Exploring the Mysterious Microbiome

Discovering the helpful inhabitants in the planet of your child!
young child observing chalkboard drawings of space
© Can Stock Photo / bialasiewicz

What’s the largest organ in the human body? You might answer skin, which contains the greatest number of human cells, or maybe you’ll go with the liver, which is the heaviest. But the largest organ in the human body is also the one that we’re still learning about: our microbiomea community of microbes uniquely adapted to each "ecosystem" within each person's body!

Organ ecosystems, microbe communities

Think of the body as a planet, home to trillions of tiny organisms, which when combined create the microbiome. The skin, mouth, nose, lungs, reproductive and digestive tracts are all ecosystems with different temperatures, water and oxygen levels, and nutrient variety. Each ecosystem is host to different communities of microbes, and each person’s microbiome is as unique as they are.

Because each microorganism also has a unique genome which interacts with our own, the microbiome has a tremendous influence on human health and well-being. The “Old Friends Hypothesis” proposed by Graham Rook in 2003 suggests that certain microbes evolved alongside human organisms and have become intricately involved in our immune defense and overall health, with both the microbes and humans depending on one another for proper functionality. While there are many aspects of this we are still trying to more fully understand, we do know that a healthy balance of bacteria in and on the body helps promote the digestion and absorption of food, encourages optimal immune system function, contributes to healthy metabolism and body composition, and affects mental health.

The Microbiota-Gut-Brain Axis

The gastrointestinal system and central nervous system enjoy two-way communication via a complex process involving hormones, neurotransmitters, and blood flow. Just as stress and anxiety can negatively impact digestive function, in part due to a change in the microbiome, the microbiome also has a significant effect on mood. Some studies have shown that probiotic supplementation can decrease perceived stress, anxiety, and depression, and improve problem solving in otherwise healthy adults.

Chart showing lifestyle factors affecting the microbiome.
Figure 1. Lifestyle factors affecting the microbiome.
Image Courtesy of L. Solomonian

The pieces of the microbiome puzzle

Babies are born with an immature, nearly sterile microbiome. The first few years of life are a critical period in which to promote its development, with a number of factors (see Figure 1) playing a role in its success or failure.

Bacteria at birth

The microbiome of the gut and vagina changes during pregnancy and creates the foundation for baby’s microbiome as she passes through the birth canal. This means that the ways in which you optimize your own microbiome during pregnancy are key to ensuring baby gets off to a great start!

Babies born via c-section develop different bacterial colonies than babies born vaginally. C-section births have been associated with higher rates of conditions involving the immune system and microbiome, including asthma, obesity, food allergies, and eczema. However, if a baby is born skyward, there are many strategies to support a healthy microbiome. Some practitioners apply “vaginal seeding” which involves swabbing a newborn baby with the mother’s vaginal secretions after delivery to mimic the introduction of the microbiome that would normally occur during vaginal birth. Since this is an emerging practice, it has limited evidence: talk to your healthcare provider for information on whether it could be right for you.

Skin-to-skin contact between parent and newborn also functions in transferring some skin co-habitants onto the baby, helping develop a diverse community of bacteria. Further, breastfeeding plays a significant role, and there are also supplemental probiotics, comprised of beneficial bacteria, that are designed for neonates and babies.

First food

In addition to the myriad excellent reasons to breastfeed, breast milk (unlike formula) contains health-promoting bacteria and antibodies required to help develop a healthy immune system. Formula feeding alters babies’ microbiomes, encouraging growth of bacterial strains that can cause disease (like C. difficile and E. coli) and decreasing protective strains, like bifidobacteria.

Unfortunately, breastfeeding isn’t an option for all parents. If possible, a fantastic alternative is pasteurized donor breast milk. While it may not be as abundant in elements beneficial to the infant microbiome, it can have a positive impact nonetheless. As mentioned, supplementation with probiotics may help, and, if donor milk isn’t available, many commercial formulas now include probiotic strains.

Daily diet

Switching from breastfeeding to solid foods is the most critical time for the maturity of the microbiome. This maturation will continue on as healthy children age, making a diet composed of a variety of different foods key to its development.

Whole foods

A varied, healthy diet full of whole foods like vegetables, fruits, and legumes, is a great way to increase levels of beneficial microbial strains. The Mediterranean Diet is a wonderful model of the whole food balance, with the addition of its emphasis on foods that contain naturally anti-inflammatory Omega-3 fatty acids like wild fish (especially mackerel, salmon, sardines, and herring), nuts and seeds (such as walnuts and flaxseeds), plant-based oils, and fortified eggs, all of which help to improve the overall health of the microbiome.


Making a conscious effort to eat more fermented and cultured foods like kimchi, kefir, sauerkraut, yogurt, miso, tempeh, kombucha, and cheese, is another way to benefit our microbiome. When foods are fermented and cultured with microbial strains, it affects the enzyme and nutritional composition, impacting the gut in a positive way by contributing to microbiome diversity and strength.


