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8 Biggest Factors Affecting the Microbiome

Now that we have covered what the microbiome actually is and what it does for our health, it’s time to discuss how we can modify the growth of the "good" vs. the "bad."

In utero, an infant was originally thought to have a sterile GI tract. Recent evidence suggests that they may have low levels of bacteria from mother’s placenta and amniotic fluid. However, the major colonization event of the GI tract happens during birth and continues until age ~2-3 years old.

1. Birth Method

How we come into the world is very important for the future health of the microbiome! Each method results in completely different species colonizing the GI tract of the infant, which has implications for future health.

Vaginal birth: Mother’s vaginal, skin, and rectal microflora inoculate baby

Caesarean section: Baby is inoculated with bacteria from hospital environment and abdominal skin

Given the association between babies born C-section and increased health risks (like obesity, Type 1 Diabetes, etc.) later in life, some progressive centres are swabbing a baby’s mouth with vaginal sample from mother if born by C-section.

2. Breast feeding

It’s recently been discovered that during the third trimester, dendritic/macrophages (cells of the immune system) travel from mother’s breast tissue to small intestine via lymphatic system to pick up bacteria and bring back to breast tissue so that it becomes incorporated in breast milk. These bacteria help with early colonization of infant’s GI tract before it’s even born! When a baby breastfeeds, it receives the bacteria from its mother’s skin in addition to these recruited bacteria in the milk.

Formulas are starting to include probiotics, but products back in the day certainly didn’t! There was a phase (that affected many baby boomers) where breast feeding was looked down on and formulas were considered the ‘high class’ option.

This is a whole topic in itself but to simplify, breastfeeding for an adequate length of time is important for baby’s future immunological health. Current guidelines recommend at least 1 year of breastfeeding.

3. Environment

Urban vs. rural up-bringing, local pollution, pesticide load, presence of pets in the home, cleanliness of home, time spent outside, presence of siblings – all affect early colonization of the microbiome. Basically, the more exposure at an early age to others, the outdoors, and bugs – the better!

Ex. A Swedish study found that kids who grew up in a house a dishwasher, had lower rates of allergic disease later in life.

This finding (and there are hundreds of other examples) supports the idea of the Hygiene Hypothesis (HH). The basis of HH is that as a society, we have become hyper-vigilent on cleanliness and our exposure to dirt, bacteria, germs, etc. has been greatly reduced. Normally, these encounters pose challenges for the maturing immune system, which is required for normal immune development. It’s one of the theories behind the recent rise in autoimmunity and cancer: too clean=lack of immune development from an early age so we have exaggerated responses to things as we age.

4. Diet

What we eat daily has a direct effect on the type, number, and location of bacteria living in our GI tract. In general, a diverse diet rich in fiber, fruits, and vegetables with minimally processed/fried food, alcohol, and refined carbohydrates is best. What we consume, our bacteria consumes too and creates metabolites that either benefits us or doesn’t. In some cases, they can cause inflammation.

Note, some research is suggesting that certain bacteria (likely early colonizers) aren’t susceptible and can’t be modified by dietary change – but that doesn’t mean you can’t have an impact on other microbiota in your GI tract to have a positive health outcome.

  • Fibre: The standard American diet is largely made up of animal protein, sugar, fat, and starch with very little fibre. In studies that look at populations across the globe, those with the greatest consumption of dietary fibre have the greatest microbial diversity. (Remember, low microbial diversity is associated with negative health outcomes.)

  • Animal protein: Diets that are high in meat (and saturated fat) are associated with increased microbial metabolic by-products, like trimethylamine-N-oxide, which promotes the development of atherosclerosis and increases risk of heart disease.

Hence the recent changes to Canada’s food Guide to decrease animal protein and shift to more fibre through plant-based choices.

5. Stress

An unexpected, short-lived stressful event has been shown to transiently shift the microbiome profile. Long-term stress has a more permanent, negative effect on the microbiome, by suppressing the growth of our “good” microbiota.

Interestingly, it works both ways. The composition and health of the microbiome influences of stress. This goes back to the Brain-Gut axis discussed in the previous post and the bi-directional communication that exists between them. When certain bacteria release fragments (ex. peptidoglycan), they can cross blood-brain barrier and modify receptors in the brain that can modify behaviour. Kind of scary!

6. Time in Nature

When we go for a walk in the forest or are in true greenspace (not pesticide laden, city park), we are surrounded by plant and organic material. Plants release volatile microbial fragments that we then inhale and this causes a favourable shift in our microbiome.

7. Exercise

Reason # 539 to exercise – it causes a favourable shift in the microbiome.

8. Medication

  • Antibiotics, obviously affect the microbiome since their intended use is to kill infectious, bad bacteria. However, our ‘good’ guys get killed too. Yeasts and resistant bacteria can then over-grow in susceptible individuals, since they’re not killed by antibiotic. Note: antibiotic exposure can occur through increased consumption of dairy and meat.

When antibiotics are used in early life (first 2 years when microbiome is still colonizing the GI tract), there’s risk of permanently losing some bacteria species and never getting them back. Consequence? Some studies have made links with early antibiotic use and increased risk of eczema, allergy, and obesity later in life.

Note – antibiotics are life-saving and should be used in appropriate circumstances. Doctors over-prescribing for viral infections has definitely been a problem in the past, but with increased awareness and many public health initiatives, this is starting to improve.

  • Proton Pump Inhibitors (PPIs) used to treat heartburn or reflux by decreasing stomach acid. Normally, an acidic environment helps orchestrate digestive enzyme release, bicarbonate release, and bile flow – all of which create a certain pH environment for our microbiome. A lot of the “good” guys thrive in acidic conditions. Acid is also required to kill pathogens that we ingest from our food.

Again, PPIs have their place when used short-term and appropriately. Please don’t stop taking your medication without first talking to your healthcare provider.


The interactions between host (us) and microbiota is extremely complex and the resulting balance of benefit vs. harm depends on the integration of factors listed above. Early life factors like birthing method, breastfeeding and antibiotic use is something that we (obviously) can’t modify. We have to do the best we can with the microbiome we have created from age 3! This may mean more dietary changes, supplement support or pre/probiotic support for some.

Next topic: Microbiome and Mood

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