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Our microbiome during a pandemic

April 19th, 2021

Microbes have long been known as the cause of numerous infectious diseases, and for even longer as an essential ingredient in making beer, wine and cheese. Over the past decade, much attention has been focused on the nature of the microorganisms living in our intestines, also known as the “microbiome.” To the surprise of many researchers, these microorganisms have proven to be beneficial to the point where some fear that hygiene measures put in place during the COVID-19 pandemic will affect the microbiome’s diversity. [1]

What is the microbiome and what is its purpose?

The microbiome is estimated to contain 10 to 100 trillion microorganisms (bacteria, viruses, yeasts, etc.), and each person is thought to have their own combination of about 1,000 different species of bacteria. A large proportion of these are believed to be inherited from our parents at birth and develop during our first years of life. [2]

The microbiome plays an essential role in the development of the human body, the proper functioning of the immune system and overall health. Many diseases, such as diabetes, Crohn’s disease, rheumatoid arthritis and multiple sclerosis, are associated with an imbalance of the microbiome. The microbiome also communicates with the brain, and problems with it may contribute to depression, schizophrenia, and certain autism spectrum disorders, among others. [3]

Read more: Understanding your Microbiome

Why is our microbiome threatened during the pandemic?

The health of our microbiome depends largely on continual exposure to bacteria of all kinds. Activities that result in the most exposure are interactions with other people or animals, outdoor activities and travel to other countries. With the pandemic and its associated precautions such as frequent hand washing, physical distancing and travel restrictions, the key measures to ensure a healthy microbiome are far from easy!

According to some experts, by reducing microbial diversity, the hygiene measures implemented to fight the pandemic could have long-term repercussions, such as a reduction in the population’s immune defenses, an increase in asthma and diabetes, and an increase in allergies.

Are children more at risk?

This situation is thought to be of particular concern for infants and young children, as the early years are important in the development of the microbiome. Studies have shown that children who have a less diverse microbiome than other children are more at risk of suffering from asthma, allergies, obesity and diabetes. [4]

During the pandemic, it is highly likely that many parents stepped up hygiene measures for newborns and children. These measures are in addition to the loss of contact between young children and extended family or other infants, which limits the opportunities to acquire bacteria.

What can we do to maintain a healthy microbiome?

While we wait to return to normal life and all the “bacterial contacts” it involves, certain practices could help us fight against microbial loss:

  • Doing outdoor activities
  • Gardening
  • Exercising
  • Eating a high-fibre diet
  • Avoiding unnecessary antibiotics
  • Increasing physical contacts between people in the same bubble

And especially for young children:

  • Choosing natural breastfeeding
  • Encouraging children to play outdoors as often as possible
  • Adopting a pet (if the whole family is willing to take care of it)
  1. Laura Dhillon Kane. “La COVID-19 aura-t-elle un impact à long terme sur les microbiomes ?” La Presse [Montreal], February 21, 2021,
  2. Marilyn Hair and Jon Sharpe. “Fast Facts About The Human Microbiome, The Center for Ecogenetics and Environmental Health,” University of Washington, January 2014,
  3. Mathieu Perreault. “Quand les intestins mènent au cerveau,” La Presse [Montreal],February 7, 2021,
  4. Anica I. Mohammadkhah, Eoin B. Simpson, Stephanie G. Patterson and Jane F. Ferguson. “Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease,” Children (2018): Vol. 5, #12, 160,