A perspective: the COVID pandemic’s negative impact on our microbiome

Written by: Nadia Siles
Edited by: Esther Melamed

As we observe the first anniversary of the COVID-19 pandemic and reflect on how the pandemic changed and continues to shape our lives.  We need to carefully assess how the pandemic control measures implemented worldwide to reduce transmission and save lives: social distancing, lockdowns, 20-second handwashing, and mask-wearing; may negatively impact our future health. 

In a perspective research article, Finlay et al. explore the many ways that COVID-19 related societal practices may be affecting our microbiome and indirectly influencing our health. The article poses essential research questions that need to be answered to know the long-term biological and social outcomes of this pandemic and future ones.

The authors explain that this pandemic superimposes a decade-long decline of microbial diversity and ancestral microbes resulting from the rise of hygiene practices, antibiotic use, and urban living worldwide. In the context of the hygiene hypothesis, exposure to a variety of microorganisms contributes to the development of our immune system and protects us from allergic diseases. This loss of diversity is likely contributing to the development of non-communicable diseases like obesity, asthma, cardiovascular, and brain diseases, understating the importance of establishing and maintaining a healthy microbiome.

For decades hygiene practices like washing hands have been essential to keeping the majority of the world’s populations safe.  The pandemic brought on drastic changes to these hygiene practices, especially in highly-resourced countries where they were intensified (i.e., frequent handwashing, daily use of hand sanitizer and surgical masks, and continual cleaning of public areas) and are likely leading to the loss of microbial diversity. If so, are there counterbalancing measures we can implement to increase healthy microbial exposures?  On the other hand, in low and middle-resourced countries, where clean water, soap, and sewage disposal are inaccessible, the pandemic has exacerbated health inequalities, prompting the need for long-term investment in essential services such as sewage systems. 

The COVID-19 pandemic and related control measures have also impacted food accessibility and practices in various ways: the food supply chain was disrupted, transportation and global trade were reduced, sit-in restaurants closed or modified to take-out, and workers at food manufacturing sites succumbing to high infection rates.  For people with the financial resources, adaptation occurred through increased home cooking practices or increased fast-food consumption, resulting in a healthier diet or fueling obesity. In contrast, socioeconomically vulnerable people facing food insecurities pre-COVID-19 were further challenged during the pandemic and were further predisposed to malnutrition and thus loss of microbial diversity.  Could the use of probiotics by these populations help them counteract the loss?

Perhaps the most critical contributor to our microbiome composition is social interactions throughout our lifespan: the people we come into close contact with at home, at work, and in social settings.  The pandemic control measure of physical distancing (i.e., social distancing, application of social bubbles, quarantine practices, mobility restrictions, and border closures) likely disrupted microbial transmission at an extraordinary scale, particularly among infants and the elderly.  Some hospital infection prevention and control measures have imposed post-partum, mother-infant separation and discouraged breastfeeding; thus, altering the “seeding and feeding” of the infant microbiomes.   The elderly, considered the most vulnerable among the population, have self-isolated or been isolated at senior care facilities reducing their social interactions and consequently their microbial transmission. 

Finlay et al. acknowledge that reducing transmission of SARS-CoV2 to prevent COVID-19 is a necessity, but he does so while emphasizing how important it is for us to investigate the effects of these pandemic control measures on our communal microbiome and the implications of these changes to our future health trajectories.  These investigations should also consider alternative strategies that allow us to implement physical distancing and hygiene practices with complementary supports that protect our microbiome’s diversity.  The author ultimately reminds us that this global pandemic is not the first and will certainly not be the last.