LivingThis is how the pandemic has changed our microbiota

This is how the pandemic has changed our microbiota


The appearance of the pandemic caused by a virus has forced us to implement strict measures to reduce the number of infections, and by extension, deaths. The scientific community has focused on investigating and understanding the mechanism of SARS-CoV-2 infection and being able to design measures based on the evidence. To this day, all experts agree that the use of masks is the most effective measure to prevent the volatile particles that contain the virus from dispersing in the air and infecting other people . During the first months of the pandemic, there was some evidence pointing to a possible contagion through surfaces through fomites. Today, it has been shown that the percentage of infections by fomites is practically irrelevant , since the vast majority continue to occur by aerosols, in the air.

What have hygienic measures achieved?

During the first months of the pandemic, early studies showed that the coronavirus could survive on surfaces long enough to spread through fomites. This first evidence led to the implementation of cleaning and disinfection measures for surfaces and objects, in addition to the use of hydroalcoholic gel . The use of these practices has limited effectiveness in preventing coronavirus infections, but they can be very effective in eliminating other types of microorganisms that do remain on surfaces for much longer and that use this route to spread.

In addition to the hygiene behaviors that have been added to the daily routine, other measures have also modulated the levels of exposure to other microorganisms. A clear example is intermittent confinement and social distance, which are still recommended today, especially indoors. Most people have also reduced the number of social interactions or the size of groups in meetings , even going so far as to create “bubble groups”. These practices also have an effect on the variety of microorganisms to which we are exposed because each person carries with them some species of bacteria and viruses that they can transfer to another person through contact such as a simple hug.

We are surrounded by microorganisms

The microbiota is made up of a set of thousands of microorganisms that include different species of viruses, bacteria and fungi . We can find them in many places in our body, but they usually play a very important role in the skin, the intestine and the respiratory tract. A correct composition in terms of numbers and variety is of vital importance, since the imbalance can generate or aggravate diseases such as intestinal infections, metabolic or even Alzheimer’s . Some microorganisms, however, can be harmful to us and if they infect us, they can cause very serious symptoms. For this reason, an adequate level of hygiene is necessary and beneficial in our society.

However, hydroalcoholic gels are not capable of distinguishing “good” bacteria from “bad” ones and eliminate them all. The same happens when we wash our hands with soap, which removes dirt and possible microorganisms that we carry with us without realizing it.

A Canadian study published in 2021 has reviewed the available evidence on the composition of the microbiota in humans and how it has been modified in patients who have suffered from COVID-19. Although it is very difficult to determine if the disease modulates the microbiota or if the change in the microbiota confers a predisposition to be infected by the coronavirus, the data shows that the species of bacteria change. An increased presence of harmful bacteria, such as Clostridium and Candida , have been detected in patients with COVID-19 .

This study has also determined that hygiene measures have been applied at different levels in different parts of the world and is closely related to the socioeconomic level of the countries . Having access to antibiotics, drinking water, soap or even hydroalcoholic gel are decisive for the control of harmful microorganisms, and in countries with resources they have been applied to extremes.

Lastly, another factor that also shapes our microbiota, especially in the intestine, is the type of food we eat. Again, in countries or cities with a high socioeconomic level, periods of confinement and restrictions in the hospitality sector have led some social groups to consume more food at home. The composition of our intestinal microbiota is constantly renewed and recycled, and the way in which the food we consume is processed is a very important variable in this regard. An excess of food at home or a reduction in the variety of foods can reduce microbial diversity.

All the factors mentioned are especially important during the development of the immune system in children and adolescents, since some infections are decisive in the development of diseases or tolerances. The pandemic has completely changed our lives, but it is still early to assess the effect on the microbiota globally in the population . More studies are necessary and the information we obtain can help adjust hygienic measures so that we only keep the benefits without affecting the proper functioning of the microbiota.


Finlay et al. 2021. The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome. PNAS . doi: 10.1073/pnas.2010217118

Chen T. 2021. Fomites and the COVID-19 pandemic: An evidence review on its role in viral transmission. Vancouver, BC: National Collaborating Center for Environmental Health. ISBN: 978-1-988234-56-4

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