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COVID-19 may forever alter our microbiomes

Members of CIFAR’s Humans & the Microbiome program shed light on how a pandemic virus (and our reactions to it) affect our health and wellbeing through the microbiome. 

We are what we eat, and also what we do, who we see, and how often we wash our hands. Research from the past several decades shows that the bacteria, fungi, and viruses that inhabit our bodies — collectively, the microbiome — have significant impacts on human health. From mental health to weight fluctuations to disease risk, a lot depends on our microbes. In turn, the composition of our microbiome is affected by how we live our lives.

The COVID-19 pandemic has upended the lives of nearly every person on the planet. So in a perspective article published in the Proceedings of the National Academy of Sciences in January 2021, members of CIFAR’s Humans & the Microbiome program lay out how the pandemic may impact our microbiomes.

The 23 co-authors, who are all fellows, advisors, or CIFAR Azrieli Global Scholars in CIFAR’s Humans & the Microbiome program, draw on their considerable multidisciplinary experience to point out the risks to our health and wellbeing caused by the intersection of COVID-19 and our microbiomes.

For B. Brett Finlay, co-director of the program, professor at the Michael Smith Laboratories at the University of British Columbia, and a lead author on the paper, the depth and extent of microbial effects is staggering. Drawing on a few examples raised in the paper, he asks, “If you’re not going on airplanes anymore, what does that do for microbial travel around the world? If you’re locked up in an apartment for a month, what does that do to your microbial exposures, especially if you are a newborn child? Homemade baked bread was off the charts when COVID-19 first hit. What is eating all of this white flour doing to the microbiome?”

Reviewing the effects of our responses to COVID-19 as well as the interaction of our microbes with the disease itself, it is clear there are many open questions. The authors hope the piece will challenge biologists, doctors, public health experts, sociologists, and political scientists to better consider the microbial dimension of the world we inhabit. 

These effects, like much of the burden of disease, will not fall equally on everyone. “The ways in which pathogens, people, political economies, ecological conditions, and historical processes all interact will manifest differently in different places,” says Tamara Giles-Vernick, a fellow in the CIFAR program, anthropologist at the Institut Pasteur in Paris, France, and a lead author on the paper. “I think it’s as much the job of social scientists as it is of biologists to take into account those highly varied consequences. We have a responsibility not to presume that everything is going to be the same everywhere.”

This kind of nuanced and discipline-spanning thinking is encouraged by CIFAR’s Humans & the Microbiome program, which asks how microbes that live in and on us affect our health, development, and even behaviour. “It’s important to think about these questions broadly, particularly because pandemics don’t end when transmission ends,” says Giles-Vernick. “Pandemics have long-term biological, social, economic, and cultural consequences. We need to be attentive to those longer-term consequences because we’re going to be living them.”

Among the drivers of long-term microbiome change, the authors point to practices like increased hygiene, travel restrictions, and isolation, which may be protecting us from the immediate threat of COVID-19, but which may also drive the loss of crucially important microbes.

“We know that with each generation, our microbial diversity is getting less and less worldly and more and more homogeneous,” says Finlay. “As any ecologist will tell you, that’s bad. You want diversity. That gives you a robust system.”

To combat this loss while staying safe, the authors suggest measures at the level of public policy and individual practice. At the societal level, they suggest keeping parks open with physical distancing, promoting breastfeeding and infant vaccination, and healthy food assistance to low-income families and children. Individual practices, they write, “could include safely spending time outdoors, gardening where possible, eating a fiber-rich diet, avoiding unnecessary antibiotics, and encouraging physical contact among co-quarantined family members and pets.”

The Perspective article, The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome, was published online in the Proceedings of the National Academy of Sciences on January 20, 2021.

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