6 min|Dr. Maya Kuczma

From Imbalance to Harmony: 6 Ways To Heal Your Gut Microbiome

Wellness, Health, Gut Health

The Symbiotic Relationship With Bacteria

Your body relies on trillions of bacteria living in your intestines and elsewhere in your body. While we used to believe bacteria were harmful, we now recognize that we are in a symbiotic relationship with these bacteria, known collectively as the microbiome.

You weren't born with all of these bacteria. We begin to acquire bacteria from our mothers - from exposure to her microbiome during passage through the birth canal. This early colonization is nourished through the process of breastfeeding. The microbiome continues to mature and diversify through early years of life (1).

These bacteria are incredibly helpful, aiding in the digestion of certain nutrients, maintaining the lining of the gut, and influencing the immune system and brain (The Gut Microbiome). Throughout our life, various factors influence whether our microbiome diversifies, or is destroyed. Imbalances in the microbiome, known as dysbiosis, are common due to our chronic exposure to harmful contributors of dysbiosis, such as:

  • Environmental toxins: herbicides, pesticides, smoking, triclosan (2, 3, 4, 5)
  • Over-medication: antibiotics, PPIs, NSAIDs such as ibuprofen (6, 7, 8)
  • Western diet (high fat, processed foods, low fibre, artificial sweeteners) (9, 10, 11)
  • Lack of early colonization: C-section birth, lack of breastfeeding (12, 13)
  • Stress (14)

What Can We Do to Heal the Gut Microbiome?

1) Remove Triggers of Dysbiosis

Whenever possible, it is ideal to remove factors that are destroying healthy bacteria and thus contributing to dysbiosis. While at times antibiotics are necessary they should not be utilized for viral illnesses, for prevention, or carelessly. Identifying the root cause of symptoms may help us to avoid unnecessary medications and their harmful side effects. Choosing organic produce, as well as organic antibiotic-free animal products decreases exposure to harmful herbicides, pesticides, and antibiotics that are regularly given to livestock.

2) Include healthy food

When the gut does not receive enough fibre, the protective mucous layer degrades, increasing susceptibility to pathogens.(10) Non-digestible carbohydrates such as fibre and resistant starch are not broken down by enzymatic processes of digestion, instead of travelling to the large intestine where they serve as 'food' for bacteria. The bacteria ferment it, producing short-chain fatty acids.(15)

This process regulates the microbiome, and the short-chain fatty acids, such as butyrate, have many protective effects on the body, such as anti-inflammatory effects to both the gut and the brain.(16) It is their quality of indigestibility that qualifies these fibres and resistant starch as prebiotics, fermentable components that directly stimulate growth and activity of the microbiome.(17)

Sources of prebiotics include dandelion greens, Jerusalem artichoke, garlic, onion, leeks, asparagus, bananas, oats, apples, flax seed, jicama, and seaweed. Fermented foods containing lactic acid bacteria serve as a source of ingestible microorganisms, and may directly affect the composition, microbial count, and immune response of the microbiome.(18,19) Examples of fermented foods include kefir, kombucha, sauerkraut, miso, tempeh, and kimchi.

3) Use a probiotic

Similarly to fermented foods, probiotics provide additional microorganisms to influence the composition of the microbiome. Many studies have shown notable shifts in beneficial bacterial strains following supplementation with probiotics.(20, 21) Additionally, improvements in anxiety, depressive-like symptoms, IBS, and many other conditions have also been recorded in trials utilizing probiotics as a treatment.(22, 23, 24)

4) Get Dirty

The environmental microbiome, both indoors and outdoors, heavily influences our own microbiome. Exposure to a rich array of bacteria may actually help our health. Children that grow up with dogs as pets have decreased the likelihood of asthma and allergic rhinitis; additionally, childhood exposure to farming appears to have a protective effect against asthma and allergies.(25, 26

As well, children with siblings have increased microbial diversity when compared to only children.(27) When deprived of exposure to a wide variety of bacteria, it appears that our immune system is more likely to misfire, losing the ability to distinguish friend from foe.