Prebiotics provide fuel for probiotic organisms. When you eat fibre-rich foods, like whole grains, flaxseed and chia, vegetables such as onions and broccoli, and fruits like berries and bananas, you are providing prebiotics for the gut. Beneficial microbes metabolize this fibre and create by-products that have anti-inflammatory, anti-cancer, and immune-protecting effects. Research shows that even small quantities of fibre intake can increase helpful strains in the microbiome. This may be a particularly important dietary addition for children who were primarily formula-fed and have reduced quantities of these strains.

kefir, yogurt, kefir grains on a blue background
Irina Rostokina /Shutterstock.com

Lifestyle links

We all know that stress can eat away at our sense of peace, security, and overall quality of life. But did you know that stress can also significantly impact the development of a child’s microbiome?

Psychological stress

Prolonged exposure to psychological stress (including social and academic) has been associated with reduced microbiome diversity and levels of Lactobacilli in particular. Research suggests that adverse childhood events not only change the composition of the gut microbiome, but that these changes last into adulthood and impact the microbiome in pregnancy, passing the impacts on to the next generation.

Environmental stress

Environmental stressors in the form of toxins and pollutants can impact the microbiome, resulting in reduced levels of good bacteria and increased levels of harmful strains.

Physical stress

Physical stress on the body such as lack of sleep has been linked to a more than 50% change in concentrations of gut microbiota. Most kids don’t get enough sleep: Canadian and US guidelines suggest that children ages 5 to 13 years old should get between 9 and 11 hours of sleep each night, and ages 14 to 17 years should get 8 to 10 hours.

Physical activity also affects children’s microbiomes. Moderate levels of exercise have been linked to increased levels of helpful strains such as Lactobacillus and Bifidobacterium, and lower levels of harmful strains. However, vigorous exercise has been associated with increased inflammation and harmful strains, so it’s important to be cautious that children are not overexerting themselves and putting too much stress on their bodies. Both the US Department of Health and Human Services and The Canadian 24-hour Movement Guidelines for Children and Youth suggest children should be physically active for a total of 60 minutes per day, and that muscle and bone strengthening exercise should be part of children’s physical activity 3 days per week. In addition to all of the known benefits of outdoor exercise, children’s exposure to microbes from nature is related to reduced risk of asthma and allergies.

child with muddy hands

Dirty dogs (and other good germs!)

More conscientious sanitation practices within the last half century have resulted in a comparatively sterile lifestyle compared to how humans used to live. This has caused a dramatic decline in the number of deaths caused by infection; however, we are seeing a simultaneous rise in the number of chronic inflammatory disorders, particularly in developed, high-income countries. Our “sterile” attitude and practices (combined with other modern lifestyle behaviours) may be contributing to an increase in conditions such as cancer, depression, atherosclerosis, neurodegenerative disorders, and type II diabetes. While hand washing is still an excellent practice to reduce the risk of harmful infections, using hand sanitizers and aiming to eradicate all bacteria in a child’s environment may be causing more harm than benefit.

Children like to stick their fingers into everything and then put those fingers in their mouths. This turns out to be an instinctive strategy to diversify a microbiome! Children who are surrounded by animals, have siblings, or live on a farm tend to have lower rates of allergic conditions than kids without similar exposures. One research study found that babies of mothers who wash and boil pacifiers have a higher risk of developing asthma, eczema, or allergies compared to babies whose moms just suck on a fallen pacifier themselves before handing it back to baby!

Antibiotic attention

Antibiotics have an important place in medicine and are sometimes lifesaving. However, in addition to eradicating harmful bacteria, they can also kill strains of beneficial bacteria. Excessive antibiotic use, both in medical care and agricultural practices, can cause an imbalance in the body, increasing the risk of microbiome-related health concerns. If antibiotics can be safely avoided, particularly in the early years, it is likely better for long term health. Conveniently, the strategies that help reduce unnecessary antibiotic use also benefit the microbiome and many other aspects of good health!

Strategies to Reduce Antibiotic Use

  • Wash hands regularly with soap and water
  • Ensure adequate sleep
  • Eat a healthy, whole foods diet
  • Get sufficient physical activity
  • Reduce excessive stress
  • Work with a healthcare professional to treat infections naturally when possible  

Probiotic prudence

Probiotics are beneficial microorganisms that can be supplemented in pill or powder form to modify the microbiome. However, there is a huge range of products delivering a dizzying array of strains and potencies, marketed for all sorts of reasons. Though they’ve been promoted as a cure-all, they aren’t always helpful, and may even cause harm (if only to your wallet). It’s ideal to promote a healthy microbiome using the strategies above and reserve probiotic use for when they are clearly indicated. There is evidence for their value where breast milk isn’t available, and in conditions such as colic, pediatric constipation and diarrhea, upper respiratory tract infections, and in childhood allergy prevention. Discuss the options and evidence with your healthcare provider to determine if supplementation is indicated for you or your child.

Although small, bacteria pack a big punch and play an important role in our health. It is vital to establish a healthy microbiome during the first few years of a child’s life by understanding not only that there are many ways to do so, but also that there are many ways we unwittingly undermine it. We can promote healthy microbiomes during pregnancy and birth through diet choices and by providing supportive environments for kids to grow and play in, and in embracing these strategies we diminish the impulse to sterilize our environment and can reduce the need for antibiotics. A healthy microbiome makes for a healthy baby and, in turn, a healthy child— take care of your microbes, they’ll be your friends for life!

Special thanks to contributions made by Dana Kolenich and Caroline Lewis