4 min|Dr. Maya Kuczma

The Gut's Hidden Universe: Unraveling the Secrets of a Diverse Microbiome

Health, Gut Health

Bacteria Is Important

We used to believe that bacteria were harmful invaders. As a result, many efforts in medicine focused on eradicating bacteria from our body. However, we now know that the bacteria within our body, known collectively as the microbiome, play a key role in our health.

There are trillions of bacteria residing throughout our body, creating a diverse ecosystem

Most of these bacteria reside in our digestive tract but they also line the respiratory tract, skin, vaginal canal, as well as many other areas. A symbiotic relationship occurs between us, the host, as well as the microbiota that we house that is mutually beneficial for both. We provide nutrients and a habitat for the bacteria while they influence our metabolism and immune system.


The presence of a variety of bacterial species appears to be a key component of the microbiome. The diversity of bacteria is linked to a diverse diet (1). Studies of groups consuming a traditional hunter-gathering diet have a more diverse collection of bacteria within their microbiota.(2) A key change in Westernized populations is a decrease in microbial species, and therefore a less diverse microbiome.(3)

But how do we develop a diverse community of bacteria, to begin with?

Both our genes and environment shape the intestinal microbiome. Our acquisition of bacteria begins early on, during birth. It is through the process of moving through the birth canal that we obtain a vast array of bacteria. Components of mother's milk passed to the baby through breastfeeding also play a role in stimulating bacterial growth.

Specific nutrients in breast milk reach the large intestine, largely undigested, where they can feed and nourish the microbiome. Additionally, bacteria are passed directly from mother to baby during breastfeeding. This early life colonization is key in creating a diverse community of bacteria; formula-fed or cesarean-delivered infants have altered microbiomes, consisting of a greater growth of bacterial families linked to food allergies and weight gain. (4)

Unfortunately, many other aspects throughout life can hinder the growth and stabilization of a diverse microbiome, creating an imbalance known as dysbiosis. A variety of behaviours have been linked to dysbiosis, such as:

  • Use of antibiotics (5)
  • Oversanitation, such as the use of triclosan-based antimicrobial hand soap (6)
  • Toxic exposure: pesticides, smoking (7,8)
  • Low fibre diet (9)
  • High sugar diet (10)
  • Born via C-section (11)
  • Lack of breastfeeding (4)
  • Stress (12)

The Role of The Microbiome

In the gut, bacteria play a key role in digesting nutrients, regulating hormones, excreting toxins, and moderating movement through the digestive tract. (13, 14, 15) Gut bacteria also regulate the epithelium, the protective lining of the intestinal tract. A healthy epithelium is crucial for preventing intestinal permeability (Do you have leaky gut?).

Dysbiosis within gut bacteria increases susceptibility to increased intestinal permeability, which has been linked to a wide variety of conditions including inflammatory bowel disease, Parkinson's disease, obesity (16, 17, 18). Recently, we have begun to understand the influence of the gut microbiome on the brain, known as the ‘gut-brain axis’. Gut bacteria produce hormones and neurotransmitters. (19)

Via these processes, the microbiome exerts substantial effects on the hypothalamic-pituitary-adrenal (HPA) axis, a hormonal pathway in our body that plays a significant role in regulating mood, behaviour, sleep, and our body’s stress response.(20) Many psychiatric and neurological conditions are influenced by chronic inflammation.(21)

Due to the microbiome’s effect on the immune system, and thus inflammation, it likely has a large influence on the development of neurological conditions related to inflammation, such as anxiety and depression.(22)

The Microbiome Connection to Health

The wide range of conditions connected to changes in the microbiome, including common conditions such as asthma, atopic eczema, and metabolic syndrome, indicate that bacteria may act as a control centre of the body, mediating health - or disease - depending on the composition, diversity, and stability.(23, 24, 25)

Due to these connections, doctors aimed at discovering the root cause of symptoms are considering the role of the microbiome in the treatment and prevention of disease, as well as creating targeted recommendations to support the balance of a diverse microbiome. Advances in microbiome testing are paving the way towards individualized health recommendations that take into consideration the current state of your microbiome.

However, the health of the microbiome can be addressed by focusing on factors that are generally helpful, regardless of the state of your microbiome, such as avoiding known contributors of dysbiosis whenever possible, reducing stress, and consuming a natural whole-foods diet.

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  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837298/
  2. https://www.ncbi.nlm.nih.gov/pubmed/24736369
  3. http://www.sciencedirect.com/science/article/pii/S0960982215006144#bib10
  4. https://www.ncbi.nlm.nih.gov/pubmed/29018787
  5. http://www.nature.com/articles/476393a
  6. https://www.ncbi.nlm.nih.gov/pubmed/28606169
  7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2022671/
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240432/
  9. http://www.cell.com/cell/fulltext/S0092-8674(16)31464-7
  10. https://www.ncbi.nlm.nih.gov/pubmed/20368178
  11. https://www.ncbi.nlm.nih.gov/pubmed/9890463
  12. https://www.ncbi.nlm.nih.gov/pubmed/22314561
  13. https://www.ncbi.nlm.nih.gov/pubmed/24075718/
  14. https://www.ncbi.nlm.nih.gov/pubmed/21531334
  15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144392/
  16. http://www.sciencedirect.com/science/article/pii/S0016508500700205
  17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353469/
  18. https://www.ncbi.nlm.nih.gov/pubmed/23084636
  19. https://www.ncbi.nlm.nih.gov/pubmed/25689247
  20. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259177/
  21. http://www.sciencedirect.com/science/article/pii/S1471490605002887
  22. http://www.sciencedirect.com/science/article/pii/S1931312815001699  
  23. https://www.ncbi.nlm.nih.gov/pubmed/24330256
  24. https://www.ncbi.nlm.nih.gov/pubmed/22153774
  25. https://www.ncbi.nlm.nih.gov/pubmed/20203013
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