5) Decrease stress

We are only beginning to understand the influence of the gut microbiome on the brain, now known as the 'gut-brain axis'. It appears that the communication between the gut and the brain is a 'two-way street'; changes in the gut can influence our brain, while stress can also influence our gut.(28) In this sense, managing our stress is an important tactic for improving our gut health, and healing our microbiome can also greatly influence our mood and behaviour.(29)

6) Start Off On the Right Track

Babies born vaginally are colonized with lactobacillus, bifidobacteria, and many other bacteria via the vaginal canal (12). Babies born via C-section have less beneficial bacteria, higher levels of hospital-acquired staph bacteria, and are more likely to experience allergies, asthma, immune defects such as autoimmunity, and obesity (12, 30, 31, 32, 33). Breast milk has a direct effect on a baby's microbiome. Human milk oligosaccharides (HMOs), an indigestible sugar in breastmilk, provides fuel for the beneficial bacteria in the baby's digestive tract, acting as the original prebiotic (34).

Additionally, breast milk contains hundreds of species of bacteria that are passed from the mother to baby during breastfeeding (35). The health benefits associated with natural birth and breastfeeding highlight the importance of these early life practices. Researchers are beginning to explore the option of vaginal seeding to expose babies born via C-section to bacteria from their mother, for use in situations in which a natural birth is not possible(36).


Clearly, the microbiome is easily influenced. Healing the microbiome requires exposure to diverse bacterial species while limiting exposure to substances that are harmful to beneficial bacteria. Various test kits have been developed to measure individual microbiome composition and we are getting closer to understanding the complex communication that occurs between the microbiome and the rest of the body.

Personalized microbiome recommendations, based on the current composition of your microbiome and levels of dysbiosis, are on the horizon. Until then, we can pursue these healthy habits that will stand the test of time and that influence the health of our microbiome, and in turn, the health of our mind and body.

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1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303825/

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756530/

3. http://aem.asm.org/content/ear...

4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240432/

5. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154632

6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555213/

7. https://www.ncbi.nlm.nih.gov/pubmed/28733944

8. http://www.sciencedirect.com/science/article/pii/S1198743X15009027

9. https://www.ncbi.nlm.nih.gov/pubmed/20368178

10. http://www.cell.com/cell/fulltext/S0092-8674(16)31464-7

11. https://www.ncbi.nlm.nih.gov/pubmed/25231862?dopt=Abstract

12.  https://www.ncbi.nlm.nih.gov/pubmed/9890463

13. https://www.ncbi.nlm.nih.gov/pubmed/10630441/

14. https://www.ncbi.nlm.nih.gov/pubmed/22314561

15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5277010/

16. https://www.ncbi.nlm.nih.gov/pubmed/10940278

17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705355/

18. https://www.ncbi.nlm.nih.gov/pubmed/20580604?dopt=Abstract

19. https://www.ncbi.nlm.nih.gov/pubmed/22759330?dopt=Abstract

20. https://www.ncbi.nlm.nih.gov/pubmed/16393305?dopt=Abstract

21. https://www.ncbi.nlm.nih.gov/pubmed/17692137?dopt=Abstract

22. https://www.ncbi.nlm.nih.gov/pubmed/27632908

23. https://www.ncbi.nlm.nih.gov/pubmed/25862297

24. https://pdfs.semanticscholar.org/8b20/bfe5e79729a2fd216ae1c1b67cca2f7da6ef.pdf

25. http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2222.1999.00534.x/full

26. https://www.ncbi.nlm.nih.gov/pubmed/11597666

27. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522135/

28. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362231/

29. https://www.ncbi.nlm.nih.gov/pubmed/18537636/

30. https://www.ncbi.nlm.nih.gov/pubmed/26620712

31. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511167/

32. http://pediatrics.aappublications.org/content/early/2014/11/25/peds.2014-0596

33. https://www.ncbi.nlm.nih.gov/pubmed/27599167

34. http://jn.nutrition.org/content/137/3/847S.full

35. https://jamanetwork.com/journals/jamapediatrics/article-abstract/2625334?redirect=true

36. https://www.nature.com/articles/nm.4039

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