sanguinarine
  83. Front Pharmacol. 2018 May 31;9:571 Berberine Regulates Treg/Th17 Balance to Treat Ulcerative Colitis Through Modulating the Gut Microbiota in the Colon
  84. Pak J Pharm Sci. 2009 Oct;22(4):421-4 Antibacterial activity of oregano (Origanum vulgare Linn.) against gram positive bacteria
  85. Food Microbiol. 2015 May;47:69-73 Application of an oregano oil nanoemulsion to the control of foodborne bacteria on fresh lettuce
  86. Curr Pharm Des. 2019;25(16):1809-1816 Essential Oil and Ethanol Extract of Oregano (Origanum vulgare L.) from Armenian Flora as a Natural Source of Terpenes, Flavonoids and other Phytochemicals with Antiradical, Antioxidant, Metal Chelating, Tyrosinase Inhibitory and Antibacterial Activity
  87. Pak J Pharm Sci. 2009 Oct;22(4):421-4 Antibacterial activity of oregano (Origanum vulgare Linn.) against gram positive bacteria
  88. J Oral Sci. 2017 Dec 27;59(4):597-601 The effects of essential oil, povidone-iodine, and chlorhexidine mouthwash on salivary nitrate/nitrite and nitrate-reducing bacteria
  89. Zhonghua Yan Ke Za Zhi. 2008 Dec;44(12):1098-102 [Comparative study of gentamycin and povidone-iodine on eliminating the conjunctival bacteria]
  90. Phys Chem Chem Phys. 2010 Oct 21;12(39):12653-7 The aluminium and iodine pentoxide reaction for the destruction of spore forming bacteria
  91. J Cataract Refract Surg. 2012 Jan;38(1):92-6. Effect of povidone-iodine concentration and exposure time on bacteria isolated from endophthalmitis cases